Transcriptome of the Female Synganglion of the Black-Legged Tick Ixodes scapularis (Acari: Ixodidae) With Comparison Between Illumina and 454 Systems

Illumina and 454 pyrosequencing were used to characterize genes from the synganglion of female Ixodes scapularis. GO term searching success for biological processes was similar for samples sequenced by both methods. However, for molecular processes, it was more successful for the Illumina samples than for 454 samples. Functional assignments of transcripts predicting neuropeptides, neuropeptide receptors, neurotransmitter receptors and other genes of interest was done, supported by strong e-values (\u3c-6), and high consensus sequence alignments. Transcripts predicting 15 putative neuropeptide prepropeptides ((allatostatin, allatotropin, bursicon α, corticotropin releasing factor (CRF), CRF-binding protein, eclosion hormone, FMRFamide, glycoprotein A, insulin-like peptide, ion transport peptide, myoinhibitory peptide, inotocin ( = neurophysin-oxytocin), Neuropeptide F, sulfakinin and SIFamide)) and transcripts predicting receptors for 14 neuropeptides (allatostatin, calcitonin, cardioacceleratory peptide, corazonin, CRF, eclosion hormone, gonadotropin-releasing hormone/AKH-like, insulin-like peptide, neuropeptide F, proctolin, pyrokinin, SIFamide, sulfakinin and tachykinin) are reported. Similar to Dermacentor variabilis, we found transcripts matching pro-protein convertase, essential for converting neuropeptide hormones to their mature form. Additionally, transcripts predicting 6 neurotransmitter/neuromodulator receptors (acetylcholine, GABA, dopamine, glutamate, octopamine and serotonin) and 3 neurotransmitter transporters (GABA transporter, noradrenalin-norepinephrine transporter and Na+-neurotransmitter/symporter) are described. Further, we found transcripts predicting genes for pheromone odorant receptor, gustatory receptor, novel GPCR messages, ecdysone nuclear receptor, JH esterase binding protein, steroidogenic activating protein, chitin synthase, chitinase, and other genes of interest. Also found were transcripts predicting genes for spermatogenesis-associated protein, major sperm protein, spermidine oxidase and spermidine synthase, genes not normally expressed in the female CNS of other invertebrates. The diversity of messages predicting important genes identified in this study offers a valuable resource useful for understanding how the tick synganglion regulates important physiological functions

Mechanisms of action of inhaled fibers, particles and nanoparticles in lung and cardiovascular diseases

<p>Abstract</p> <p>Background</p> <p>A symposium on the mechanisms of action of inhaled airborne particulate matter (PM), pathogenic particles and fibers such as silica and asbestos, and nanomaterials, defined as synthetic particles or fibers less than 100 nm in diameter, was held on October 27 and 28, 2005, at the Environmental Protection Agency (EPA) Conference Center in Research Triangle Park, North Carolina. The meeting was the eighth in a series of transatlantic conferences first held in Penarth, Wales, at the Medical Research Council Pneumoconiosis Unit (1979), that have fostered long-standing collaborations between researchers in the fields of mineralogy, cell and molecular biology, pathology, toxicology, and environmental/occupational health.</p> <p>Results</p> <p>The goal of this meeting, which was largely supported by a conference grant from the NHLBI, was to assemble a group of clinical and basic research scientists who presented and discussed new data on the mechanistic effects of inhaled particulates on the onset and development of morbidity and mortality in the lung and cardiovascular system. Another outcome of the meeting was the elucidation of a number of host susceptibility factors implicated in adverse health effects associated with inhaled pathogenic particulates.</p> <p>Conclusion</p> <p>New models and data presented supported the paradigm that both genetic and environmental (and occupational) factors affect disease outcomes from inhaled particulates as well as cardiopulmonary responses. These future studies are encouraged to allow the design of appropriate strategies for prevention and treatment of particulate-associated morbidity and mortality, especially in susceptible populations.</p

Associations Between Daily Affect and Sleep Vary by Sleep Assessment Type: What Can Ambulatory EEG Add to the Picture?

Objective/Background Disrupted sleep can be a cause and a consequence of affective experiences. However, daily longitudinal studies show sleep assessed via sleep diaries is more consistently associated with positive and negative affect than sleep assessed via actigraphy. The objective of the study was to test whether sleep parameters derived from ambulatory electroencephalography (EEG) in a naturalistic setting were associated with day-to-day changes in affect. Participants/Method Eighty adults (mean age = 32.65 years, 63% female) completed 7 days of affect and sleep assessments. We examined bidirectional associations between morning positive affect and negative affect with sleep assessed via diary, actigraphy, and ambulatory EEG. Results Mornings with lower positive affect than average were associated with higher diary- and actigraphy-determined sleep efficiency that night. Mornings with higher negative affect than average were associated with longer actigraphy-determined total sleep time that night. Nights with longer diary-determined total sleep time, greater sleep efficiency, and shorter sleep onset latency than average were associated with higher next-morning positive affect, and nights with lower diary-determined wake-after-sleep-onset were associated with lower next-morning negative affect. EEG-determined sleep and affect results were generally null in both directions: only higher morning negative affect was associated with longer rapid eye movement (REM) sleep that night. Conclusions Self-reported sleep and affect may occur in a bidirectional fashion for some sleep parameters. EEG-determined sleep and affect associations were inconsistent but may still be important to assess in future studies to holistically capture sleep. Single-channel EEG represents a novel, ecologically valid tool that may provide information beyond diaries and actigraphy

