Effect of Nitrogen Sources on Omega-3 Polyunsaturated Fatty Acid Biosynthesis and Gene Expression in Thraustochytriidae sp.

The molecular mechanism that contributes to nitrogen source dependent omega-3 polyunsaturated fatty acid (n-3 PUFA) synthesis in marine oleaginous protists Thraustochytriidae sp., was explored in this study. The fatty acid (FA) synthesis was significantly influenced by the supplement of various levels of sodium nitrate (SN) (1-50 mM) or urea (1-50 mM). Compared with SN (50 mM) cultivation, cells from urea (50 mM) cultivation accumulated 1.16-fold more n-3 PUFAs (49.49% docosahexaenoic acid (DHA) (w/w, of total FAs) and 5.28% docosapentaenoic acid (DPA) (w/w, of total FAs)). Strikingly higher quantities of short chain FAs (<18 carbons) (52.22-fold of that in urea cultivation) were produced from SN cultivation. Ten candidate reference genes (RGs) were screened by using four statistical methods (geNorm, NormFinder, Bestkeeper and RefFinder). MFT (Mitochondrial folate transporter) and NUC (Nucleolin) were determined as the stable RGs to normalize the RT-qPCR (real-time quantitative polymerase chain reaction) data of essential genes related to n-3 PUFAs-synthesis. Our results elucidated that the gene transcripts of delta(3,5)-delta(2,4)-dienoyl-CoA isomerase, enoyl-CoA hydratase, fatty acid elongase 3, long-chain fatty acid acyl-CoA ligase, and acetyl-CoA carboxylase were up-regulated under urea cultivation, contributing to the extension and unsaturated bond formation. These findings indicated that regulation of the specific genes through nitrogen source could greatly stimulate n-3 PUFA production in Thraustochytriidae sp.

Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes.

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

Enhancement of marinacarboline A biosynthesis by optimizing the riboflavin supplement in marine derived Nocardiopsis flavescens CGMCC 4.5723.

OBJECTIVES: To improve the bioproductivity of secondary metabolites of marine derived Nocardiopsis flavescens CGMCC 4.5723 by enhancing its riboflavin supplement. RESULTS: The NfRibA, type II guanosine triphosphate (GTP) cyclohydrolase (GCH II) of Nocardiopsis flavescens CGMCC 4.5723, was biochemically identified and showed that NfRibA could efficiently catalyze the first step of riboflavin biosynthesis to hydrolyze GTP into 2, 5-diamino-6-ribosylamino-4(3H)-pyrimidinedione 5'-phosphate (DARPP) with Km value of 160.11 ± 26.81 µM in vitro. The overexpression of NfribA could obviously increase riboflavin bioproduction to the titers of 0.41 ± 0.19 mg/l by comparing with the wild type counterpart. Consequently, this rise of riboflavin bioproduction did not disturb the expression of genes involved in marinacarboline A biosynthesis, but could significantly enhance its bioproduction with the titer of 5.5 ± 0.17 mg/l through comparing with wild type control. CONCLUSIONS: Optimization of riboflavin supplement could be a new promising strategy in actinomycetic marinacarboline A exploitation.

Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis.

The long-chain omega-3 polyunsaturated fatty acids (n-3 LC-PUFAs) EPA (20:5n-3) and DHA (22:6n-3) are widely recognized as beneficial to human health and development. Select lineages of cosmopolitan marine prokaryotic and eukaryotic microorganisms synthesize these compounds via a unique fatty acid synthase/polyketide synthase mechanism that is distinct from the canonical desaturase/elongase-mediated pathway employed by the majority of eukaryotic single-cell microorganisms and metazoans. This "Pfa synthase" mechanism is highly efficient and has been co-opted for the large-scale industrial production of n-3 LC-PUFAs for commercial applications. Both prokaryotic and eukaryotic microbes containing this pathway can be readily isolated from marine environments and maintained in culture under laboratory conditions. Some strains are genetically tractable and have established methods for genetic modification. The discussion and methods presented here should be useful for the exploitation and optimization of n-3 LC-PUFA products from marine microorganisms.

Distinct Patterns of Selection in Selenium-Dependent Genes between Land and Aquatic Vertebrates.

