Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain.

The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.

Examining the Transcriptomic and Biochemical Signatures of Bacillus subtilis Strains: Impacts on Plant Growth and Abiotic Stress Tolerance.

Rhizobacteria from various ecological niches display variations in physiological characteristics. This study investigates the transcriptome profiling of two Bacillus subtilis strains, BsCP1 and BsPG1, each isolated from distinct environments. Gene expression linked to the synthesis of seven types of antibiotic compounds was detected in both BsCP1 and BsPG1 cultures. Among these, the genes associated with plipastatin synthesis were predominantly expressed in both bacterial strains. However, genes responsible for the synthesis of polyketide, subtilosin, and surfactin showed distinct transcriptional patterns. Additionally, genes involved in producing exopolysaccharides (EPS) showed higher expression levels in BsPG1 than in BsCP1. Consistently with this, a greater quantity of EPS was found in the BsPG1 culture compared to BsCP1. Both bacterial strains exhibited similar effects on Arabidopsis seedlings, promoting root branching and increasing seedling fresh weight. However, BsPG1 was a more potent enhancer of drought, heat, and copper stress tolerance than BsCP1. Treatment with BsPG1 had a greater impact on improving survival rates, increasing starch accumulation, and stabilizing chlorophyll content during the post-stress stage. qPCR analysis was used to measure transcriptional changes in Arabidopsis seedlings in response to BsCP1 and BsPG1 treatment. The results show that both bacterial strains had a similar impact on the expression of genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Likewise, genes associated with stress response, root development, and disease resistance showed comparable responses to both bacterial strains. However, treatment with BsCP1 and BsPG1 induced distinct activation of genes associated with the ABA signaling pathway. The results of this study demonstrate that bacterial strains from different ecological environments have varying abilities to produce beneficial metabolites for plant growth. Apart from the SA and JA signaling pathways, ABA signaling triggered by PGPR bacterial strains could play a crucial role in building an effective resistance to various abiotic stresses in the plants they colonize.

Multiple model species selection for transcriptomics analysis of non-model organisms.

BACKGROUND: Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in gene functional annotation, gene regulation analysis, and environmental factor verification. However, with increasing amounts of sequenced reads and reference model species, the selection of appropriate reference species for gene annotation has become a new challenge. METHODS: We proposed a novel approach for finding the most effective reference model species through taxonomic associations and ultra-conserved orthologous (UCO) gene comparisons among species. An online system for multiple species selection (MSS) for RNA-seq differential expression analysis was developed, and comprehensive genomic annotations from 291 reference model eukaryotic species were retrieved from the RefSeq, KEGG, and UniProt databases. RESULTS: Using the proposed MSS pipeline, gene ontology and biological pathway enrichment analysis can be efficiently achieved, especially in the case of transcriptomic analysis of non-model organisms. The results showed that the proposed method solved problems related to limitations in annotation information and provided a roughly twenty-fold reduction in computational time, resulting in more accurate results than those of traditional approaches of using a single model reference species or the large non-redundant reference database. CONCLUSIONS: Selection of appropriate reference model species helps to reduce missing annotation information, allowing for more comprehensive results than those obtained with a single model reference species. In addition, adequate model species selection reduces the computational time significantly while retaining the same order of accuracy. The proposed system indeed provides superior performance by selecting appropriate multiple species for transcriptomic analysis compared to traditional approaches.

Retinoic Acid Protects and Rescues the Development of Zebrafish Embryonic Retinal Photoreceptor Cells from Exposure to Paclobutrazol.

