Better Understanding of the Metamorphosis of Pregnancy (BUMP): protocol for a digital feasibility study in women from preconception to postpartum.

The Better Understanding the Metamorphosis of Pregnancy (BUMP) study is a longitudinal feasibility study aimed to gain a deeper understanding of the pre-pregnancy and pregnancy symptom experience using digital tools. The present paper describes the protocol for the BUMP study. Over 1000 participants are being recruited through a patient provider-platform and through other channels in the United States (US). Participants in a preconception cohort (BUMP-C) are followed for 6 months, or until conception, while participants in a pregnancy cohort (BUMP) are followed into their fourth trimester. Participants are provided with a smart ring, a smartwatch (BUMP only), and a smart scale (BUMP only) alongside cohort-specific study apps. Participant centric engagement strategies are used that aim to co-design the digital approach with participants while providing knowledge and support. The BUMP study is intended to lay the foundational work for a larger study to determine whether participant co-designed digital tools can be used to detect, track and return multimodal symptoms during the perinatal window to inform individual level symptom trajectories.

Black sea bass are a host in the developmental cycle of Lernaeenicus radiatus (Copepoda: Pennellidae): insights into parasite morphology, gill pathology and genetics.

Lernaeenicus radiatus, a mesoparasitic pennellid copepod, has long been known in the northwest Atlantic with metamorphosed females infecting the muscle of marine fish. The study herein is the first to identify a definitive first host, black sea bass Centropristis striata, for L. radiatus supporting larval development to adults and sexual reproduction in the gills. This finding suggests a two-host life cycle for L. radiatus, with black sea bass as the first host. Heavy infections in the gill were associated with considerable pathology related to a unique and invasive attachment process that penetrated the gill and selectively attached to the gill filament cartilage. The morphology of the developing copepod was highly conserved with that of a related pennellid copepod, Lernaeocera branchialis, though was distinguished by the attachment process, unique pigmentation and other morphologic features described herein. Sequencing the small and large subunits of the ribosomal RNA and mitochondrial cytochrome c oxidase subunit I genes demonstrated L. radiatus to share closer identities with Lernaeocera and Haemobaphes spp. pennellid copepods rather than other Lernaeenicus spp. available in GenBank to date. Taxonomy of L. radiatus is discussed in relation to life cycles, tissue tropism, morphology and genetics of other closely related pennellid copepods.

First report of carp edema virus in the mortality of wild common carp Cyprinus carpio in North America.

Carp edema virus (CEV) is an unclassified poxvirus that infects skin and gill tissue to cause koi sleepy disease. In the USA, CEV was first detected in 1996 in a California koi wholesaler, and has since been reported sporadically only within imported and domestic koi. Common carp Cyprinus carpio are a non-native species now present in most waterways in the USA. In May 2017, >526 large adult common carp in spawning condition died in Mill Pond, Park Ridge, NJ, USA. The water temperature during the kill was 15°C and the affected fish displayed marked lethargy prior to death. The presence of CEV was confirmed by endpoint PCR, real-time quantitative PCR (qPCR), and transmission electron microscopy (TEM), making this the first report of CEV associated with a wild carp kill in North America. Phylogenetic analysis of a region of the 4a gene encoding the major core protein clustered the CEV strain among others in genogroup I, which includes CEV strains previously detected in common carp cultured in Europe. Gill histopathology included severe lamellar fusion and apoptosis in the interlamellar region and TEM identified cytoplasmic virions consistent in morphology with CEV in the branchial epithelial cells. Five months following the mortality, surviving fish were collected and screened for CEV by purifying and concentrating virus from the gills and testing with qPCR. No evidence of CEV was found, supporting previous studies showing CEV is not detectable in gills after abatement of clinical signs.

Phylogeny and morphology of Ovipleistophora diplostomuri n. sp. (Microsporidia) with a unique dual-host tropism for bluegill sunfish and the digenean parasite Posthodiplostomum minimum (Strigeatida).

Microsporidia are diverse opportunistic parasites abundant in aquatic organisms with some species hyperparasitic in digenean parasites. In the current study, we describe a unique microsporidian parasite, Ovipleistophora diplostomuri n. sp. that has a tropism for both the bluegill sunfish Lepomis macrochirus, and its digenean parasite Posthodiplostomum minimum. Though the microsporidium first infects a fish, the subsequent infection causes hypertrophy of the metacercarial wall and degeneration of the P. minimum metacercariae within the fish tissue. Genetic analysis placed this species within Ovipleistophora and ultrastructural characteristics were consistent with the genus, including the presence of dimorphic spores within sporophorous vesicles. Meronts did not have a surface coat of dense material, which has been previously reported for the genus. This is the first Ovipleistophora species described that does not have a tropism for ovary. Genetics demonstrated that O. diplostomuri n. sp. groups closely within fish microsporidia and not other species known to be hyperparasitic in digeneans, suggesting that it evolved from fish-infecting microsporidians and developed a secondary tropism for a common and widespread digenean parasite. The high genetic identity to Ovipleistophora species demonstrates the close relationship of this unique microsporidian with other microsporidia that infect ovary.