Selenium (Se), a sparse element on earth, is an essential micronutrient in the vertebrate diet and its intake depends on its content in soils and waters worldwide. Selenium is required due to its function in selenoproteins, which contain selenocysteine (Sec), the 21st amino acid in the genetic code, as one of their constituent residues. Selenocysteine is analogous to the amino acid cysteine (Cys), which uses the abounding element sulfur instead. Despite the irregular distribution of Se worldwide, its distinct biochemical properties have made the substitution of Sec for Cys rare in vertebrate proteins. Still, vertebrates inhabited environments with different amounts of Se and may have distinctly adapted to it. To address this question, we compared the evolutionary forces acting on the coding sequences of selenoprotein genes and genes that regulate Se between vertebrate clades and between the Se-dependent genes and their paralogs with Cys. We find that the strength of natural selection in genes that use or regulate Se is distinct between land vertebrates and teleost fishes and more variable than in the Cys paralogs, particularly in genes involved in the preferential supply of Se to some organs and the tissue-specific expression of selenoproteins. This is compatible with vertebrates adapting to Se scarcity in land and its abundance in waters. In agreement, teleost fishes duplicated and subfunctionalized or neofunctionalized selenoprotein genes and maintained their capacity for Se transport in the body, which declined (under neutrality) for millions of years in terrestrial vertebrates. Dietary Se has thus distinctly shaped vertebrate evolution.

Limited pollen dispersal, small genetic neighborhoods, and biparental inbreeding in Vallisneria americana.

PREMISE OF THE STUDY: Pollen dispersal is a key process that influences ecological and evolutionary dynamics of plant populations by facilitating sexual reproduction and gene flow. Habitat loss and fragmentation have the potential to reduce pollen dispersal within and among habitat patches. We assessed aquatic pollen dispersal and mating system characteristics in Vallisneria americana-a water-pollinated plant with a distribution that has been reduced from historic levels. METHODS: We examined pollen neighborhood size, biparental inbreeding, and pollen dispersal, based on seed paternity using the indirect paternity method KinDist, from samples of 18-39 mothers and 14-20 progeny per mother from three sites across 2 years. KEY RESULTS: On average, fruits contained seeds sired by seven fathers. We found significant biparental inbreeding and limited pollen dispersal distances (0.8-4.34 m). However, in a number of cases, correlated paternity did not decline with distance, and dispersal could not be reliably estimated. CONCLUSIONS: Frequent pollen dispersal is not expected among patches, and even within patches, gene flow via pollen will be limited. Limited pollen dispersal establishes genetic neighborhoods, which, unless overcome by seed and propagule dispersal, will lead to genetic differentiation even in a continuous population. Unless loss and fragmentation drive populations to extreme sex bias, local pollen dispersal is likely to be unaffected by habitat loss and fragmentation per se because the spatial scale of patch isolation already exceeds pollen dispersal distances. Therefore, managing specifically for pollen connectivity is only relevant over very short distances.

Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions.

The effect of pressure and temperature on microbial communities of marine environments contaminated with petroleum hydrocarbons is understudied. This study aims to reveal the responses of marine bacterial communities to low temperature, high pressure, and contamination with petroleum hydrocarbons using seawater samples collected near an offshore Brazilian platform. Microcosms containing only seawater and those containing seawater contaminated with 1% crude oil were subjected to three different treatments of temperature and pressure as follows: (1) 22°C/0.1 MPa; (2) 4°C/0.1 MPa; and (3) 4°C/22 MPa. The effect of depressurization followed by repressurization on bacterial communities was also evaluated (4°C/22 MPaD). The structure and composition of the bacterial communities in the different microcosms were analyzed by PCR-DGGE and DNA sequencing, respectively. Contamination with oil influenced the structure of the bacterial communities in microcosms incubated either at 4°C or 22°C and at low pressure. Incubation at low temperature and high pressure greatly influenced the structure of bacterial communities even in the absence of oil contamination. The 4°C/22 MPa and 4°C/22 MPaD treatments resulted in similar DGGE profiles. DNA sequencing (after 40 days of incubation) revealed that the diversity and relative abundance of bacterial genera were related to the presence or absence of oil contamination in the nonpressurized treatments. In contrast, the variation in the relative abundances of bacterial genera in the 4°C/22 MPa-microcosms either contaminated or not with crude oil was less evident. The highest relative abundance of the phylum Bacteroidetes was observed in the 4°C/22 MPa treatment.

Changes in the abundance of cell wall apiogalacturonan and xylogalacturonan and conservation of rhamnogalacturonan II structure during the diversification of the Lemnoideae.