Paclobutrazol (PBZ) is a widely used fungicide that shows toxicity to aquatic embryos, probably through rain-wash. Here, we specifically focus on its toxic effect on eye development in zebrafish, as well as the role of retinoic acid (RA), a metabolite of vitamin A that controls proliferation and differentiation of retinal photoreceptor cells, in this toxicity. Embryos were exposed to PBZ with or without RA from 2 to 72 h post-fertilization (hpf), and PBZ-treated embryos (2-72 hpf) were exposed to RA for additional hours until 120 hpf. Eye size and histology were examined. Expression levels of gnat1 (rod photoreceptor marker), gnat2 (cone photoreceptor marker), aldehyde dehydrogenases (encoding key enzymes for RA synthesis), and phospho-histone H3 (an M-phase marker) in the eyes of control and treated embryos were examined. PBZ exposure dramatically reduces photoreceptor proliferation, thus resulting in a thinning of the photoreceptor cell layer and leading to a small eye. Co-treatment of PBZ with RA, or post-treatment of PBZ-treated embryos with RA, partially rescues photoreceptor cells, revealed by expression levels of marker proteins and by retinal cell proliferation. PBZ has strong embryonic toxicity to retinal photoreceptors, probably via suppressing the production of RA, with effects including impaired retinal cell division.

Ftr82 Is Critical for Vascular Patterning during Zebrafish Development.

Cellular components and signaling pathways are required for the proper growth of blood vessels. Here, we report for the first time that a teleost-specific gene ftr82 (finTRIM family, member 82) plays a critical role in vasculature during zebrafish development. To date, there has been no description of tripartite motif proteins (TRIM) in vascular development, and the role of ftr82 is unknown. In this study, we found that ftr82 mRNA is expressed during the development of vessels, and loss of ftr82 by morpholino (MO) knockdown impairs the growth of intersegmental vessels (ISV) and caudal vein plexus (CVP), suggesting that ftr82 plays a critical role in promoting ISV and CVP growth. We showed the specificity of ftr82 MO by analyzing ftr82 expression products and expressing ftr82 mRNA to rescue ftr82 morphants. We further showed that the knockdown of ftr82 reduced ISV cell numbers, suggesting that the growth impairment of vessels is likely due to a decrease of cell proliferation and migration, but not cell death. In addition, loss of ftr82 affects the expression of vascular markers, which is consistent with the defect of vascular growth. Finally, we showed that ftr82 likely interacts with vascular endothelial growth factor (VEGF) and Notch signaling. Together, we identify teleost-specific ftr82 as a vascular gene that plays an important role for vascular development in zebrafish.

Tumor Suppressor Lzap Suppresses Wnt/ß-Catenin Signaling to Promote Zebrafish Embryonic Ventral Cell Fates via the Suppression of Inhibitory Phosphorylation of Glycogen Synthase Kinase 3.

Wnt/ß-catenin signaling controls various cell fates in metazoan development, and its dysregulation is often associated with cancer formation. However, regulations of this signaling pathway are not completely understood. Here, we report that Lzap, a tumor suppressor, controls nuclear translocation of ß-catenin. In zebrafish embryos disruption of lzap increases the expression of chordin (chd), which encodes a bone morphogenetic protein (BMP) antagonist that is localized in prospective dorsal cells and promotes dorsal fates. Consistently, lzap-deficient embryos with attenuated BMP signaling are dorsalized, which can be rescued by overexpression of zebrafish lzap or bmp2b or human LZAP. The expansion of chd expression in embryos lacking lzap is due to the accumulation of nuclear ß-catenin in ventral cells, in which ß-catenin is usually degraded. Furthermore, the activity of GSK3, a master regulator of ß-catenin degradation, is suppressed in lzap-deficient embryos via inhibitory phosphorylation. Finally, we also report that a similar regulatory axis is also likely to be present in a human tongue carcinoma cell line, SAS. Our results reveal that Lzap is a novel regulator of GSK3 for the maintenance of ventral cell properties and may prevent carcinogenesis via the regulation of ß-catenin degradation.

Gremlin 2 promotes differentiation of embryonic stem cells to atrial fate by activation of the JNK signaling pathway.

