High‐throughput methods for visualizing the teleost skeleton: capturing autofluorescence of alizarin red

For nearly a century, Alizarin red S (alizarin sodium sulfonate) has been used by morphologists to stain calcified bone matrix. More recently, its traditional use has frequently been replaced by more modern techniques; however, its auto fluorescent property continues to contribute to research well beyond the context of bone development and regeneration. The purpose of this study is to describe detailed methods that can be used to capture the autofluorescence of Alizarin red‐stained mineralized tissues in juvenile zebrafish. These methods allow for in situ analyses of minute skeletal elements, such as pharyngeal teeth, and preclude the need for dissection.     

Development of the pharyngeal arch skeleton in Catostomus commersonii (Teleostei: Cypriniformes)

Skeletal elements of the gill arches of adult cypriniform fishes vary widely in number, size, and shape and are important characters in morphologically based phylogenetic studies. Understanding the developmental basis for this variation is thus phylogenetically significant but also important in relation to the many developmental genetic and molecularly based studies of the early developing and hence experimentally tractable gill arches in the zebrafish, a cyprinid cypriniform. We describe the sequence of the chondrification and ossification of the pharyngeal arches and associated dermal bones from Catostomus commersonii (Catostomidae, Cypriniformes) and make selected comparisons to other similarly described pharyngeal arches. We noted shared spatial trends in arch development including the formation of ventral cartilages before dorsal and anterior cartilages before posterior. Qualitatively variable gill arch elements in Cypriniformes including pharyngobranchial 1, pharyngobranchial 4, and the sublingual are the last such elements to chondrify in C. commersonii. We show that the sublingual bone in C. commersonii has two cartilaginous precursors that fuse and ossify to form the single bone in adults. This indicates homology of the sublingual in catostomids to the two sublingual bones in the adults of cobitids and balitorids. Intriguing patterns of fusion and segmentation of the cartilages in the pharyngeal arches were discovered. These include the individuation of the basihyal and anterior copula through segmentation of a single cartilage rod, fusion of cartilaginous basibranchials 4 and 5, and fusion of hypobranchial 4 with ceratobranchial 4. Such “fluidity” in cartilage patterning may be widespread in fishes and requires further comparative developmental studies. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc.     

Genetic analysis of craniofacial development in the vertebrate embryo

Every cartilage and bone in the vertebrate skeleton has a precise shape and position. The head skeleton develops in the embryo from the neural crest, which emigrates from the neural ectoderm and forms the skull and pharyngeal arches. Recent genetic data from mice and zebrafish suggest that cells in the pharyngeal segments are specified by positional information in at least two dimensions, Hox genes along the anterior-posterior axis and other homeobox genes along the dorsal-ventral axis within a segment. Many zebrafish and human mutant phenotypes indicate that additional genes are required for the development of groups of adjacent pharyngeal arches and for patterning along the mediolateral axis of the skull. The complementary genetic approaches in humans, mice and fish reveal networks of genes that specify the complex morphology of the head skeleton along a relatively simple set of coordinates.     

Divergent requirements for fibroblast growth factor signaling in zebrafish maxillary barbel and caudal fin regeneration

