Richard G. Manzon

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next‐generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double‐digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0‐, 12‐, 48‐ and 96‐h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12–48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96‐h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2‐ to 16‐fold), and additional read‐length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.

Critical windows in embryonic development: Shifting incubation temperatures alter heart rate and oxygen consumption of Lake Whitefish (Coregonus clupeaformis) embryos and hatchlings

Critical windows are periods of developmental susceptibility when the phenotype of an embryonic, juvenile or adult animal may be vulnerable to environmental fluctuations. Temperature has pervasive effects on poikilotherm physiology, and embryos are especially vulnerable to temperature shifts. To identify critical windows, we incubated whitefish embryos at control temperatures of 2°C, 5°C, or 8°C, and shifted treatments among temperatures at the end of gastrulation or organogenesis. Heart rate (fH) and oxygen consumption ( [Formula: see text] ) were measured across embryonic development, and [Formula: see text] was measured in 1-day old hatchlings. Thermal shifts, up or down, from initial incubation temperatures caused persistent changes in fH and [Formula: see text] compared to control embryos measured at the same temperature (2°C, 5°C, or 8°C). Most prominently, when embryos were measured at organogenesis, shifting incubation temperature after gastrulation significantly lowered [Formula: see text] or fH. Incubation at 2°C or 5°C through gastrulation significantly lowered [Formula: see text] (42% decrease) and fH (20% decrease) at 8°C, incubation at 2°C significantly lowered [Formula: see text] (40% decrease) and fH (30% decrease) at 5°C, and incubation at 5°C and 8°C significantly lowered [Formula: see text] at 2°C (27% decrease). Through the latter half of development, [Formula: see text] and fH in embryos were not different from control values for thermally shifted treatments. However, in hatchlings measured at 2°C, [Formula: see text] was higher in groups incubated at 5°C or 8°C through organogenesis, compared to 2°C controls (43 or 65% increase, respectively). Collectively, these data suggest that embryonic development through organogenesis represents a critical window of embryonic and hatchling phenotypic plasticity. This study presents an experimental design that identified thermally sensitive periods for fish embryos.

Hormetic effects of gamma radiation on the stress axis of natural populations of meadow voles (Microtus pennsylvanicus)

We tested the hypothesis that low doses of gamma radiation have beneficial, hormetic effects on the stress axis (the hypothalamic-pituitary-adrenocortical axis) of free-ranging meadow vole populations (Microtus pennsylvanicus). Voles were exposed to chronic gamma radiation from a 137Cs field irradiator. In isolated populations, voles received one of three treatments over a four-year period: Controls (0.19-0.42 microGy/h--levels that were 2-5x above background levels [0.1 microGy/h] and live-trapped in all years--1982--1985), low doses (22.6 microGy/h--50-200x background, live-trapped from November 1982--April 1985), or high doses (3,840 microGy/h--40,000x background, live-trapped from November 1983--April 1985). Voles exposed to a low dose had levels of free and total corticosterone that were significantly higher than those in the control or high-dose groups. Differences in response to radiation between the sexes were apparent for maximum corticosterone-binding capacity, with females exposed to low doses having higher binding capacity than control or high-dose females, whereas males exposed to low doses had lower binding capacity than control or high-dose males. Low-dose voles had higher counts of neutrophils than either the controls or high-dose voles; hematocrit was greater in the controls than in irradiated voles. These results indicate that voles display a hormetic response to radiation, wherein low doses of an otherwise harmful agent produce a beneficial effect. The stimulation of the stress axis resulting in the increased secretion of glucocorticoids, which may protect against the excessive actions of the immune and inflammatory responses, may be a key mechanism producing this effect.

A Self-Contained, Controlled Hatchery System for Rearing Lake Whitefish Embryos for Experimental Aquaculture

AbstractA self-contained, small-scale research hatchery was constructed in a modified chromatography refrigerator equipped with a filtered and UV-sterilized water recirculation system. Lake Whitefish Coregonus clupeaformis embryos were raised in conventional upwelling hatching jars, in dishes with a continuous slow “drip feed,” and in a variety of static water incubation systems in petri dishes and multiwell plates. The optimal rearing density for petri dishes was found to be 50 embryos per dish, with weekly water changes. The highest survival in multiwell plates was seen in the 6- and 24-well sizes. Survival rates in most multiwell plates and petri dishes, as well as in the hatching jar incubators, were between 40% and 60%, which is in line with survival rates seen in commercial large-scale rearing. Overall, these techniques permitted the rearing of large numbers of whitefish in separate batches and under controlled conditions, while greatly reducing space requirements and material costs. Our system is w...