The bone morphogenetic protein antagonist Gremlin 2 (Grem2) is required for atrial differentiation and establishment of cardiac rhythm during embryonic development. A human Grem2 variant has been associated with familial atrial fibrillation, suggesting that abnormal Grem2 activity causes arrhythmias. However, it is not known how Grem2 integrates into signaling pathways to direct atrial cardiomyocyte differentiation. Here, we demonstrate that Grem2 expression is induced concurrently with the emergence of cardiovascular progenitor cells during differentiation of mouse embryonic stem cells (ESCs). Grem2 exposure enhances the cardiogenic potential of ESCs by 20-120-fold, preferentially inducing genes expressed in atrial myocytes such as Myl7, Nppa, and Sarcolipin. We show that Grem2 acts upstream to upregulate proatrial transcription factors CoupTFII and Hey1 and downregulate atrial fate repressors Irx4 and Hey2. The molecular phenotype of Grem2-induced atrial cardiomyocytes was further supported by induction of ion channels encoded by Kcnj3, Kcnj5, and Cacna1d genes and establishment of atrial-like action potentials shown by electrophysiological recordings. We show that promotion of atrial-like cardiomyocytes is specific to the Gremlin subfamily of BMP antagonists. Grem2 proatrial differentiation activity is conveyed by noncanonical BMP signaling through phosphorylation of JNK and can be reversed by specific JNK inhibitors, but not by dorsomorphin, an inhibitor of canonical BMP signaling. Taken together, our data provide novel mechanistic insights into atrial cardiomyocyte differentiation from pluripotent stem cells and will assist the development of future approaches to study and treat arrhythmias.

FOXO/Fringe is necessary for maintenance of the germline stem cell niche in response to insulin insufficiency.

The stem cell niche houses and regulates stem cells by providing both physical contact and local factors that regulate stem cell identity. The stem cell niche also plays a role in integrating niche-local and systemic signals, thereby ensuring that the balance of stem cells meets the needs of the organism. However, it is not clear how these signals are merged within the niche. Nutrient-sensing insulin/FOXO signaling has been previously shown to directly control Notch activation in the Drosophila female germline stem cell (GSC) niche, which maintains the niche and GSC identity. Here, we demonstrate that FOXO directly activates transcription of fringe, a gene encoding a glycosyltransferase that modulates Notch glycosylation. Fringe facilitates Notch inactivation in the GSC niche when insulin signaling is low. We also show that the Notch ligand predominantly involved is GSC niche-derived Delta. These results reveal that FOXO-mediated regulation of fringe links the insulin and Notch signaling pathways in the GSC niche in response to nutrition, and emphasize that stem cells are regulated by complex interactions between niche-local and systemic signals.

Effects of maternal cadmium exposure on female reproductive functions, gamete quality, and offspring development in zebrafish (Danio rerio).

Impacts of maternal Cd(2+) exposure on female zebrafish (Danio rerio) were observed in females as well as their offspring. In females, Cd disturbed fecundity and other reproductive functions. In their offspring, it retarded gamete development and growth and influenced gene expression. There was a positive relationship between Cd(2+) contents in ovaries of females and treatment doses of 0-8.9 µM of Cd(2+). The mating rate decreased by 60 % when females were exposed to 8.9-35.6 µM of Cd(2+) for 72 h compared with the control group. It was observed that growth is delayed by one somite stage in maternal-Cd(2+) embryos compared with control embryos, which grew at the sixth-somite stage. The ceratohyal angles of larvae of Cd-exposed adults (maternal Cd(2+)) at 72 h postfertilization (hpf) appeared to have a positive response after doses of maternal Cd. In addition, approximately 30 % of 96-hpf larvae that were treated with a dose of 35.6 µM of maternal Cd(2+) appeared to have pericardial edema. At the 5-hpf stage of maternal Cd(2+) exposure, embryos showed 33 and 37 target genes, respectively, that were significantly downregulated and upregulated as shown by cDNA microarray analysis. A major effect of maternal Cd(2+) exposure on zebrafish embryo genes is that 18.9% of transcription functions were upregulated. In addition, 33.3% of transcripts relative to the function of protein biosynthesis were downregulated. These results showed that maternal Cd(2+) exposure influenced the reproduction ability of females and also caused their embryos to develop with abnormal gene expression.

Tfap2a and Foxd3 regulate early steps in the development of the neural crest progenitor population.