The zebrafish maxillary barbel is an integumentary organ containing skin, glands, pigment cells, taste buds, nerves, and endothelial vessels. The maxillary barbel can regenerate (LeClair & Topczewski 2010); however, little is known about its molecular regulation. We have studied fibroblast growth factor (FGF) pathway molecules during barbel regeneration, comparing this system to a well‐known regenerating appendage, the zebrafish caudal fin. Multiple FGF ligands (fgf20a, fgf24), receptors (fgfr1‐4) and downstream targets (pea3, il17d) are expressed in normal and regenerating barbel tissue, confirming FGF activation. To test if specific FGF pathways were required for barbel regeneration, we performed simultaneous barbel and caudal fin amputations in two temperature‐dependent zebrafish lines. Zebrafish homozygous for a point mutation in fgf20a, a factor essential for caudal fin blastema formation, regrew maxillary barbels normally, indicating that the requirement for this ligand is appendage‐specific. Global overexpression of a dominant negative FGF receptor, Tg(hsp70l:dn‐fgfr1:EGFP)^pd1 completely blocked fin outgrowth but only partially inhibited barbel outgrowth, suggesting reduced requirements for FGFs in barbel tissue. Maxillary barbels expressing dn‐fgfr1 regenerated peripheral nerves, dermal connective tissue, endothelial tubes, and a glandular epithelium; in contrast to a recent report in which dn‐fgfr1 overexpression blocks pharyngeal taste bud formation in zebrafish larvae (Kapsimali et al. 2011), we observed robust formation of calretinin‐positive tastebuds. These are the first experiments to explore the molecular mechanisms of maxillary barbel regeneration. Our results suggest heterogeneous requirements for FGF signaling in the regeneration of different zebrafish appendages (caudal fin versus maxillary barbel) and taste buds of different embryonic origin (pharyngeal endoderm versus barbel ectoderm).     

Rapid evolution of thermal plasticity in mountain lake Daphnia populations

Populations at risk of extinction due to climate change may be rescued by adaptive evolution or plasticity. Selective agents, such as introduced predators, may enhance or constrain plastic or adaptive responses to temperature. We tested responses of Daphnia to temperature by collecting populations from lakes across an elevational gradient in the presence and absence of fish predators (long‐term selection). We subsequently grew these populations at two elevations in field mesocosms over two years (short‐term selection), followed by a common‐garden experiment at two temperatures in the lab to measure life‐history traits. Both long‐term and short‐term selection affected traits, suggesting that genetic variation of plasticity within populations enabled individuals to rapidly evolve plasticity in response to high temperature. We found that short‐term selection by high temperature increased plasticity for growth rate in all populations. Fecundity was higher in populations from fishless lakes and body size showed greater plasticity in populations from warm lakes (long‐term selection). Neither body size nor fecundity were affected by short‐term thermal selection. These results demonstrate that plasticity is an important component of the life‐history response of Daphnia, and that genetic variation within populations enabled rapid evolution of plasticity in response to selection by temperature.     

Integration of Zebrafish Model and Network Pharmacology to Explore Possible Action Mechanisms of Morinda officinalis for Treating Osteoporosis

Osteoporosis (OP) is a metabolic bone disease affecting nearly 200 million individuals globally. Morinda officinalis F.C.How (MOH) has long been used as a traditional herbal medicine for the treatment of bone fractures and joint diseases in China. However, it still remains unclear how the compounds in MOH work synergistically for treating OP. In this study, we used prednisolone (PNSL)‐induced zebrafish OP model to screen the antiosteoporosis components in MOH. A network pharmacology approach was further proposed to explore the underlying mechanism of MOH on OP. The PNSL‐induced zebrafish model validated that two anthraquinones, one iridoid glycoside, and two saccharides exerted antiosteoporotic effect. We constructed the components‐targets network and obtained the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 26 candidate compounds of MOH and 257 related targets could probably treat OP through regulating osteoclast differentiation and MAPK signaling pathway. Our work developed a strategy to screen the antiosteoporosis components and explore the underlying mechanism of MOH for treating OP at a network pharmacology level.     

Mate competition and evolutionary outcomes in genetically modified zebrafish (Danio rerio)

Demonstrating relationships between sexual selection mechanisms and trait evolution is central to testing evolutionary theory. Using zebrafish, we found that wild‐type males possessed a significant advantage in mate competition over transgenic RFP Glofish® males. In mating trials, wild‐type males were aggressively superior to transgenic males in male–male chases and male–female chases; as a result, wild‐type males sired 2.5× as many young as did transgenic males. In contrast, an earlier study demonstrated that female zebrafish preferred transgenic males as mates when mate competition was excluded experimentally. We tested the evolutionary consequence of this conflict between sexual selection mechanisms in a long‐term study. The predicted loss of the transgenic phenotype was confirmed. More than 18,500 adults collected from 18 populations across 15 generations revealed that the frequency of the transgenic phenotype declined rapidly and was eliminated entirely in all but one population. Fitness component data for both sexes indicated that only male mating success differed between wild‐type and transgenic individuals. Our predictive demographic model based on fitness components closely matched the rate of transgenic phenotype loss observed in the long‐term study, thereby supporting its utility for studies assessing evolutionary outcomes of escaped or released genetically modified animals.     