Changes in the Gut Microbiome of the Sea Lamprey during Metamorphosis

ABSTRACT Vertebrate metamorphosis is often marked by dramatic morphological and physiological changes of the alimentary tract, along with major shifts in diet following development from larva to adult. Little is known about how these developmental changes impact the gut microbiome of the host organism. The metamorphosis of the sea lamprey (Petromyzon marinus) from a sedentary filter-feeding larva to a free-swimming sanguivorous parasite is characterized by major physiological and morphological changes to all organ systems. The transformation of the alimentary canal includes closure of the larval esophagus and the physical isolation of the pharynx from the remainder of the gut, which results in a nonfeeding period that can last up to 8 months. To determine how the gut microbiome is affected by metamorphosis, the microbial communities of feeding and nonfeeding larval and parasitic sea lamprey were surveyed using both culture-dependent and -independent methods. Our results show that the gut of the filter-feeding larva contains a greater diversity of bacteria than that of the blood-feeding parasite, with the parasite gut being dominated by Aeromonas and, to a lesser extent, Citrobacter and Shewanella. Phylogenetic analysis of the culturable Aeromonas from both the larval and parasitic gut revealed that at least five distinct species were represented. Phenotypic characterization of these isolates revealed that over half were capable of sheep red blood cell hemolysis, but all were capable of trout red blood cell hemolysis. This suggests that the enrichment of Aeromonas that accompanies metamorphosis is likely related to the sanguivorous lifestyle of the parasitic sea lamprey.

Embryonic development of lake whitefish Coregonus clupeaformis: a staging series, analysis of growth and effects of fixation

A reference staging series of 18 morphological stages of laboratory reared lake whitefish Coregonus clupeaformis is provided. The developmental processes of blastulation, gastrulation, neurulation as well as development of the eye, circulatory system, chromatophores and mouth are included and accompanied by detailed descriptions and live imaging. Quantitative measurements of embryo size and mass were taken at each developmental stage. Eggs were 3·19 ± 0·16 mm (mean ± s.d.) in diameter at fertilization and embryos reached a total length (LT ) of 14·25 ± 0·41 mm at hatch. Separated yolk and embryo dry mass were 0·25 ± 0·08 mg and 1·39 ± 0·17 mg, respectively, at hatch. The effects of two common preservatives (formalin and ethanol) were examined throughout development and post hatch. Embryo LT significantly decreased following fixation at all points in development. A correction factor to estimate live LT from corresponding fixed LT was determined as live LT = (fixed LT )(1·025) . Eye diameter and yolk area measurements significantly increased in fixed compared with live embryos up to 85-90% development for both measurements. The described developmental stages can be generalized to teleost species, and is particularly relevant for the study of coregonid development due to additionally shared developmental characteristics. The results of this study and staging series are therefore applicable across various research streams encompassing numerous species that require accurate staging of embryos and descriptions of morphological development.

Thermal stress and the heat shock response in embryonic and young of the year juvenile lake whitefish.

We investigated the effects of thermal stress on embryonic (fin flutter, vitelline circulation stage) and young of the year (YOY) juvenile lake whitefish by characterizing the kinetics of the heat shock response (HSR). Lake whitefish were subjected to one of three different heat shock (HS) temperatures (3, 6, or 9 °C above control) for six different lengths of time (0.25, 0.50, 1, 2, 3, or 4h) followed by a 2h recovery period at the control temperature of 2 °C or 14 °C for embryos and YOY juveniles, respectively. The duration of the HSR was examined by allowing the fish to recover for 1, 2, 4, 8, 12, 16, 24, 36, or 48 h following a 2h HS. In embryos, at the fin flutter stage, only hsp70 mRNA levels were upregulated in response to the various HS treatments. By comparison, all three typically inducible hsps, hsp90α, hsp70 and hsp47, were upregulated in the YOY juveniles. In both instances the HSR was long lasting, but much more so in embryos where hsp70 mRNA levels continued to increase for 48 h after a 2h HS and remained significantly higher than untreated controls. Collectively our data indicate that both embryo and YOY juvenile lake whitefish have a robust HSR which permits them to survive a 4h, 9 °C HS. Moreover, both life history stages are capable of triggering a HSR following a moderate 3 °C HS which is likely an important protective mechanism against environmental stressors during embryogenesis and early life history stages of lake whitefish.

Thyroid hormone and retinoid X receptor function and expression during sea lamprey (Petromyzon marinus) metamorphosis