MAIN CONCLUSION: The diversification of the Lemnoideae was accompanied by a reduction in the abundance of cell wall apiogalacturonan and an increase in xylogalacturonan whereas rhamnogalacturonan II structure and cross-linking are conserved. The subfamily Lemnoideae is comprised of five genera and 38 species of small, fast-growing aquatic monocots. Lemna minor and Spirodela polyrhiza belong to this subfamily and have primary cell walls that contain large amounts of apiogalacturonan and thus are distinct from the primary walls of most other flowering plants. However, the pectins in the cell walls of other members of the Lemnoideae have not been investigated. Here, we show that apiogalacturonan decreased substantially as the Lemnoideae diversified since Wolffiella and Wolffia walls contain between 63 and 88% less apiose than Spirodela, Landoltia, and Lemna walls. In Wolffia, the most derived genus, xylogalacturonan is far more abundant than apiogalacturonan, whereas in Wolffiella pectic polysaccharides have a high arabinose content, which may arise from arabinan sidechains of RG I. The apiose-containing pectin rhamnogalacturonan II (RG-II) exists in Lemnoideae walls as a borate cross-linked dimer and has a glycosyl sequence similar to RG-II from terrestrial plants. Nevertheless, species-dependent variations in the extent of methyl-etherification of RG-II sidechain A and arabinosylation of sidechain B are discernible. Immunocytochemical studies revealed that pectin methyl-esterification is higher in developing daughter frond walls than in mother frond walls, indicating that methyl-esterification is associated with expanding cells. Our data support the notion that a functional cell wall requires conservation of RG-II structure and cross-linking but can accommodate structural changes in other pectins. The Lemnoideae provide a model system to study the mechanisms by which wall structure and composition has changed in closely related plants with similar growth habits.

Impacts of discarded coffee waste on human and environmental health.

Coffee is one of the most widely consumed beverages throughout the world. So far, many studies have shown the properties of coffee beverages, but little is known about its impacts on human and environmental health from its discard in the environment. So, the present work aims to investigate the mutagenic, genotoxic, cytotoxic and ecotoxic effects of leached (LE) and solubilized (SE) extracts from coffee waste, simulating the disposal of this residue in landfills and via sewage systems, respectively. Chemical analyses were also carried out. LE and SE induced mutagenicity in the TA98 Salmonella strain with and without exogenous metabolization (S9). In the TA100 only SE induced mutagenicity, what was observed without S9. An increase in the frequency of micronuclei was observed in HepG2 cell line after 3 and 24h of exposure to both extracts. No cytotoxic effects were observed in HepG2 cells by WST-1 assay. The EC50 values for the LE and SE were 1.5% and 11.26% for Daphnia similis, 0.12% and 1.39% for Ceriodaphnia dubia and 6.0% and 5.5% for Vibrio fischeri, respectively. Caffeine and several transition metals were found in both extracts. Coffee waste discarded in the environment may pose a risk to human and environmental health, since this compound can cause DNA damage and present toxicity to aquatic organisms.

35 Years of Marine Natural Product Research in Sweden: Cool Molecules and Models from Cold Waters.

Currents efforts in marine biodiscovery have essentially focused on temperate to tropical shallow water organisms. With more than 6000 species of marine plants and animals, the Kosterfjord area has the richest marine biodiversity in Swedish waters, but it remains understudied. The overall objective of our marine pharmacognosy research is to explore and reveal the pharmacological potential of organisms from this poorly explored region. More generally, we wish to understand aspects of structure-activity relationships of chemical interactions in cold-water marine environment (shallow and deep). Our strategy is based on ecologically guided search for compounds through studies of physiology and organism interactions coupled to identification of bioactive molecules guided by especially in vivo assays. The research programme originated in the beginning of the 1980s with a broad screening of Swedish marine organisms using both in vitro and in vivo assays, resulting in isolation and identification of several different bioactive molecules. Two congenerous cyclopeptides, i.e. barettin and 8,9-dihydrobarettin, were isolated from the deep-sea sponge Geodia barretti, and structurally elucidated, guided by their antifouling activity and their affinity to a selection of human serotonin receptors. To optimize the activity a number of analogues of barettin were synthezised and tested for antifouling activity. Within the EU project BlueGenics, two larger homologous peptides, barrettides A and B, were isolated from G. baretti. Also, metabolic fingerprinting combined with sponge systematics was used to further study deep-sea natural product diversity in the genus Geodia. Finally, the chemical property space model 'ChemGPS-NP' has been developed and used in our research group, enabling a more efficient use of obtained compounds and exploration of possible biological activities and targets. Another approach is the broad application of phylogenetic frameworks, which can be used in prediction of where-in which organisms-to search for novel molecules or better sources of known molecules in marine organisms. In a further perspective, the deeper understanding of evolution and development of life on Earth can also provide answers to why marine organisms produce specific molecules.

