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.     

Personality‐Dependent Survival in the Marine Isopod Idotea balthica

We studied the fitness effects of animal personality by measuring activity and its relation to survival in the marine isopod Idotea balthica. We asked (1) whether activity could be considered to be a personality trait, (2) whether this trait is connected to survival, and (3) whether personality and survival exhibit sex differences. We found that activity fulfilled the criteria of personality as individuals had consistent between‐individual differences over time and across situations. Consistent individual differences in activity were associated with fitness as the survival probability of active individuals was lower, but this did not depend on sex. Our results demonstrate that personality exists in I. balthica and support recent suggestions that the association between personality and life‐history traits is a central component in mediating animal personality.     

Melanoma‐associated GRM3 variants dysregulate melanosome trafficking and cAMP signaling

Large‐scale sequencing studies have revealed several genes that are recurrently mutated in melanomas. To annotate the melanoma genome, we have expressed tumor‐associated variants of these genes in zebrafish and characterized their effects on melanocyte development and function. Here, we describe expression of tumor‐associated variants of the recurrently mutated metabotropic glutamate receptor 3 (GRM3) gene. Unlike wild‐type GRM3, tumor‐associated GRM3 variants disrupted trafficking of melanosomes, causing their aggregation in the cell body. Melanosomes are trafficked in a cAMP‐dependent manner, and drugs that directly or indirectly increased cAMP levels were able to suppress melanosome aggregation in mutant GRM3‐expressing melanocytes. Our data show that oncogenic GRM3 variants dysregulate cAMP signaling, a heretofore unknown role for these oncogenes. cAMP signaling has been implicated in melanoma progression and drug resistance, and our data show that oncogenic properties of GRM3 could be mediated, at least in part, by alterations in cAMP signaling.     

Copy number variations of CBF genes at the Fr‐A2 locus are essential components of winter hardiness in wheat

Winter hardiness is important for the adaptation of wheat to the harsh winter conditions in temperate regions and is thus also an important breeding goal. Here, we employed a panel of 407 European winter wheat cultivars to dissect the genetic architecture of winter hardiness. We show that copy number variation (CNV) of CBF (C‐repeat Binding Factor) genes at the Fr‐A2 locus is the essential component for winter survival, with CBF‐A14 CNV being the most likely causal polymorphism, accounting for 24.3% of the genotypic variance. Genome‐wide association mapping identified several markers in the Fr‐A2 chromosomal region, which even after accounting for the effects of CBF‐A14 copy number explained approximately 15% of the genotypic variance. This suggests that additional, as yet undiscovered, polymorphisms are present at the Fr‐A2 locus. Furthermore, CNV of Vrn‐A1 explained an additional 3.0% of the genotypic variance. The allele frequencies of all loci associated with winter hardiness were found to show geographic patterns consistent with their role in adaptation. Collectively, our results from the candidate gene analysis, association mapping and genome‐wide prediction show that winter hardiness in wheat is a quantitative trait, but with a major contribution of the Fr‐A2 locus.     

Altering PI3K—Akt signalling in zebrafish embryos affects PTEN phosphorylation and gastrulation

Background information. PTEN (phosphatase and tensin homologue deleted on chromosome 10) is a negative regulator of the PI3K (phosphoinositide 3‐kinase)–Akt (also called protein kinase B) signalling pathway and is essential for embryogenesis, but its function in early vertebrate embryos is unclear. Results. To address how PTEN functions in early embryos, we overexpressed one of the four zebrafish PTEN isoforms at the 1–2‐cell stage. Overexpression of Ptena454 alters phospho‐Akt levels and impairs cell movements associated with gastrulation. Heat shocking embryos increases phospho‐Akt levels and lowers phospho‐Ptena454 levels. Inhibiting CK2 (protein kinase CK2) activity reduces phospho‐Pten levels and augments the effects due to Ptena454 overexpression. Low phospho‐Akt and corresponding low phospho‐GSK‐3 (glycogen synthase kinase‐3) and high phospho‐Pten levels accompany wortmannin or LY294002 treatment, which inhibit PI3K activity. Conclusions. These results suggest that Ptena454 regulation is correlated to changes in phospho‐Akt levels. We propose a model in which homoeostasis in rapidly dividing and migrating embryonic cells depends on a counterbalance between pro‐survival signalling employing CK2 and GSK‐3 and the pro‐apoptotic activity of Ptena454.     