Directive and non-directive food-related parenting practices: Associations between an expanded conceptualization of food-related parenting practices and child dietary intake and weight outcomes.

This study examines associations between an expanded conceptualization of food-related parenting practices, specifically, directive and non-directive control, and child weight (BMI z-score) and dietary outcomes [Healthy Eating Index (HEI) 2010, daily servings fruits/vegetables] within a sample of parent-child dyads (8-12 years old; n = 160). Baseline data from the Healthy Home Offerings via the Mealtime Environment (HOME Plus) randomized controlled trial was used to test associations between directive and non-directive control and child dietary outcomes and weight using multiple regression analyses adjusted for parental education. Overall variance explained by directive and non-directive control constructs was also calculated. Markers of directive control included pressure-to-eat and food restriction, assessed using subscales from the Child Feeding Questionnaire; markers of non-directive control were assessed with a parental role modeling scale and a home food availability inventory in which an obesogenic home food environment score was assigned based on the types and number of unhealthful foods available within the child's home food environment. DIRECTIVE CONTROL: Food restriction and pressure-to-eat were positively and negatively associated with BMI z-scores, respectively, but not with dietary outcomes. NON-DIRECTIVE CONTROL: An obesogenic home food environment was inversely associated with both dietary outcomes; parental role modeling of healthful eating was positively associated with both dietary outcomes. Neither non-directive behavioral construct was significantly associated with BMI z-scores. TOTAL VARIANCE: Greater total variance in BMI-z was explained by directive control; greater total variance in dietary outcomes was explained by non-directive control. Including a construct of food-related parenting practices with separate markers for directive and non-directive control should be considered for future research. These concepts address different forms of parental control and, in the present study, yielded unique associations with child dietary and weight outcomes.

Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology.

BACKGROUND: Comparative genomic hybridization (CGH) arrays are increasingly used in personalized medicine programs to identify gene copy number aberrations (CNAs) that may be used to guide clinical decisions made during molecular tumor boards. However, analytical processes such as the centralization step may profoundly affect CGH array results and therefore may adversely affect outcomes in the precision medicine context. PATIENTS AND METHODS: The effect of three different centralization methods: median, maximum peak, alternative peak, were evaluated on three datasets: (i) the NCI60 cell lines panel, (ii) the Cancer Cell Line Encyclopedia (CCLE) panel, and (iii) the patients enrolled in prospective molecular screening trials (SAFIR-01 n = 283, MOSCATO-01 n = 309), and compared with karyotyping, drug sensitivity, and patient-drug matching, respectively. RESULTS: Using the NCI60 cell lines panel, the profiles generated by the alternative peak method were significantly closer to the cell karyotypes than those generated by the other centralization strategies (P < 0.05). Using the CCLE dataset, selected genes (ERBB2, EGFR) were better or equally correlated to the IC50 of their companion drug (lapatinib, erlotinib), when applying the alternative centralization. Finally, focusing on 24 actionable genes, we observed as many as 7.1% (SAFIR-01) and 6.8% (MOSCATO-01) of patients originally not oriented to a specific treatment, but who could have been proposed a treatment based on the alternative peak centralization method. CONCLUSION: The centralization method substantially affects the call detection of CGH profiles and may thus impact precision medicine approaches. Among the three methods described, the alternative peak method addresses limitations associated with existing approaches.

Cyprinid herpesvirus-2 causing mass mortality in goldfish: applying electron microscopy to histological samples for diagnostic virology.