The African turquoise killifish: A research organism to study vertebrate aging and diapause

The African turquoise killifish has recently gained significant traction as a new research organism in the aging field. Our understanding of aging has strongly benefited from canonical research organisms—yeast, C. elegans, Drosophila, zebrafish, and mice. Many characteristics that are essential to understand aging—for example, the adaptive immune system or the hypothalamo‐pituitary axis—are only present in vertebrates (zebrafish and mice). However, zebrafish and mice live more than 3 years and their relatively long lifespans are not compatible with high‐throughput studies. Therefore, the turquoise killifish, a vertebrate with a naturally compressed lifespan of only 4–6 months, fills an essential gap to understand aging. With a recently developed genomic and genetic toolkit, the turquoise killifish not only provides practical advantages for lifespan and longitudinal experiments, but also allows more systematic characterizations of the interplay between genetics and environment during vertebrate aging. Interestingly, the turquoise killifish can also enter a long‐term dormant state during development called diapause. Killifish embryos in diapause already have some organs and tissues, and they can last in this state for years, exhibiting exceptional resistance to stress and to damages due to the passage of time. Understanding the diapause state could give new insights into strategies to prevent the damage caused by aging and to better preserve organs, tissues, and cells. Thus, the African turquoise killifish brings two interesting aspects to the aging field—a compressed lifespan and a long‐term resistant diapause state, both of which should spark new discoveries in the field.     

Visualization of skeletons and intervertebral disks in live fish larvae by fluorescent calcein staining and disk specific GFP expression

Zebrafish and medaka have become popular models for studying skeletal development because of high fecundity, shorter generation period, and transparency of fish embryo. The first step to study skeletal development is visualizing bone and cartilage. Live animal staining with fluorescent calcein have several advantages over the standard skeletal staining protocol by using alizarin red and alcian blue for bone and cartilage. However, there is no detailed study examining skeletal development of live marine fish larvae by calcein staining. Here we applied calcein staining to examine skeletal development in red sea bream larvae. In addition, green fluorescent protein (GFP) reporter zebrafish was employed to trace lineage analysis of intervertebral disk cells in live fish larvae. Calcein staining of red sea bream larvae successfully visualized development of craniofacial skeletons as well as urinary calculus. Histochemical detection of alkaline phosphatase (ALP) activity revealed that abnormal segmentation of notochord induced by RA during vertebral development in zebrafish. Immunohistochemistry clearly revealed that GFP‐positive cells in intervertebral space was nucleus polposus like cell in twhh‐GFP transgenic zebrafish. It was demonstrated usefulness of calcein and ALP staining and twhh‐GFP transgenic zebrafish for studying skeletal development in live fish larvae.     