Does eutrophication-driven evolution change aquatic ecosystems?

Eutrophication increases primary production and changes the relative abundance, taxonomic composition and spatial distribution of primary producers within an aquatic ecosystem. The changes in composition and location of resources alter the distribution and flow of energy and biomass throughout the food web. Changes in productivity also alter the physico-chemical environment, which has further effects on the biota. Such ecological changes influence the direction and strength of natural and sexual selection experienced by populations. Besides altering selection, they can also erode the habitat gradients and/or behavioural mechanisms that maintain ecological separation and reproductive isolation among species. Consequently, eutrophication of lakes commonly results in reduced ecological specialization as well as genetic and phenotypic homogenization among lakes and among niches within lakes. We argue that the associated loss in functional diversity and niche differentiation may lead to decreased carrying capacity and lower resource-use efficiency by consumers. We show that in central European whitefish species radiations, the functional diversity affected by eutrophication-induced speciation reversal correlates with community-wide trophic transfer efficiency (fisheries yield per unit phosphorus). We take this as an example of how evolutionary dynamics driven by anthropogenic environmental change can have lasting effects on biodiversity and ecosystem functioning.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake.

Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.

Loss of heterophylly in aquatic plants: not ABA-mediated stress but exogenous ABA treatment induces stomatal leaves in Potamogeton perfoliatus.

Heterophyllous aquatic plants produce aerial (i.e., floating and terrestrial) and submerged leaves-the latter lack stomata-while homophyllous plants contain only submerged leaves, and cannot survive on land. To identify whether differences in morphogenetic potential and/or physiological stress responses are responsible for variation in phenotypic plasticity between two plants types, responses to abscisic acid (ABA) and salinity stress were compared between the closely related, but ecologically diverse pondweeds, Potamogeton wrightii (heterophyllous) and P. perfoliatus (homophyllous). The ABA-treated (1 or 10 µM) P. wrightii plants exhibited heterophylly and produced leaves with stomata. The obligate submerged P. perfoliatus plants were able to produce stomata on their leaves, but there were no changes to leaf shape, and stomatal production occurred only at a high ABA concentration (10 µM). Under salinity stress conditions, only P. wrightii leaves formed stomata. Additionally, the expression of stress-responsive NCED genes, which encode a key enzyme in ABA biosynthesis, was consistently up-regulated in P. wrightii, but only temporarily in P. perfoliatus. The observed species-specific gene expression patterns may be responsible for the induction or suppression of stomatal production during exposure to salinity stress. These results suggest that the two Potamogeton species have an innate morphogenetic ability to form stomata, but the actual production of stomata depends on ABA-mediated stress responses specific to each species and habitat.

Genetic assessment of meiobenthic community composition and spatial distribution in coastal sediments along northern Gulf of Mexico.

Meiobenthic (meiofauna and micro-eukaryotes) organisms are important contributors to ecosystem functioning in aquatic environments through their roles in nutrient transport, sediment stability, and food web interactions. Despite their ecological importance, information pertaining to variation of these communities at various spatial and temporal scales is not widely known. Many studies in the Gulf of Mexico (GOM) have focused either on deep sea or continental shelf areas, while little attention has been paid to bays and coastal regions. Herein, we take a holistic approach by using high-throughput sequencing approaches to examine spatial variation in meiobenthic communities within Alabama bays and the coastal northern GOM region. Sediment samples were collected along three transects (Mississippi Sound: MS, FOCAL: FT, and Orange Beach: OB) from September 2010 to April 2012 and community composition was determined by metabarcoding the V9 hypervariable region of the nuclear18S rRNA gene. Results showed that Stramenopiles (diatoms), annelids, arthropods (copepods), and nematodes were the dominate groups within samples, while there was presence of other phyla throughout the dataset. Location played a larger role than time sampled in community composition. However, samples were collected over a short temporal scale. Samples clustered in reference to transect, with the most eastern transect (OB) having a distinct community composition in comparison to the other two transects (MS and FT). Communities also differed in reference to region (Bay versus Shelf). Bulk density and percent inorganic carbon were the only measured environmental factors that were correlated with community composition.

Examination of metabolic responses to phosphorus limitation via proteomic analyses in the marine diatom Phaeodactylum tricornutum.