The neural crest is a stem cell-like population exclusive to vertebrates that gives rise to many different cell types including chondrocytes, neurons and melanocytes. Arising from the neural plate border at the intersection of Wnt and Bmp signaling pathways, the complexity of neural crest gene regulatory networks has made the earliest steps of induction difficult to elucidate. Here, we report that tfap2a and foxd3 participate in neural crest induction and are necessary and sufficient for this process to proceed. Double mutant tfap2a (mont blanc, mob) and foxd3 (mother superior, mos) mob;mos zebrafish embryos completely lack all neural crest-derived tissues. Moreover, tfap2a and foxd3 are expressed during gastrulation prior to neural crest induction in distinct, complementary, domains; tfap2a is expressed in the ventral non-neural ectoderm and foxd3 in the dorsal mesendoderm and ectoderm. We further show that Bmp signaling is expanded in mob;mos embryos while expression of dkk1, a Wnt signaling inhibitor, is increased and canonical Wnt targets are suppressed. These changes in Bmp and Wnt signaling result in specific perturbations of neural crest induction rather than general defects in neural plate border or dorso-ventral patterning. foxd3 overexpression, on the other hand, enhances the ability of tfap2a to ectopically induce neural crest around the neural plate, overriding the normal neural plate border limit of the early neural crest territory. Although loss of either Tfap2a or Foxd3 alters Bmp and Wnt signaling patterns, only their combined inactivation sufficiently alters these signaling gradients to abort neural crest induction. Collectively, our results indicate that tfap2a and foxd3, in addition to their respective roles in the differentiation of neural crest derivatives, also jointly maintain the balance of Bmp and Wnt signaling in order to delineate the neural crest induction domain.

Tumor suppressor Lzap regulates cell cycle progression, doming, and zebrafish epiboly.

Initial stages of embryonic development rely on rapid, synchronized cell divisions of the fertilized egg followed by a set of morphogenetic movements collectively called epiboly and gastrulation. Lzap is a putative tumor suppressor whose expression is lost in 30% of head and neck squamous cell carcinomas. Lzap activities include regulation of cell cycle progression and response to therapeutic agents. Here, we explore developmental roles of the lzap gene during zebrafish morphogenesis. Lzap is highly conserved among vertebrates and is maternally deposited. Expression is initially ubiquitous during gastrulation, and later becomes more prominent in the pharyngeal arches, digestive tract, and brain. Antisense morpholino-mediated depletion of Lzap resulted in delayed cell divisions and apoptosis during blastomere formation, resulting in fewer, larger cells. Cell cycle analysis suggested that Lzap loss in early embryonic cells resulted in a G2/M arrest. Furthermore, the Lzap-deficient embryos failed to initiate epiboly--the earliest morphogenetic movement in animal development--which has been shown to be dependent on cell adhesion and migration of epithelial sheets. Our results strongly implicate Lzap in regulation of cell cycle progression, adhesion and migratory activity of epithelial cell sheets during early development. These functions provide further insight into Lzap activity that may contribute not only to development, but also to tumor formation.

GTP-Binding Protein 1-Like (GTPBP1l) Regulates Vascular Patterning during Zebrafish Development.

Genetic regulation of vascular patterning is not fully understood. Here, we report a novel gene, gtpbp1l (GTP-binding protein 1-like), that regulates vascular development in zebrafish. Amino acid sequence comparison and a phylogenetic study showed that gtpbp1l is conserved in vertebrates. Gtpbp1l mRNA is expressed in the vasculature during embryogenesis. Knockdown of gtpbp1l by morpholino impairs the patterning of the intersegmental vessel (ISV) and caudal vein plexus (CVP), indicating the role of gtpbp1l in vasculature. Further apoptosis assays and transgenic fish tests suggested that vascular defects in gtpbp1l morphants are not due to cell death but are likely caused by the impairment of migration and proliferation. Moreover, the altered expression of vessel markers is consistent with the vascular defects in gtpbp1l morphants. Finally, we revealed that gtpbp1l is regulated by VEGF/notch and BMP signaling. Collectively, these findings showed that gtpbp1l plays a critical role in vascular patterning during zebrafish development.