Mevalonate-Farnesal Biosynthesis in Ticks: Comparative Synganglion Transcriptomics and a New Perspective

Juvenile hormone (JH) controls the growth, development, metamorphosis, and reproduction of insects. For many years, the general assumption has been that JH regulates tick and other acarine development and reproduction the same as in insects. Although researchers have not been able to find the common insect JHs in hard and soft tick species and JH applications appear to have no effect on tick development, it is difficult to prove the negative or to determine whether precursors to JH are made in ticks. The tick synganglion contains regions which are homologous to the corpora allata, the biosynthetic source for JH in insects. Next-gen sequencing of the tick synganglion transcriptome was conducted separately in adults of the American dog tick, Dermacentor variabilis, the deer tick, Ixodes scapularis, and the relapsing fever tick, Ornithodoros turicata as a new approach to determine whether ticks can make JH or a JH precursor. All of the enzymes that make up the mevalonate pathway from acetyl-CoA to farnesyl diphosphate (acetoacetyl-CoA thiolase, HMG-S, HMG-R, mevalonate kinase, phosphomevalonate kinase, diphosphomevalonate decarboxylase, and farnesyl diphosphate synthase) were found in at least one of the ticks studied but most were found in all three species. Sequence analysis of the last enzyme in the mevalonate pathway, farnesyl diphosphate synthase, demonstrated conservation of the seven prenyltransferase regions and the aspartate rich motifs within those regions typical of this enzyme. In the JH branch from farnesyl diphosphate to JH III, we found a putative farnesol oxidase used for the conversion of farnesol to farnesal in the synganglion transcriptome of I. scapularis and D. variabilis. Methyltransferases (MTs) that add a methyl group to farnesoic acid to make methyl farnesoate were present in all of the ticks studied with similarities as high as 36% at the amino acid level to insect JH acid methyltransferase (JHAMT). However, when the tick MTs were compared to the known insect JHAMTs from several insect species at the amino acid level, the former lacked the farnesoic acid binding motif typical in insects. The P450s shown in insects to add the C10,11 epoxide to methyl farnesoate, are in the CYP15 family; this family was absent in our tick transcriptomes and in the I. scapularis genome, the only tick genome available. These data suggest that ticks do not synthesize JH III but have the mevalonate pathway and may produce a JH III precursor

Combined Effects of Acute Temperature Change and Elevated pCO2 on the Metabolic Rates and Hypoxia Tolerances of Clearnose Skate (Rostaraja eglanteria), Summer Flounder (Paralichthys dentatus), and Thorny Skate (Amblyraja radiata)

Understanding how rising temperatures, ocean acidification, and hypoxia affect the performance of coastal fishes is essential to predicting species-specific responses to climate change. Although a population’s habitat influences physiological performance, little work has explicitly examined the multi-stressor responses of species from habitats differing in natural variability. Here, clearnose skate (Rostaraja eglanteria) and summer flounder (Paralichthys dentatus) from mid-Atlantic estuaries, and thorny skate (Amblyraja radiata) from the Gulf of Maine, were acutely exposed to current and projected temperatures (20, 24, or 28 °C; 22 or 30 °C; and 9, 13, or 15 °C, respectively) and acidification conditions (pH 7.8 or 7.4). We tested metabolic rates and hypoxia tolerance using intermittent-flow respirometry. All three species exhibited increases in standard metabolic rate under an 8 °C temperature increase (Q10 of 1.71, 1.07, and 2.56, respectively), although this was most pronounced in the thorny skate. At the lowest test temperature and under the low pH treatment, all three species exhibited significant increases in standard metabolic rate (44–105%; p \u3c 0.05) and decreases in hypoxia tolerance (60–84% increases in critical oxygen pressure; p \u3c 0.05). This study demonstrates the interactive effects of increasing temperature and changing ocean carbonate chemistry are species-specific, the implications of which should be considered within the context of habitat. Associated dataset: Gail D. Schweiterman, Daniel P. Crear et al. 2019. Metabolic Rates and Hypoxia Tolerences of clearnose skate (Rostaraja eglanteria), summer flounder (Paralichthys dentatus), and thorny skate (Amblyraja radiata) https://doi.org/10.25773/qmew-c18

Metabolic Rates and Hypoxia Tolerences of clearnose skate (Rostaraja eglanteria), summer flounder (Paralichthys dentatus), and thorny skate (Amblyraja radiata)