Sea lampreys (Petromyzon marinus) are members of the ancient class Agnatha and undergo a metamorphosis that transforms blind, sedentary, filter-feeding larvae into free-swimming, parasitic juveniles. Thyroid hormones (THs) appear to be important for lamprey metamorphosis, however, serum TH concentrations are elevated in the larval phase, decline rapidly during early metamorphosis and remain low until metamorphosis is complete; these TH fluctuations are contrary to those of other metamorphosing vertebrates. Moreover, thyroid hormone synthesis inhibitors (goitrogens) induce precocious metamorphosis and exogenous TH treatments disrupt natural metamorphosis in P. marinus. Given that THs exert their effects by binding to TH nuclear receptors (TRs) that often act as heterodimers with retinoid X receptors (RXRs), we cloned and characterized these receptors from P. marinus and examined their expression during metamorphosis. Two TRs (PmTR1 and PmTR2) and three RXRs (PmRXRs) were isolated from P. marinus cDNA. Phylogenetic analyses group the PmTRs together on a branch prior to the gnathostome TRα/β split. The three RXRs also group together, but our data indicated that these transcripts are most likely either allelic variants of the same gene locus, or the products of a lamprey-specific duplication event. Importantly, these P. marinus receptors more closely resemble vertebrate as opposed to invertebrate chordate receptors. Functional analysis revealed that PmTR1 and PmTR2 can activate transcription of TH-responsive genes when treated with nanomolar concentrations of TH and they have distinct pharmacological profiles reminiscent of vertebrate TRβ and TRα, respectively. Also similar to other metamorphosing vertebrates, expression patterns of the PmTRs during lamprey metamorphosis suggest that PmTR1 has a dynamic, tissue-specific expression pattern that correlates with tissue morphogenesis and biochemical changes and PmTR2 has a more uniform expression pattern. This TR expression data suggests that THs, either directly or via a metabolite, may function to positively modulate changes at the tissue or organ levels during lamprey metamorphosis. Collectively the results presented herein support the hypothesis that THs have a dual functional role in the lamprey life cycle whereby high levels promote larval feeding, growth and lipogenesis and low levels promote metamorphosis.

Sea lamprey (Petromyzon marinus) contain four developmentally regulated serum thyroid hormone distributor proteins.

Thyroid hormones (THs) are very lipophilic molecules which require a distribution network for efficient transport in serum. Despite observations that THs function in a wide variety of processes, including aspects of fish development (i.e., flat fish metamorphosis and smoltification), the proteins responsible for TH distribution in fish serum remain poorly studied. We chose to investigate the serum TH distributor proteins (THDPs) in lampreys. As one of only two extant agnathans, data on lamprey THDPs may offer new insights into the evolution of the vertebrate TH distribution network and serum proteins in general. Moreover, lampreys appear to contradict the vertebrate model of an increase in TH concentrations initiating and driving vertebrate metamorphosis. We show for the first time that sea lamprey serum contains at least four THDPs and that their presence in serum is temporally regulated throughout the life cycle. The albumin, glycoprotein AS is the dominant THDP present in the sera of larval and metamorphosing sea lamprey. In stage seven of metamorphosis, three additional THDPs appear, including the albumin, glycoprotein SDS-1; the glycolipoprotein CB-III; and an unidentified low molecular weight protein temporarily named Spot-5. The sera of parasitic and upstream migrant sea lampreys lack AS; their serum THDPs are SDS-1, CB-III, and Spot-5. Our data indicate that despite the change in type and number of THDPs, the overall total TH binding capacity of sea lamprey serum remains fairly stable until stage 7 of metamorphosis when a only modest decrease in total binding capacity is observed. Collectively these data indicate that the decline in serum TH concentrations observed during lamprey metamorphosis is not a consequence of a reduction in the distribution and storage capacity of the serum.

CRH peptide evolution occurred in three phases: Evidence from characterizing sea lamprey CRH system members

The corticotropin releasing hormone (CRH) system, which includes the CRH family of peptides, their receptors (CRHRs) and a binding protein (CRHBP), has been strongly conserved throughout vertebrate evolution. The identification of invertebrate homologues suggests this system evolved over 500 million years ago. However, the early vertebrate evolution of the CRH system is not understood. Current theory indicates that agnathans (hagfishes and lampreys) are monophyletic with a conservative evolution over the past 500million years and occupy a position at the root of vertebrate phylogeny. We isolated the cDNAs for three CRH family members, two CRHRs and a CRHBP from the sea lamprey, Petromyzon marinus. Two of the CRH peptides are related to the CRH/urotensin-1 (UI) lineage, whereas the other is a urocortin (Ucn) 3 orthologue. The predicted amino acid identity of CRH and UI is 61% but they possess distinct motifs indicative of each peptide, suggesting an early divergence of the two genes. Based on our findings we propose the CRH peptides evolved in at least 3 distinct phases. The first occurring prior to the agnathans gave rise to the CRH/UI-like and Ucn2/3-like paralogous lineages. The second was a partial sub-genomic duplication of the ancestral CRH/UI-like gene, but not the Ucn2/3-like gene, giving rise to the CRH and UI (Ucn) lineages. The third event which resulted in the appearance of Ucn2 and Ucn3 must have occurred after the evolution of the cartilaginous fishes. Interestingly, unlike other vertebrate CRHRs, we were unable to classify our two P. marinus receptors (designated CRHRα and CRHRβ) as either type 1 or type 2, indicating that this split evolved later in vertebrate evolution. A single CRHBP gene was found suggesting that either this gene has not been affected by the vertebrate genome duplications or there have been a series of paralogous gene deletions. This study suggests that P. marinus possess a functional CRH system that differs from that of the gnathostomes and may represent a model for the earliest functioning CRH system in vertebrates.