Phosphorus (P) is an essential macronutrient for the survival of marine phytoplankton. In the present study, phytoplankton response to phosphorus limitation was studied by proteomic profiling in diatom Phaeodactylum tricornutum in both cellular and molecular levels. A total of 42 non-redundant proteins were identified, among which 8 proteins were found to be upregulated and 34 proteins were downregulated. The results also showed that the proteins associated with inorganic phosphate uptake were downregulated, whereas the proteins involved in organic phosphorus uptake such as alkaline phosphatase were upregulated. The proteins involved in metabolic responses such as protein degradation, lipid accumulation and photorespiration were upregulated whereas energy metabolism, photosynthesis, amino acid and nucleic acid metabolism tend to be downregulated. Overall our results showed the changes in protein levels of P. tricornutum during phosphorus stress. This study preludes for understanding the role of phosphorous in marine biogeochemical cycles and phytoplankton response to phosphorous scarcity in ocean. It also provides insight into the succession of phytoplankton community, providing scientific basis for elucidating the mechanism of algal blooms.

Luteimonas dalianensis sp. nov., an obligate marine bacterium isolated from seawater.

A marine bacterial strain, designated OB44-3(T), was isolated from a crude oil-contaminated seawater sample collected near Dalian Bay, China. Cells of strain OB44-3(T) were Gramnegative, aerobic, rod-shaped, and oxidase- and catalasepositive. The major fatty acids were branched-chain saturated iso-C15:0 (27.9%) and unsaturated iso-C17:1 ω9c (14.8%). The DNA G+C content was 64.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain OB44-3(T) was a member of the genus Luteimonas (95-96% 16S rRNA gene sequence similarity); its closest neighbors were the type strains of Luteimonas terricola (96% sequence similarity), Luteimonas mephitis (96%), and Luteimonas lutimaris (96%). On the basis of phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain OB44-3(T) was considered to represent a novel species of the genus Luteimonas. The name Luteimonas dalianensis sp. nov. is proposed, with strain OB44-3(T) (=CGMCC 1.12191(T) =JCM 18136(T)) as the type strain.

A ferritin from Dendrorhynchus zhejiangensis with heavy metals detoxification activity.

Ferritin, an iron homeostasis protein, has important functions in transition and storage of toxic metal ions. In this study, the full-length cDNA of ferritin was isolated from Dendrorhynchus zhejiangensis by cDNA library and RACE approaches. The higher similarity and conserved motifs for ferritin were also identified in worm counterparts, indicating that it belonged to a new member of ferritin family. The temporal expression of worm ferritin in haemocytes was analyzed by RT-PCR, and revealed the ferritin could be induced by Cd(2+), Pb(2+) and Fe(2+). The heavy metal binding activity of recombinant ferritin was further elucidated by atomic force microscopy (AFM). It was observed that the ferritin protein could form a chain of beads with different size against three metals exposure, and the largest one with 35~40 nm in height was identified in the Cd(2+) challenge group. Our results indicated that worm ferritin was a promising candidate for heavy metals detoxification.

Ecological and evolutionary consequences of linked life-history stages in the sea.

Naturalists and scientists have been captivated by the diversity of marine larval forms since they were discovered following the advent of the microscope. Because they often bear little resemblance to adults, larvae were identified initially as new life forms, classified into different groups based on the similarity of their body plans and given new names that are still with us today. The radically different body plans and lifestyles of marine larvae and adults have led most investigators historically to study the two phases of complex life cycles in isolation. More recently, important ecological insights have sprung from taking a holistic view of marine life cycles. Meanwhile, the evolutionary (phenotypic and genetic) links among life-history phases remain less appreciated. In this review, our objective is to evaluate the evolutionary links within marine life cycles, and explore their ecological and evolutionary consequences. We provide a brief overview of marine life histories, discuss the phenotypic and genetic links between the two phases of the life cycle and pose challenges to advance our understanding of the evolutionary constraints acting on marine life histories.

In situ labeling of transcription sites in marine medaka.

Transcription factories have been characterized in cultured mammalian cells, but little is known about the regulation of these nuclear structures in different primary cell types. Using marine medaka, we observed transcription sites labeled by the metabolic incorporation of 5-fluorouridine (5-FU) into nascent RNA. Medaka was permeable to 5-FU in ambient water and became fully labeled within 4 hr of incubation. The incorporation of 5-FU was inhibited by the transcription inhibitor actinomycin D. The 5-FU incorporation sites were detected in the cell nucleus, and could be abolished by RNase digestion. The tissue distribution of 5-FU incorporation was visualized by immunocytochemistry on whole-mount specimens and histological sections. The 5-FU labeling appeared highly cell type specific, suggesting a regulation of the overall transcription activities at tissue level. Mapping of transcription factories by 5-FU incorporation in fish provides a useful and physiologically relevant model for studying the control of gene expression in the context of the functional organization of the cell nucleus. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.