Sensation‐seeking genes and physical activity in youth

Many studies examining genetic influences on physical activity (PA) have evaluated the impact of single nucleotide polymorphisms (SNPs) related to the development of lifestyle‐related chronic diseases, under the hypothesis that they would be associated with PA. However, PA is a multidetermined behavior and associated with a multitude of health consequences. Thus, examining a broader range of candidate genes associated with a broader range of PA correlates may provide new insights into the genetic underpinnings of PA. In this study, we focus on one such correlate – sensation‐seeking behavior. Participants (N = 1130 Mexican origin youth) provided a saliva sample and data on PA and sensation‐seeking tendencies in 2008–2009. Participants were genotyped for 630 functional and tagging variants in the dopamine, serotonin and cannabinoid pathways. Overall 30% of participants (males – 37.6% and females – 22.0%) reported ≥60 min of PA on 5 of 7 days. After adjusting for gender, age and population stratification, and applying the Bayesian False Discovery Probability approach for assessing noteworthiness, four gene variants were significantly associated with PA. In a multivariable model, being male, having higher sensation‐seeking tendencies and at least one copy of the minor allele for SNPs in angiotensin I‐converting enzyme gene [ACE; rs8066276 odds ratio (OR) = 1.44; P = 0.012] and tryptophan hydroxylase 2 gene (TPH2; rs11615016 OR = 1.73; P = 0.021) were associated with increased likelihood of meeting PA recommendations. Participants with at least one copy of the minor allele for SNPs in synaptosomal‐associated protein 25 gene (SNAP25; rs363035 OR = 0.53; P = 0.005) and cannabinoid receptor 1 gene (CNR1; rs6454672 OR = 0.62; P = 0.022) have decreased likelihood of meeting PA recommendations. Our findings extend current knowledge of the complex relationship between PA and possible genetic underpinnings.     

Resveratrol derivative,trans‐3,5,4′‐trimethoxystilbene,exerts antiangiogenic and vascular‐disrupting effects in zebrafish through the downregulation of VEGFR2 and cell‐cycle modulation

Angiogenesis plays an important role in the development of neoplastic diseases such as cancer. Resveratrol and its derivatives exert antiangiogenic effects, but the mechanisms of their actions remain unclear. The aim of this study was to evaluate the antiangiogenic activity of resveratrol and its derivative trans‐3,5,4′‐trimethoxystilbene in vitro using human umbilical vein endothelial cells (HUVECs) and in vivo using transgenic zebrafish, and to clarify their mechanisms of action in zebrafish by gene expression analysis of the vascular endothelial growth factor (VEGF) receptor (VEGFR2/KDR) and cell‐cycle analysis. trans‐3,5,4′‐Trimethoxystilbene showed significantly more potent antiangiogenic activity than that of resveratrol in both assays. In zebrafish, trans‐3,5,4′‐trimethoxystilbene caused intersegmental vessel regression and downregulated VEGFR2 mRNA expression. Trans‐3,5,4′‐trimethoxystilbene also induced G2/M cell‐cycle arrest, most specifically in endothelial cells of zebrafish embryos. We propose that the antiangiogenic and vascular‐targeting activities of trans‐3,5,4′‐trimethoxystilbene result from the downregulation of VEGFR2 expression and cell‐cycle arrest at G2/M phase. J. Cell. Biochem. 109: 339–346, 2010. © 2009 Wiley‐Liss, Inc.     

Molecular characterization of SLC24A5 variants and evaluation of Nitisinone treatment efficacy in a zebrafish model of OCA6

Skin pigmentation is a highly heterogeneous trait with diverse consequences worldwide. SLC24A5, encoding a potent K⁺‐dependent Na⁺/Ca²⁺ exchanger, is among the known color‐coding genes that participate in melanogenesis by maintaining pH in melanosomes. Deficient SLC24A5 activity results in oculocutaneous albinism (OCA) type 6 in humans. In this study, by utilizing a exome sequencing (ES) approach, we identified two new variants [p. (Gly110Arg) and p. (IIe189Ilefs*1)] of SLC24A5 cosegregating with the OCA phenotype, including nystagmus, strabismus, foveal hypoplasia, albinotic fundus, and vision impairment, in three large consanguineous Pakistani families. Both of these variants failed to rescue the pigmentation in zebrafish slc24a5 morphants, confirming the pathogenic effects of the variants. We also phenotypically characterized a commercially available zebrafish mutant line (slc24a5^ko) that harbors a nonsense (p.Tyr208*) allele of slc24a5. Similar to morphants, homozygous slc24a5^ko mutants had significantly reduced melanin content and pigmentation. Next, we used these slc24a5^ko zebrafish mutants to test the efficacy of nitisinone, a compound known to increase ocular and fur pigmentation in OCA1 (TYR) mutant mice. Treatment of slc24a5^ko mutant zebrafish embryos with varying doses of nitisinone did not improve melanin production and pigmentation, suggesting that treatment with nitisinone is unlikely to be therapeutic in OCA6 patients.     