Novel model of restricted mobility induced osteopenia in zebrafish

Immobilization, such as prolonged bed rest, is a risk factor for bone loss in humans. Motivated by the emerging utility of zebrafish (Danio rerio) as an animal of choice for the study of musculoskeletal disease, here we report a model of restricted mobility induced osteopenia in adult zebrafish. Aquatic tanks with small cubical compartments to restrict the movement and locomotion of single fish were designed and fabricated for this study. Adult zebrafish were divided into two groups: a normal control (CONT) and a restricted mobility group (RMG) (18 fish/group). Six fish from each group were euthanized on days 14, 21 and 35 of the movement restriction. By using microcomputed tomography (micro-CT), we assessed bone volume/tissue volume (BV/TV) and bone density in the whole skeleton of the fish. Furthermore, we assessed skeletal shape in the vertebrae (radius, length, volume, neural and haemal arch aperture areas, neural and haemal arch angle, and thickness of the intervertebral space), single vertebra bone volume and bone density. Movement restriction significantly decreased vertebral skeletal parameters such as radius, length, volume, arch aperture areas and angles as well as the thickness of the intervertebral space in RMG. Furthermore, restricted mobility significantly (P < 0.001) decreased BV/TV and bone density as compared to the CONT group, starting as early as 14 days. By analysing zebrafish from CONT and RMG, we show that micro-CT imaging is a sensitive method to quantify distinct skeletal properties in zebrafish. We further defined the micro-CT parameters which can be used to examine the effects of restricted mobility on the skeleton of the fish. Our findings propose a rapid and effective osteopenia “stabulation” model, which could be used widely for osteoporosis drug screening.     

Aggression and social support predict long‐term cortisol levels in captive tufted capuchin monkeys (Cebus [Sapajus] apella)

Many nonhuman primates live in complex social groups in which they regularly encounter both social stressors such as aggression and social support such as that provided by long‐term affiliative relationships. Repeated exposure to social stressors may result in chronically elevated cortisol levels that can have deleterious physical effects such as impaired immune function, cardiovascular disease, and reduced brain function. In contrast, affiliative social relationships may act as a buffer, dampening the release of cortisol in response to acute and chronic stressors. Understanding how social stressors and social support predict cortisol levels is therefore essential to understanding how social situations relate to health and welfare. We studied this relationship in 16 socially housed captive brown capuchin monkeys (Cebus [Sapajus] apella) by comparing long‐term hair cortisol levels with behavioral measures of social stress (dominance rank, rank certainty, and amount of aggression received) and social support (amount of affiliation and centrality in the affiliative social network of the group). Dominance rank, rank certainty, amount of affiliation, and age were not significant predictors of long‐term cortisol levels in this population. Instead, long‐term cortisol levels were positively related to the amount of aggression received and negatively related to centrality in the affiliative social network of the group. This pattern may be attributed to the species’ socially tolerant dominance system and to the availability of social support across the dominance hierarchy.     

Accumulation of apoptosis‐insensitive human bone marrow‐mesenchymal stromal cells after long‐term expansion

Cells undergo replicative senescence during in vitro expansion, which is induced by the accumulation of cellular damage caused by excessive reactive oxygen species. In this study, we investigated whether long‐term‐cultured human bone marrow mesenchymal stromal cells (MSCs) are insensitive to apoptotic stimulation. To examine this, we established replicative senescent cells from long‐term cultures of human bone marrow MSCs. Senescent cells were identified based on declining population doublings, increased expression of senescence markers p16 and p53 and increased senescence‐associated β‐gal activity. In cell viability assays, replicative senescent MSCs in late passages (i.e. 15–19 passages) resisted damage induced by oxidative stress more than those in early passages did (i.e. 7–10 passages). This resistance occurred via caspase‐9 and caspase‐3 rather than via caspase‐8. The senescent cells are gradually accumulated during long‐term expansion. The oxidative stress‐sensitive proteins ataxia‐telangiectasia mutated and p53 were phosphorylated, and the expression of apoptosis molecules Bax increased, and Bcl‐2 decreased in early passage MSCs; however, the expression of the apoptotic molecules did less change in response to apoptotic stimulation in late‐passage MSCs, suggesting that the intrinsic apoptotic signalling pathway was not induced by oxidative stress in long‐term‐cultured MSCs. Based on these results, we propose that some replicative senescent cells may avoid apoptosis signalling via impairment of signalling molecules and accumulation during long‐term expansion. Copyright © 2016 John Wiley & Sons, Ltd.     

