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.

Screening patients for heterozygous p53 mutations using a functional assay in yeast.

Inherited mutations of the p53 gene significantly increase the risk of developing diverse malignancies, and germline p53 mutations can be detected by assaying the transcriptional activity of the p53 protein in mammalian cells. Here we describe a method starting with lymphocytes that allows detection of germline p53 mutations by 'functional' analysis of p53 protein expressed in Saccharomyces cerevisiae. The p53 PCR products are directly cloned into yeast expression vectors in vivo and subsequently tested for transcriptional activity in a simple growth assay. This technique, functional analysis of separated alleles in yeast (FASAY), requires only a few steps, can be automated readily and should permit screening for germline or somatic heterozygous mutations in any gene whose function can be monitored in yeast.

Functional analysis of human MLH1 mutations in Saccharomyces cerevisiae.

Hereditary non-polyposis colorectal cancer (HNPCC; OMIM 120435-6) is a cancer-susceptibility syndrome linked to inherited defects in human mismatch repair (MMR) genes. Germline missense human MLH1 (hMLH1) mutations are frequently detected in HNPCC (ref. 3), making functional characterization of mutations in hMLH1 critical to the development of genetic testing for HNPCC. Here, we describe a new method for detecting mutations in hMLH1 using a dominant mutator effect of hMLH1 cDNA expressed in Saccharomyces cerevisiae. The majority of hMLH1 missense mutations identified in HNPCC patients abolish the dominant mutator effect. Furthermore, PCR amplification of hMLH1 cDNA from mRNA from a HNPCC patient, followed by in vivo recombination into a gap expression vector, allowed detection of a heterozygous loss-of-function missense mutation in hMLH1 using this method. This functional assay offers a simple method for detecting and evaluating pathogenic mutations in hMLH1.

Widespread aneuploidy revealed by DNA microarray expression profiling.

Expression profiling using DNA microarrays holds great promise for a variety of research applications, including the systematic characterization of genes discovered by sequencing projects. To demonstrate the general usefulness of this approach, we recently obtained expression profiles for nearly 300 Saccharomyces cerevisiae deletion mutants. Approximately 8% of the mutants profiled exhibited chromosome-wide expression biases, leading to spurious correlations among profiles. Competitive hybridization of genomic DNA from the mutant strains and their isogenic parental wild-type strains showed they were aneuploid for whole chromosomes or chromosomal segments. Expression profile data published by several other laboratories also suggest the use of aneuploid strains. In five separate cases, the extra chromosome harboured a close homologue of the deleted gene; in two cases, a clear growth advantage for cells acquiring the extra chromosome was demonstrated. Our results have implications for interpreting whole-genome expression data, particularly from cells known to suffer genomic instability, such as malignant or immortalized cells.

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.

Drug target validation and identification of secondary drug target effects using DNA microarrays.

We describe here a method for drug target validation and identification of secondary drug target effects based on genome-wide gene expression patterns. The method is demonstrated by several experiments, including treatment of yeast mutant strains defective in calcineurin, immunophilins or other genes with the immunosuppressants cyclosporin A or FK506. Presence or absence of the characteristic drug 'signature' pattern of altered gene expression in drug-treated cells with a mutation in the gene encoding a putative target established whether that target was required to generate the drug signature. Drug dependent effects were seen in 'targetless' cells, showing that FK506 affects additional pathways independent of calcineurin and the immunophilins. The described method permits the direct confirmation of drug targets and recognition of drug-dependent changes in gene expression that are modulated through pathways distinct from the drug's intended target. Such a method may prove useful in improving the efficiency of drug development programs.

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.

Integrating genetic approaches into the discovery of anticancer drugs.

The discovery of anticancer drugs is now driven by the numerous molecular alterations identified in tumor cells over the past decade. To exploit these alterations, it is necessary to understand how they define a molecular context that allows increased sensitivity to particular compounds. Traditional genetic approaches together with the new wealth of genomic information for both human and model organisms open up strategies by which drugs can be profiled for their ability to selectively kill cells in a molecular context that matches those found in tumors. Similarly, it may be possible to identify and validate new targets for drugs that would selectively kill tumor cells with a particular molecular context. This article outlines some of the ways that yeast genetics can be used to streamline anticancer drug discovery.

Genetic selection of peptide inhibitors of biological pathways.

Genetic selections were used to find peptides that inhibit biological pathways in budding yeast. The peptides were presented inside cells as peptamers, surface loops on a highly expressed and biologically inert carrier protein, a catalytically inactive derivative of staphylococcal nuclease. Peptamers that inhibited the pheromone signaling pathway, transcriptional silencing, and the spindle checkpoint were isolated. Putative targets for the inhibitors were identified by a combination of two-hybrid analysis and genetic dissection of the target pathways. This analysis identified Ydr517w as a component of the spindle checkpoint and reinforced earlier indications that Ste50 has both positive and negative roles in pheromone signaling. Analysis of transcript arrays showed that the peptamers were highly specific in their effects, which suggests that they may be useful reagents in organisms that lack sophisticated genetics as well as for identifying components of existing biological pathways that are potential targets for drug discovery.

Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.

Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. Genetic manipulations allowed analysis of changes in gene expression underlying pheromone signaling, cell cycle control, and polarized morphogenesis. A two-dimensional hierarchical clustered matrix, covering 383 of the most highly regulated genes, was constructed from 46 diverse experimental conditions. Diagnostic subsets of coexpressed genes reflected signaling activity, cross talk, and overlap of multiple mitogen-activated protein kinase (MAPK) pathways. Analysis of the profiles specified by two different MAPKs-Fus3p and Kss1p-revealed functional overlap of the filamentous growth and mating responses. Global transcript analysis reflects biological responses associated with the activation and perturbation of signal transduction pathways.

An information-intensive approach to the molecular pharmacology of cancer.

Since 1990, the National Cancer Institute (NCI) has screened more than 60,000 compounds against a panel of 60 human cancer cell lines. The 50-percent growth-inhibitory concentration (GI50) for any single cell line is simply an index of cytotoxicity or cytostasis, but the patterns of 60 such GI50 values encode unexpectedly rich, detailed information on mechanisms of drug action and drug resistance. Each compound's pattern is like a fingerprint, essentially unique among the many billions of distinguishable possibilities. These activity patterns are being used in conjunction with molecular structural features of the tested agents to explore the NCI's database of more than 460,000 compounds, and they are providing insight into potential target molecules and modulators of activity in the 60 cell lines. For example, the information is being used to search for candidate anticancer drugs that are not dependent on intact p53 suppressor gene function for their activity. It remains to be seen how effective this information-intensive strategy will be at generating new clinically active agents.

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.

The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome). Of the deleted ORFs, 17 percent were essential for viability in rich medium. The phenotypes of more than 500 deletion strains were assayed in parallel. Of the deletion strains, 40 percent showed quantitative growth defects in either rich or minimal medium.