Neither single‐marker nor haplotype analyses support an association between the dopamine transporter gene and heroin dependence in Han Chinese

Much evidence suggests that dysfunction of dopamine transporter‐mediated dopamine transmission may be involved in the pathophysiology of substance abuse and dependence. The aim of this study was to examine whether the dopamine transporter gene (DAT1; SLC6A3) is associated with the development of heroin dependence (HD) and whether DAT1 influences personality traits in patients with HD. Polymorphisms of DAT1 were analyzed in a case–control study of 1046 Han Chinese (615 patients and 431 controls). All participants were screened using a Chinese version of the modified Schedule of Affective Disorder and Schizophrenia‐Lifetime and all patients met the criteria for HD. Furthermore, a Chinese version of the Tridimensional Personality Questionnaire (TPQ) was used to assess personality traits in the patient group and examine the association between their personality traits and DAT1 polymorphisms. Of the patient group, 271 completed the TPQ. No statistically significant differences in allele or genotype frequencies of all investigated variants between HD patients and controls were observed. In haplotype analyses, four haplotype blocks of DAT1 were not associated with the development of HD. These DAT1 polymorphisms did not influence novelty seeking and harm avoidance scores in HD patients. This study suggests that the DAT1 gene may not contribute to the risk of HD and specific personality traits in HD among the Han Chinese population.     

Pigment‐dispersing factor signaling in the circadian system of Caenorhabditis elegans

The neuropeptide pigment‐dispersing factor (PDF) is important for the generation and entrainment of circadian rhythms in the fruitfly Drosophila melanogaster. Recently two pdf homologs, pdf‐1 and pdf‐2, and a PDF receptor, pdfr‐1, have been found in Caenorhabditis elegans and have been implicated in locomotor activity. In this work, we have studied the role of the PDF neuropeptide in the circadian system of C. elegans and found that both pdf‐1 and pdf‐2 mutants affect the normal locomotor activity outputs. In particular, loss of pdf‐1 induced circadian arrhythmicity under both light–dark (LD) and constant dark (DD) conditions. These defects can be rescued by a genomic copy of the pdf‐1 locus. Our results indicate that PDF‐1 is involved in rhythm generation and in the synchronization to LD cycles, as rhythmic patterns of activity rapidly disappear when pdf‐1 mutants are recorded under both entrained and free‐running conditions. The role of PDF‐2 and the PDF receptors is probably more complex and involves the interaction between the two pdf paralogues found in the nematode.     

Extreme‐phenotype genome‐wide association study (XP‐GWAS): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number trait, which was selected to enable comparisons between the results of XP‐GWAS and conventional GWAS. An exome‐sequencing strategy was used to focus sequencing resources on genes and their flanking regions. A total of 0.94 million variants were identified and served as evaluation markers; comparisons among pools showed that 145 of these variants were statistically associated with the kernel row number phenotype. These trait‐associated variants were significantly enriched in regions identified by conventional GWAS. XP‐GWAS was able to resolve several linked QTL and detect trait‐associated variants within a single gene under a QTL peak. XP‐GWAS is expected to be particularly valuable for detecting genes or alleles responsible for quantitative variation in species for which extensive genotyping resources are not available, such as wild progenitors of crops, orphan crops, and other poorly characterized species such as those of ecological interest.     

DNA methylation regulates gabrb2 mRNA expression: developmental variations and disruptions in l‐methionine‐induced zebrafish with schizophrenia‐like symptoms

Single nucleotide polymorphisms (SNPs) in the human type A gamma‐aminobutyric acid (GABA) receptor β₂ subunit gene (GABRB2) have been associated with schizophrenia and quantitatively correlated with mRNA expression in the postmortem brain tissue of patients with schizophrenia. l ‐Methionine (MET) administration has been reported to cause a recrudescence of psychotic symptoms in patients with schizophrenia, and similar symptoms have been generated in MET‐induced mice. In this study, a zebrafish animal model was used to evaluate the relationship between the gabrb2 mRNA expression and its promoter DNA methylation in developmental and MET‐induced schizophrenia‐like zebrafish. The results indicated developmental increases in global DNA methylation and decreases in gabrb2 promoter methylation in zebrafish. A significant increase in gabrb2 mRNA levels was observed after GABA was synthesized. Additionally, the MET‐triggered schizophrenia‐like symptoms in adult zebrafish, involving social withdrawal and cognitive dysfunction analyzed with social interaction and T‐maze behavioral tests, were accompanied by significantly increased DNA methylation levels in the global genome and the gabrb2 promoter. Furthermore, the significant correlation between gabrb2 mRNA expression and gabrb2 promoter methylation observed in the developmental stages became non‐significant in MET‐triggered adult zebrafish. These findings demonstrate that gabrb2 mRNA expression is associated with DNA methylation varies by developmental stage and show that these epigenetic association mechanisms are disrupted in MET‐triggered adult zebrafish with schizophrenia‐like symptoms. In conclusion, these results provide plausible epigenetic evidence of the GABA_A receptor β₂ subunit involvement in the schizophrenia‐like behaviors and demonstrate the potential use of zebrafish models in neuropsychiatric research.     