A selective glial barrier at motor axon exit points prevents oligodendrocyte migration from the spinal cord.

Nerve roots have specialized transition zones that permit axon extension but limit cell movement between the CNS and PNS. Boundary cap cells prevent motor neuron soma from following their axons into the periphery, thereby contributing to a selective barrier. Transition zones also restrict movement of glial cells. Consequently, axons that cross the CNS-PNS interface are insulated by central and peripheral myelin. The mechanisms that prevent the migratory progenitors of oligodendrocytes and Schwann cells, the myelinating cells of the CNS and PNS, respectively, from crossing transition zones are not known. Here, we show that interactions between myelinating glial cells prevent their movements across the interface. Using in vivo time-lapse imaging in zebrafish we found that, in the absence of Schwann cells, oligodendrocyte progenitors cross ventral root transition zones and myelinate motor axons. These studies reveal that distinct mechanisms regulate the movement of axons, neurons, and glial cells across the CNS-PNS interface.

Waterborne Exposure of Paclobutrazol at Environmental Relevant Concentration Induce Locomotion Hyperactivity in Larvae and Anxiolytic Exploratory Behavior in Adult Zebrafish.

The available arable land is unable to fulfill the food production need of rapidly the exponentially growing human population in the world. Pesticides are one of those different measures taken to meet this demand. As a plant growth regulator to block gibberellin, paclobutrazol (PBZ) is used excessively throughout the world to promote early fruit setting, and to increase seed setting which might be harmful because PBZ is a very stable compound; therefore, it can bioaccumulate into the food chain of an ecosystem. In the present study, we discovered unexpected effects of PBZ on zebrafish larvae and adult behaviors by challenging them with low dose exposure. Zebrafish larvae aged 4 days post-fertilization (dpf) were exposed for 24 h at 10 µg/L (0.01 ppm) and 100 µg/L (0.1 ppm) of PBZ, respectively, and adults were incubated at 100 µg/L (0.1 ppm) and 1000 µg/L (1 ppm) concentrations of PBZ, respectively, for fourteen days. After incubation, the locomotor activity, burst, and rotation movement for the larvae; and multiple behavioral tests such as novel tank exploration, mirror biting, shoaling, predator avoidance, and social interaction for adult zebrafish were evaluated. Brain tissues of the adult fish were dissected and subjected to biochemical analyses of the antioxidant response, oxidative stress, superoxide dismutase (SOD), and neurotransmitter levels. Zebrafish larvae exposed to PBZ exhibited locomotion hyperactivity with a high burst movement and swimming pattern. In adult zebrafish, PBZ resulted in anxiolytic exploratory behavior, while no significant results were found in social interaction, shoal making, and predator avoidance behaviors. Interestingly, high dose PBZ exposure significantly compromised the innate aggressive behavior of the adult fish. Biochemical assays for oxidative stress, antioxidant response, and superoxide dismutase (SOD) showed significant reductions in their relative contents. In conclusion, for the first time, our behavior assays revealed that chronic PBZ exposure induced behavioral alterations in both larvae and the adult zebrafish. Because PBZ is a widely-used plant growth regulator, we suggest that it is necessary to conduct more thorough tests for its biosafety and bioaccumulation.

Integrated Hypoxia Signaling and Oxidative Stress in Developmental Neurotoxicity of Benzo[a]Pyrene in Zebrafish Embryos.

Benzo[a]pyrene (B[a]P) is a polycyclic aromatic hydrocarbon formed by the incomplete combustion of organic matter. Environmental B[a]P contamination poses a serious health risk to many organisms because the pollutant may negatively affect many physiological systems. As such, chronic exposure to B[a]P is known to lead to locomotor dysfunction and neurodegeneration in several organisms. In this study, we used the zebrafish model to delineate the acute toxic effects of B[a]P on the developing nervous system. We found that embryonic exposure of B[a]P downregulates shh and isl1, causing morphological hypoplasia in the telencephalon, ventral thalamus, hypothalamus, epiphysis and posterior commissure. Moreover, hypoxia-inducible factors (hif1a and hif2a) are repressed upon embryonic exposure of B[a]P, leading to reduced expression of the Hif-target genes, epo and survivin, which are associated with neural differentiation and maintenance. During normal embryogenesis, low-level oxidative stress regulates neuronal development and function. However, our experiments revealed that embryonic oxidative stress is greatly increased in B[a]P-treated embryos. The expression of catalase was decreased and sod1 expression increased in B[a]P-treated embryos. These transcriptional changes were coincident with increased embryonic levels of H2O2 and malondialdehyde, with the levels in B[a]P-treated fish similar to those in embryos treated with 120-µM H2O2. Together, our data suggest that reduced Hif signaling and increased oxidative stress are involved in B[a]P-induced acute neurotoxicity during embryogenesis.