In June 2013, a major fish kill of adult goldfish Carassius auratus occurred in Runnemede Lake, New Jersey, USA: an estimated 3000 to 5000 fish died within ~5 d. Necropsy of 4 moribund fish revealed severely pale gills, and histopathology showed type I and II fusion of the gills, diffuse necrosis of hematopoietic tissue in anterior and posterior kidney, and multifocal necrosis of the spleen. Within necrotic areas, pyknosis and enlarged nuclei with marginalized chromatin were observed. Cyprinid herpesvirus-2, the etiological agent for herpesviral hematopoietic necrosis disease, was confirmed in all 4 fish using PCR. We assessed the efficacy of identifying herpesviral infections (viral morphogenesis and cellular ultrastructure) using transmission electron microscopy (TEM) when applied to tissues fixed in 10% neutral buffered formalin (NBF) and tissue that was removed from paraffin blocks. Both sample types could be used to detect the virus within cells at similar concentrations. Tissues reprocessed from 10% NBF contained all the known stages of viral morphogenesis including empty capsids, capsids with an inner linear concentric density, capsids with an electron-dense core, and in the cytoplasm, mature capsids containing an envelope. Paraffin-embedded tissues showed similar stages, but viral capsids with an inner linear concentric density were rare and mature enveloped virions were not observed. In previously paraffin-embedded tissues, cellular membranes were not preserved, making identification of cell types and organelles difficult, whereas membrane preservation was good in tissues processed from 10% NBF. The results demonstrated that routinely fixed and paraffin-embedded samples can be successfully utilized to diagnose herpesviruses, and formalin-fixed tissue could be used to describe viral morphogenesis by TEM, making this a useful and reliable method for diagnostic virology when other samples are not available.

CpG inclusion in feed reduces sea lice, Lepeophtheirus salmonis, numbers following re-infection.

Lepeophtheirus salmonis infections in Atlantic salmon, Salmo salar, have been characterized by little to no hyperplastic response and a biphasic immune response that results in chronic inflammation with tissue repair as the infection progresses. We hypothesized that CpG administration with prior lice exposure would enhance epithelial inflammatory mechanisms and boost the Atlantic salmon immune response to L. salmonis, leading to greater protection against infection. We administered multiple exposures of L. salmonis to two groups of Atlantic salmon and compared responses against first-time exposed Atlantic salmon. Following re-exposure, CpG fed fish exhibited increased skin expression of interleukin (IL)-1ß and IL-12 ß compared to control previously exposed (CPE) and control first-time exposed (CFE) animals, respectively. This inflammatory enhancement occurred with significantly lower expression of matrix metalloproteinase-9 (MMP 9), both systemically (spleen) and locally (skin). Reduced MMP 9 expression was a hallmark of the re-infected fish (occurred in both tissues at both times). When significant differences were present in the skin or spleen, the two re-exposed groups showed greater similarity than with the first exposure group. Lice numbers on CpG fed fish were significantly lower than CFE fish at 7 days post-re-infection (dpri), and although they were not significantly different at 17 dpri, the trend of lower lice levels remained. CpG fed fish also showed nearly twofold greater protection than CPE when compared to the CFE group (48.5% vs. 27.0% reductions at 7 dpri and 27.2% vs. 13.1% reductions at 17 dpri, respectively). The enhanced protection of CpG oligodeoxynucleotide administration to previous exposure was consistent across all body surfaces and suggests that CpG can not only enhance innate responses to L. salmonis in Atlantic salmon, but also further stimulate adaptive responses.

The need for precompetitive integrative bionetwork disease model building.

If you doubt that there are enormous gaps in the current drug discovery process, you should probably skip to the next article. Yet even while critiques rightly highlight inefficiencies or operational issues, they often miss a fundamental reality: until we better understand diseases as altered bionetworks and view diseases at an individual patient level, efforts to develop effective biomarkers and therapies will be inefficient at best.

Induction of aneuploidy by single-walled carbon nanotubes.

Engineered carbon nanotubes are newly emerging manufactured particles with potential applications in electronics, computers, aerospace, and medicine. The low density and small size of these biologically persistent particles makes respiratory exposures to workers likely during the production or use of commercial products. The narrow diameter and great length of single-walled carbon nanotubes (SWCNT) suggest the potential to interact with critical biological structures. To examine the potential of nanotubes to induce genetic damage in normal lung cells, cultured primary and immortalized human airway epithelial cells were exposed to SWCNT or a positive control, vanadium pentoxide. After 24 hr of exposure to either SWCNT or vanadium pentoxide, fragmented centrosomes, multiple mitotic spindle poles, anaphase bridges, and aneuploid chromosome number were observed. Confocal microscopy demonstrated nanotubes within the nucleus that were in association with cellular and mitotic tubulin as well as the chromatin. Our results are the first to report disruption of the mitotic spindle by SWCNT. The nanotube bundles are similar to the size of microtubules that form the mitotic spindle and may be incorporated into the mitotic spindle apparatus.

Genomic affinities in Arachis section Arachis (Fabaceae): molecular and cytogenetic evidence.