How specialized volatiles respond to chronic and short‐term physiological and shock heat stress in Brassica nigra

Brassicales release volatile glucosinolate breakdown products upon tissue mechanical damage, but it is unclear how the release of glucosinolate volatiles responds to abiotic stresses such as heat stress. We used three different heat treatments, simulating different dynamic temperature conditions in the field to gain insight into stress‐dependent changes in volatile blends and photosynthetic characteristics in the annual herb Brassica nigra (L.) Koch. Heat stress was applied by either heating leaves through temperature response curve measurements from 20 to 40 °C (mild stress), exposing plants for 4 h to temperatures 25–44 °C (long‐term stress) or shock‐heating leaves to 45–50 °C. Photosynthetic reduction through temperature response curves was associated with decreased stomatal conductance, while the reduction due to long‐term stress and collapse of photosynthetic activity after heat shock stress were associated with non‐stomatal processes. Mild stress decreased constitutive monoterpene emissions, while long‐term stress and shock stress resulted in emissions of the lipoxygenase pathway and glucosinolate volatiles. Glucosinolate volatile release was more strongly elicited by long‐term stress and lipoxygenase product released by heat shock. These results demonstrate that glucosinolate volatiles constitute a major part of emission blend in heat‐stressed B. nigra plants, especially upon chronic stress that leads to induction responses.     

Low divergence in Dlx gene expression between dentitions of the medaka (Oryzias latipes) versus high level of expression shuffling in osteichtyans

SUMMARY Serially homologous structures are believed to originate from the redeployment of a genetic cascade in different locations of the body. Serial homologs may diverge at the genetic and morphological level and acquire developmental independency (individualization). Teeth are repeated units that form dentitions found on different bones of the oral–pharyngeal cavity in gnathostomes and provide a good model to study such processes. Previous comparisons of dlx gene expression patterns between mouse oral teeth and zebrafish pharyngeal teeth showed a high level of divergence. Furthermore, these genes are differentially expressed in different teeth of the zebrafish, and in the mouse they are responsible for tooth identity (incisors vs. molars). We examined the potential divergence of dlx gene expression between oral and pharyngeal teeth by examining the expression pattern in the development of the first generation teeth of the medaka and comparing it with data from the zebrafish and the mouse. Out of the seven medaka dlx genes, five are expressed during odontogenesis compared with six in both the zebrafish and the mouse. The only difference observed between oral and pharyngeal teeth in the medaka is an earlier expression of dlx5a in the oral dental epithelium. The subset of dlx genes expressed in the medaka, zebrafish, and mouse is slightly different but their detailed expression patterns are highly divergent. Our results demonstrate a low constraint on dlx gene expression shuffling in the odontogenic cascade within osteichtyans but the non-individualization of oral and pharyngeal dentitions in the medaka.     

Apple (Malus pumila var. domestica) phenology is advancing due to rising air temperature in northern Japan

Recent studies show advancing onset of plant growing season in many regions for the last several decades. With the well‐established dependence of plant phenology on temperature, these trends are interpreted as an indication of global warming. For several decades, however, other determinants of plant phenology, e.g. varieties and trends in managed systems, may have changed and confounded the phenological trends. In this study, we tested if long‐term changes in phenology of apple (Malus pumila var. domestica) are attributable to long‐term changes in temperature by comparing the phenological response to long‐term trend in air temperature, which is of our interest, with that to year‐to‐year fluctuation in air temperature, which should represent the real effect of temperature on phenology. We collected records of air temperature and phenological events (budding and flowering) in apple from 1977 to 2004 at six locations in Japan. Linear trends in flowering showed advancing rate in the range from 0.21 to 0.35 day yr^?1, statistically significant at three locations (P<0.05). We also found a warming trend in mean air temperature throughout March and April, with which flowering was closely correlated, in the range from 0.047 to 0.077 °C yr^?1, statistically significant at five locations (P<0.05). We separated the temperature time‐series into two components: a long‐term trend and a year‐to‐year fluctuation, by fitting smoothing spline to the trend and taking the residuals as the anomaly. We then fit a multiple regression model of phenological response to air temperature with separate coefficients for long‐term trend and anomaly. Flowering date responded to the long‐term trend at ?3.8 day °C^?1 and to the anomaly at ?4.6 day °C^?1. The temperature coefficients were not statistically different from each other or among locations, suggesting that the advance of apple phenology has predominantly been caused by the temperature increase across the locations studied. The same result was also observed with budding.     