Protocadherin‐17 function in Zebrafish retinal development

Cadherin cell adhesion molecules play crucial roles in vertebrate development including the development of the retina. Most studies have focused on examining functions of classic cadherins (e.g. N‐cadherin) in retinal development. There is little information on the function of protocadherins in the development of the vertebrate visual system. We previously showed that protocadherin‐17 mRNA was expressed in developing zebrafish retina during critical stages of the retinal development. To gain insight into protocadherin‐17 function in the formation of the retina, we analyzed eye development and differentiation of retinal cells in zebrafish embryos injected with protocadherin‐17 specific antisense morpholino oligonucleotides (MOs). Protocadherin‐17 knockdown embryos (pcdh17 morphants) had significantly reduced eyes due mainly to decreased cell proliferation. Differentiation of several retinal cell types (e.g. retinal ganglion cells) was also disrupted in the pcdh17 morphants. Phenotypic rescue was achieved by injection of protocadherin‐17 mRNA. Injection of a vivo‐protocadherin‐17 MO into one eye of embryonic zebrafish resulted in similar eye defects. Our results suggest that protocadherin‐17 plays an important role in the normal formation of the zebrafish retina. © 2012 Wiley Periodicals, Inc. Develop Neurobiol, 2013     

Bayesian genome‐wide association analysis for body weight in farmed Atlantic salmon (Salmo salar L.)

We performed a genome‐wide association study to detect markers associated with growth traits in Atlantic salmon. The analyzed traits included body weight at tagging (BWT) and body weight at 25 months (BW25M). Genotypes of 4662 animals were imputed from the 50K SNP chip to the 200K SNP chip using fimpute software. The markers were simultaneously modeled using Bayes C to identify genomic regions associated with the traits. We identified windows explaining a maximum of 3.71% and 3.61% of the genetic variance for BWT and BW25M respectively. We found potential candidate genes located within the top ten 1‐Mb windows for BWT and BW25M. For instance, the vitronectin (VTN) gene, which has been previously reported to be associated with cell growth, was found within one of the top ten 1‐Mb windows for BWT. In addition, the WNT1‐inducible‐signaling pathway protein 3, melanocortin 2 receptor accessory protein 2, myosin light chain kinase, transforming growth factor beta receptor type 3 and myosin light chain 1 genes, which have been reported to be associated with skeletal growth in humans, growth stimulation during the larval stage in zebrafish, body weight in pigs, feed conversion in chickens and growth rate of sheep skeletal muscle respectively, were found within some of the top ten 1‐Mb windows for BW25M. These results indicate that growth traits are most likely controlled by many variants with relatively small effects in Atlantic salmon. The genomic regions associated with the traits studied here may provide further insight into the functional regions underlying growth traits in this species.     

New Isocoumarins from a Cold‐Adapted Fungal Strain Mucor sp. and Their Developmental Toxicity to Zebrafish Embryos

Three new isocoumarin derivatives, mucorisocoumarins A–C ( 1 – 3 , resp.), together with seven known compounds, 4 – 10 , were isolated from the cold‐adapted fungal strain Mucor sp. (No. XJ07027‐5). The structures of the new compounds were identified by detailed IR, MS, and 1D‐ and 2D‐NMR analyses. It was noteworthy that compounds 1, 2, 4 , and 5 were successfully resolved by chiral HPLC, indicating that 1 – 7 should exist as enantiomers. In an embryonic developmental toxicity assay using a zebrafish model, compound 3 produced developmental abnormalities in the zebrafish embryos. This is the first report of isocoumarins with developmental toxicity to zebrafish embryos.     

Adriamycin inhibits embryonic development in zebrafish through downregulation of Kruppel‐like factor4

Adriamycin is an effective anticancer drug used in a wide range of cancers. Anticancer drugs modulate oncogenes and nodal regulatory molecules that affect cell differentiation and organismal development. In this study, we explore the effect of adriamycin on Kruppel‐like factor4 (Klf4), an essential pluripotent factor by choosing zebrafish embryos as a model system. Klf4 is involved in the regulation of cellular growth, proliferation, and differentiation. In zebrafish embryogenesis, Klf4 is a major regulator of differentiation of polster in the anterior mesendoderm region of cells into hatching gland cells. The importance of this study is to check the effect of adriamycin on embryonic development. We found, adriamycin dose dependently altered the gene expression level of Klf4 that occurs in parallel to its detrimental effect on hatching. Supportively, cathepsin L and cyclase‐associated protein1 are the other two markers of hatching that are altered along with Klf4.