Section Arachis is the largest of nine sections in the genus Arachis and includes domesticated peanut, A. hypogaea L. Most species are diploids (x = 10) with two tetraploids and a few aneuploids. Three genome types have been recognized in this section (A, B and D), but the genomes are not well characterized and relationships of several newly described species are uncertain. To clarify genomic relationships in section Arachis, cytogenetic information and molecular data from amplified fragment length polymorphism (AFLP) and the trnT-F plastid region were used to provide an additional insight into genome composition and species relationships. Cytogenetic information supports earlier observations on genome types of A. cruziana, A. herzogii, A. kempff-mercadoi and A. kuhlmannii but was inconclusive about the genome composition of A. benensis, A. hoehnei, A. ipaensis, A. palustris, A. praecox and A. williamsii. An AFLP dendrogram resolved species into four major clusters and showed A. hypogaea grouping closely with A. ipaensis and A. williamsii. Sequence data of the trnT-F region provided genome-specific information and showed for the first time that the B and D genomes are more closely related to each other than to the A genome. Integration of information from cytogenetics and biparentally and maternally inherited genomic regions show promise in understanding genome types and relationships in Arachis.

Emerging approaches in molecular profiling affecting oncology drug discovery.

The purpose of this paper is to provide some perspectives on whether we are at a tipping point in understanding oncology and oncology drug discovery. It describes how model organisms have prepared us for more efficient drug discovery, lessons that are in use today. It provides examples of the emerging integration of biomarkers in patient care. It also details how over the next several years the processes of carrying out target identification and identifying responders to drugs will become more and more similar. In conclusion, a discussion is provided about who can do what to link the various components of this information-rich drug discovery process together.

A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets.

Application of statistical genetics approaches to variations in mRNA transcript abundances in segregating populations can be used to identify genes and pathways associated with common human diseases. The combination of this genetic information with gene expression and clinical trait data can also be used to identify subtypes of a disease and the genetic loci specific to each subtype. Here we highlight results from some of our recent work in this area and further explore the many possibilities that exist in employing a more comprehensive genetics and functional genomics approach to the functional annotation of genomes, and in applying such methods to the validation of targets for complex traits in the drug discovery process.

Necrosis of nasal and airway epithelium in rats inhaling vapors of artificial butter flavoring.

As the result of a high prevalence of fixed airways obstruction in workers at a microwave popcorn manufacturing plant, we examined the hypothesis that vapors of butter flavoring used in the manufacture of microwave popcorn and other foods can produce airway injury in rats. Rats were exposed to vapors liberated from heated butter flavoring. Rats were exposed for 6 h by inhalation and were necropsied 1 day after exposure. The exposure was found by GC-MS analysis to be a complex mixture of various organic gases with the major peaks consisting of diacetyl (2,3-butanedione), acetic acid, acetoin (3-hydroxy-2-butanone), butyric acid, acetoin dimers, 2-nonanone, and delta-alkyl lactones. Diacetyl was used as a marker of exposure concentration. In the lung, butter flavoring vapors containing 285-371 ppm diacetyl caused multifocal, necrotizing bronchitis, which was most consistently present in the mainstem bronchus. Alveoli were unaffected. Butter flavoring vapors containing 203-371 ppm diacetyl caused necrosuppurative rhinitis, which affected all four levels of the nose. Within the posterior two nasal levels (T3 and T4), necrosis and inflammation was principally localized to the nasopharyngeal duct. Control rats were unaffected. Therefore, concentrations of butter flavoring vapors that can occur during the manufacture of foods are associated with epithelial injury in the nasal passages and pulmonary airways of rats.

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer.

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.

Molecular cloning and biological characterization of a novel murine lymphoid growth factor.

Using a bioassay consisting of the proliferation of a murine B cell line, a cDNA of a gene whose product supports the growth of that cell line was isolated from a thymic stromal cell line. This factor, termed thymic stromal lymphopoietin (TSLP), is a protein of 140 amino acids. The gene encoding TSLP was mapped to murine chromosome 18. Purified recombinant TSLP supported the growth of pre-B cell colonies in vitro, but had no myelopoietic activity. TSLP had comitogenic activity for fetal thymocytes, but was not as potent as interleukin 7 in lobe submersion cultures. Injection of TSLP into neonatal mice induced the expansion of B220(+)BP-1(+) pre-B cells.

Functional discovery via a compendium of expression profiles.

Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to monitor hundreds of different cellular functions simultaneously. We constructed a reference database or "compendium" of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and we show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. The utility of this approach is validated by examining profiles caused by deletions of uncharacterized genes: we identify and experimentally confirm that eight uncharacterized open reading frames encode proteins required for sterol metabolism, cell wall function, mitochondrial respiration, or protein synthesis. We also show that the compendium can be used to characterize pharmacological perturbations by identifying a novel target of the commonly used drug dyclonine.