These data were collected following methods described in the associated publication: LINK “Combined Effects of Acute Temperature Change and Elevated pCO2 on the Metabolic Rates and Hypoxia Tolerances of Clearnose Skate (Rostaraja eglanteria), Summer Flounder (Paralichthys dentatus), and Thorny Skate (Amblyraja radiata)”. Schweiterman, G.D. et al. 2019 Biology, 8(3), 56

Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation

AbstractThe majority of colorectal cancers (CRCs) arise from adenomatous polyps. In this study, we sought to present the underrecognized CRC with the residual polyp of origin (CRC RPO+) as an entity to be utilized as a model to study colorectal carcinogenesis. We identified all subjects with biopsy-proven CRC RPO+ that were evaluated over 10 years at Mayo Clinic, Rochester, MN, and compared their clinical and pathologic characteristics to CRC without remnant polyps (CRC RPO−). Overall survival and disease-free survival overlap with an equivalent hazard ratio between CRC RPO+ and RPO− cases when age, stage, and grade are adjusted. The somatic genomic profile obtained by whole genome sequencing and the gene expression profiles by RNA-seq for CRC RPO+ tumors were compared with that of age -and gender-matched CRC RPO− evaluated by The Cancer Genome Atlas. CRC RPO+ cases were more commonly found with lower-grade, earlier-stage disease than CRC RPO−. However, within the same disease stage and grade, their clinical course is very similar to that of CRC RPO−. The mutation frequencies of commonly mutated genes in CRC are similar between CRC RPO+ and RPO− cases. Likewise, gene expression patterns are indistinguishable between the RPO+ and RPO− cases. We have confirmed that CRC RPO+ is clinically and biologically similar to CRC RPO− and may be utilized as a model of the adenoma to carcinoma transition

Evolutionary comparisons of chelonid alphaherpesvirus 5 (ChHV5) genomes from fibropapillomatosis-afflicted green (chelonia mydas), Ooive ridley (lepidochelys olivacea) and kemp’s ridley (lepidochelys kempii) sea turtles

peer-reviewedThe spreading global sea turtle fibropapillomatosis (FP) epizootic is threatening some of Earth’s ancient reptiles, adding to the plethora of threats faced by these keystone species. Understanding this neoplastic disease and its likely aetiological pathogen, chelonid alphaherpesvirus 5 (ChHV5), is crucial to understand how the disease impacts sea turtle populations and species and the future trajectory of disease incidence. We generated 20 ChHV5 genomes, from three sea turtle species, to better understand the viral variant diversity and gene evolution of this oncogenic virus. We revealed previously underappreciated genetic diversity within this virus (with an average of 2035 single nucleotide polymorphisms (SNPs), 1.54% of the ChHV5 genome) and identified genes under the strongest evolutionary pressure. Furthermore, we investigated the phylogeny of ChHV5 at both genome and gene level, confirming the propensity of the virus to be interspecific, with related variants able to infect multiple sea turtle species. Finally, we revealed unexpected intra-host diversity, with up to 0.15% of the viral genome varying between ChHV5 genomes isolated from different tumours concurrently arising within the same individual. These findings offer important insights into ChHV5 biology and provide genomic resources for this oncogenic viru

Galaxy Zoo : 3D – crowdsourced bar, spiral, and foreground star masks for MaNGA target galaxies

Funding: Funding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. We gratefully acknowledge the National Science Foundation’s support of the Keck Northeast Astronomy Consortium’s REU program through grants AST-1005024 and AST-1950797, the KINSC (Koshland Integrated Natural Sciences Centre) at Haverford College for Summer Scholar funding, and the Ogden Trust, UK for support for summer undergraduate internships.The challenge of consistent identification of internal structure in galaxies – in particular disc galaxy components like spiral arms, bars, and bulges – has hindered our ability to study the physical impact of such structure across large samples. In this paper we present Galaxy Zoo: 3D (GZ:3D) a crowdsourcing project built on the Zooniverse platform that we used to create spatial pixel (spaxel) maps that identify galaxy centres, foreground stars, galactic bars, and spiral arms for 29 831 galaxies that were potential targets of the MaNGA survey (Mapping Nearby Galaxies at Apache Point Observatory, part of the fourth phase of the Sloan Digital Sky Surveys or SDSS-IV), including nearly all of the 10 010 galaxies ultimately observed. Our crowdsourced visual identification of asymmetric internal structures provides valuable insight on the evolutionary role of non-axisymmetric processes that is otherwise lost when MaNGA data cubes are azimuthally averaged. We present the publicly available GZ:3D catalogue alongside validation tests and example use cases. These data may in the future provide a useful training set for automated identification of spiral arm features. As an illustration, we use the spiral masks in a sample of 825 galaxies to measure the enhancement of star formation spatially linked to spiral arms, which we measure to be a factor of three over the background disc, and how this enhancement increases with radius.Publisher PDFPeer reviewe