Piwi reduction in the aged niche eliminates germline stem cells via Toll-GSK3 signaling.

Transposons are known to participate in tissue aging, but their effects on aged stem cells remain unclear. Here, we report that in the Drosophila ovarian germline stem cell (GSC) niche, aging-related reductions in expression of Piwi (a transposon silencer) derepress retrotransposons and cause GSC loss. Suppression of Piwi expression in the young niche mimics the aged niche, causing retrotransposon depression and coincident activation of Toll-mediated signaling, which promotes Glycogen synthase kinase 3 activity to degrade ß-catenin. Disruption of ß-catenin-E-cadherin-mediated GSC anchorage then results in GSC loss. Knocking down gypsy (a highly active retrotransposon) or toll, or inhibiting reverse transcription in the piwi-deficient niche, suppresses GSK3 activity and ß-catenin degradation, restoring GSC-niche attachment. This retrotransposon-mediated impairment of aged stem cell maintenance may have relevance in many tissues, and could represent a viable therapeutic target for aging-related tissue degeneration.

Toxic Effects of Paclobutrazol on Developing Organs at Different Exposure Times in Zebrafish.

To enhance crop productivity and economic profit, farmers often use pesticides that modulate plant growth and prevent disease. However, contamination of ecosystems with agricultural pesticides may impair the health of resident biota. Paclobutrazol (PBZ), an aromatic-containing triazole, is widely applied to many crops in order to promote flowering and fruit setting, while also regulating plant growth and preventing fungus-related diseases. Due to its high mobility, high stability and potential for bioaccumulation, the risks of PBZ to the health of organisms and ecological systems have become a serious concern. In previous studies, we documented the toxicity of PBZ on developing heart, eyes, liver, pancreas and intestine of zebrafish. In this study, we sought to further understand the developmental stage-specific impacts of PBZ on digestive organs and other tissues. Zebrafish were exposed to PBZ beginning at different embryonic stages, and the toxic effects on organs were evaluated at 120 hpf (hours post-fertilization) by in situ hybridization staining with tissue-specific marker genes, such as liver, intestine and pancreas. Unsurprisingly, early-stage embryos exhibited higher sensitivity to PBZ-induced death and developmental hypoplasia of digestive organs. Interestingly, the developing liver and pancreas were more sensitive to PBZ than intestine when embryos were exposed at early stages, but these tissues showed lower sensitivity at later stages. Our delineation of the differential toxic effects of PBZ on developing organs at different exposure timings can serve as a powerful reference for further studies into the mechanisms of PBZ organ toxicity.

Functional enrichment analysis based on long noncoding RNA associations.