The spatio‐temporal forest patch dynamics inferred from the fine‐scale synchronicity in growth chronology

Question: Abrupt increments in tree radial growth chronology are associated with gap formations derived from disturbances. If a forest has been primarily controlled by fine‐scale disturbances such as single tree‐fall, do these release events spatio‐temporally synchronize at a fine scale such as 10 m and 5 years? Is it possible to quantify spatio‐temporal patterns of synchronicity from tree rings and long‐term inventories, and associate them with spatial forest patch dynamics? How and to what extent can we reconstruct the fine‐scale synchronized growth and spatio‐temporal forest patch dynamics from currently available information? Location: Cores were taken from Abies sachalinensis trees in a coniferous/deciduous mixed forest in the Shiretoko Peninsula, Hokkaido, northern Japan. Methods: We first eliminated short‐term fluctuations and highlighted growth trends over the mid‐term using a time‐series smoothing technique. This helped identify release events, we then conducted fine‐scale spatial analyses on released A. sachalinensis primarily with cluster analysis. Results: We specified the unit scale of synchronicity at 10 m, and classified released A. sachalinensis trees into spatially separated regions. Only once during the recent 50 years was extensive synchronicity over 40 m found. Most of the released A. sachalinensis were isolated, with non‐released A. sachalinensis present in nearby, implying imperfect synchronization. The ambiguous 20–30 m A. sachalinensis patches present in the current forest were the result of connected and overlapping patches smaller than 10 m associated with different disturbances and different responses of understorey trees. Conclusion: Tree‐ring series, long‐term census and fine‐scale spatio‐temporal analyses revealed that this forest community has been controlled by two types of disturbance: frequent small disturbances such as single tree‐fall and less frequent multiple tree‐falls.     

Long‐term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods,data management,and long‐term population trends

Long‐term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long‐term viability of species, but large‐scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long‐term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long‐term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long‐term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year‐to‐year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large‐scale and long‐term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long‐term observational studies. For instance, in the case of the Glanville fritillary project, the long‐term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life‐history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long‐term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.     

Label‐free quantitative analysis of the membrane proteome of Bace1 protease knock‐out zebrafish brains

The aspartyl protease BACE1 cleaves neuregulin 1 and is involved in myelination and is a candidate drug target for Alzheimer's disease, where it acts as the β‐secretase cleaving the amyloid precursor protein. However, little is known about other substrates in vivo. Here, we provide a proteomic workflow for BACE1 substrate identification from whole brains, combining filter‐aided sample preparation, strong‐anion exchange fractionation, and label‐free quantification. We used bace1‐deficient zebrafish and quantified differences in protein levels between wild‐type and bace1 ?/? zebrafish brains. Over 4500 proteins were identified with at least two unique peptides and quantified in both wild‐type and bace1 ?/? zebrafish brains. The majority of zebrafish membrane proteins did not show altered protein levels, indicating that Bace1 has a restricted substrate specificity. Twenty‐four membrane proteins accumulated in the bace1 ?/? brains and thus represent candidate Bace1 substrates. They include several known BACE1 substrates, such as the zebrafish homologs of amyloid precursor protein and the cell adhesion protein L1, which validate the proteomic workflow. Additionally, several candidate substrates with a function in neurite outgrowth and axon guidance, such as plexin A3 and glypican‐1 were identified, pointing to a function of Bace1 in neurodevelopment. Taken together, our study provides the first proteomic analysis of knock‐out zebrafish tissue and demonstrates that combining gene knock‐out models in zebrafish with quantitative proteomics is a powerful approach to address biomedical questions.