BACKGROUND: Differential gene expression analysis using RNA-seq data is a popular approach for discovering specific regulation mechanisms under certain environmental settings. Both gene ontology (GO) and KEGG pathway enrichment analysis are major processes for investigating gene groups that participate in common biological responses or possess related functions. However, traditional approaches based on differentially expressed genes only detect a few significant GO terms and pathways, which are frequently insufficient to explain all-inclusive gene regulation mechanisms. METHODS: Transcriptomes of survivin (birc5) gene knock-down experimental and wild-type control zebrafish embryos were sequenced and assembled, and a differential expression (DE) gene list was obtained for traditional functional enrichment analysis. In addition to including DE genes with significant fold-change levels, we considered additional associated genes near or overlapped with differentially expressed long noncoding RNAs (DE lncRNAs), which may directly or indirectly activate or inhibit target genes and play important roles in regulation networks. Both the original DE gene list and the additional DE lncRNA-associated genes were combined to perform a comprehensive overrepresentation analysis. RESULTS: In this study, a total of 638 DE genes and 616 DE lncRNA-associated genes (lncGenes) were leveraged simultaneously in searching for significant GO terms and KEGG pathways. Compared to the traditional approach of only using a differential expression gene list, the proposed method of employing DE lncRNA-associated genes identified several additional important GO terms and KEGG pathways. In GO enrichment analysis, 60% more GO terms were obtained, and several neuron development functional terms were retrieved as complete annotations. We also observed that additional important pathways such as the FoxO and MAPK signaling pathways were retrieved, which were shown in previous reports to play important roles in apoptosis and neuron development functions regulated by the survivin gene. CONCLUSIONS: We demonstrated that incorporating genes near or overlapped with DE lncRNAs into the DE gene list outperformed the traditional enrichment analysis method for effective biological functional interpretations. These hidden interactions between lncRNAs and target genes could facilitate more comprehensive analyses.

Aryl hydrocarbon receptor 2 mediates the toxicity of Paclobutrazol on the digestive system of zebrafish embryos.

Paclobutrazol (PBZ), a trazole-containing fungicide and plant growth retardant, has been widely used for over 30 years to regulate plant growth and promote early fruit setting. Long-term usage of PBZ in agriculture and natural environments has resulted in residual PBZ in the soil and water. Chronic exposure to waterborne PBZ can cause various physiological effects in fish, including hepatic steatosis, antioxidant activity, and disruption of spermatogenesis. We have previously shown that PBZ also affects the rates of zebrafish embryonic survival and hatching, and causes developmental failure of the head skeleton and eyes; here, we further show that PBZ has embryonic toxic effects on digestive organs of zebrafish, and describe the underlying mechanisms. PBZ treatment of embryos resulted in dose-dependent morphological and functional abnormalities of the digestive organs. Real-time RT-PCR and in situ hybridization were used to show that PBZ strongly induces cyp1a1 expression in the digestive system, and slightly induces ahr2 expression in zebrafish embryos. Knockdown of ahr2 with morpholino oligonucleotides prevents PBZ toxicity. Thus, the toxic effect of PBZ on digestive organs is mediated by AhR2, as was previously reported for retene and TCDD. These findings have implications for understanding the potential toxicity of PBZ during embryogenesis, and thus the potential impact of fungicides on public health and the environment.

Animal model of Sar1b deficiency presents lipid absorption deficits similar to Anderson disease.

Anderson disease (ANDD) or chylomicron retention disease (CMRD) is a rare, hereditary lipid malabsorption syndrome associated with mutations in the SAR1B gene that is characterized by failure to thrive and hypocholesterolemia. Although the SAR1B structure has been resolved and its role in formation of coat protein II (COPII)-coated carriers is well established, little is known about the requirement for SAR1B during embryogenesis. To address this question, we have developed a zebrafish model of Sar1b deficiency based on antisense oligonucleotide knockdown. We show that zebrafish sar1b is highly conserved among vertebrates; broadly expressed during development; and enriched in the digestive tract organs, brain, and craniofacial skeleton. Consistent with ANDD symptoms of chylomicron retention, we found that dietary lipids in Sar1b-deficient embryos accumulate in enterocytes. Transgenic expression analysis revealed that Sar1b is required for growth of exocrine pancreas and liver. Furthermore, we found abnormal differentiation and maturation of craniofacial cartilage associated with defects in procollagen II secretion and absence of select, neuroD-positive neurons of the midbrain and hindbrain. The model presented here will help to systematically dissect developmental roles of Sar1b and to discover molecular and cellular mechanisms leading to organ-specific ANDD pathology. Key messages: Sar1b depletion phenotype in zebrafish resembles Anderson disease deficits. Sar1b deficiency results in multi-organ developmental deficits. Sar1b is required for dietary cholesterol uptake into enterocytes.