Land Use, Not Stream Order, Controls N2O Concentration and Flux in the Upper Mara River Basin, Kenya.

Anthropogenic activities have led to increases in nitrous oxide (N2O) emissions from river systems, but there are large uncertainties in estimates due to lack of data in tropical rivers and rapid increase in human activity. We assessed the effects of land use and river size on N2O flux and concentration in 46 stream sites in the Mara River, Kenya, during the transition from the wet (short rains) to dry season, November 2017 to January 2018. Flux estimates were similar to other studies in tropical and temperate systems, but in contrast to other studies, land use was more related to N2O concentration and flux than stream size. Agricultural stream sites had the highest fluxes (26.38 ± 5.37 N2O-N µg·m-2·hr-1) compared to both forest and livestock sites (5.66 ± 1.38 N2O-N µg·m-2·hr-1 and 6.95 ± 2.96 N2O-N µg·m-2·hr-1, respectively). N2O concentrations in forest and agriculture streams were positively correlated to stream carbon dioxide (CO2-C(aq)) but showed a negative correlation with dissolved organic carbon, and the dissolved organic carbon:dissolved inorganic nitrogen ratio. N2O concentration in the livestock sites had a negative relationship with CO2-C(aq) and a higher number of negative fluxes. We concluded that in-stream chemoautotrophic nitrification was likely the main biogeochemical process driving N2O production in agricultural and forest streams, whereas complete denitrification led to the consumption of N2O in the livestock stream sites. These results point to the need to better understand the relative importance of nitrification and denitrification in different habitats in producing N2O and for process-based studies.

Twelve testable hypotheses on the geobiology of weathering.

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earth's surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby controlling the location and extent of biological weathering. (2) Biological stoichiometry drives changes in mineral stoichiometry and distribution through weathering. (3) On landscapes experiencing little erosion, biology drives weathering during initial succession, whereas weathering drives biology over the long term. (4) In eroding landscapes, weathering-front advance at depth is coupled to surface denudation via biotic processes. (5) Biology shapes the topography of the Critical Zone. (6) The impact of climate forcing on denudation rates in natural systems can be predicted from models incorporating biogeochemical reaction rates and geomorphological transport laws. (7) Rising global temperatures will increase carbon losses from the Critical Zone. (8) Rising atmospheric P(CO2) will increase rates and extents of mineral weathering in soils. (9) Riverine solute fluxes will respond to changes in climate primarily due to changes in water fluxes and secondarily through changes in biologically mediated weathering. (10) Land use change will impact Critical Zone processes and exports more than climate change. (11) In many severely altered settings, restoration of hydrological processes is possible in decades or less, whereas restoration of biodiversity and biogeochemical processes requires longer timescales. (12) Biogeochemical properties impart thresholds or tipping points beyond which rapid and irreversible losses of ecosystem health, function, and services can occur.

Notch-Delta signaling is required for spatial patterning and Müller glia differentiation in the zebrafish retina.

Notch-Delta signaling has been implicated in several alternative modes of function in the vertebrate retina. To further investigate these functions, we examined retinas from zebrafish embryos in which bidirectional Notch-Delta signaling was inactivated either by the mind bomb (mib) mutation, which disrupts E3 ubiquitin ligase activity, or by treatment with gamma-secretase inhibitors, which prevent intramembrane proteolysis of Notch and Delta. We found that inactivating Notch-Delta signaling did not prevent differentiation of retinal neurons, but it did disrupt spatial patterning in both the apical-basal and planar dimensions of the retinal epithelium. Retinal neurons differentiated, but their laminar arrangement was disrupted. Photoreceptor differentiation was initiated normally, but its progression was slowed. Although confined to the apical retinal surface as in normal retinas, the planar organization of cone photoreceptors was disrupted: cones of the same spectral subtype were clumped rather than regularly spaced. In contrast to neurons, Müller glia failed to differentiate suggesting an instructive role for Notch-Delta signaling in gliogenesis.

Cadherin expression in the inner ear of developing zebrafish.

Cadherins are cell adhesion molecules that have been implicated in development of a variety of organs including the ear. In this study we analyzed expression patterns of three zebrafish cadherins (Cadherin-2, -4, and -11) in the embryonic and larval zebrafish inner ear using both in situ hybridization and immunocytochemical methods. All three Cadherins exhibit distinct spatiotemporal patterns of expression during otic vesicle morphogenesis. Cadherin-2 and Cadherin-4 proteins and their respective mRNAs were detected mainly in the sensory patches and the statoacoustic ganglion (SAg), respectively. In contrast, cadherin-11mRNA was widely expressed earlier in the otic placode, and later became restricted to a subset of cells in the inner ear, including hair cells.

Up-regulation of cadherin-2 and cadherin-4 in regenerating visual structures of adult zebrafish.

Cadherins are homophilic cell adhesion molecules that control development of a variety of tissues and maintenance of adult structures. In this study, we examined expression of zebrafish cadherin-2 (Cdh2, N-cadherin) and cadherin-4 (Cdh4, R-cadherin) in the visual system of adult zebrafish after eye or optic nerve lesions using immunocytochemistry and immunoblotting. Both Cdh2 and Cdh4 immunoreactivities were specifically up-regulated in regenerating retina and/or the optic pathway. Furthermore, temporal expression patterns of these two cadherins were distinct during the regeneration of the injured tissues. Cadherins have been shown to regulate axonal outgrowth in the developing nervous system, but this is the first report, to our knowledge, of increased cadherin expression associated with axonal regeneration in the vertebrate central nervous system. Our results suggest that both Cdh2 and Cdh4 may be important for regeneration of injured retinal ganglion cell axons.

Cadherin-4 expression in the zebrafish central nervous system and regulation by ventral midline signaling.

In this study we show that zebrafish cadherin-4 (R-cadherin) transcript (cad4) and protein are expressed in several defined regions in the embryonic forebrain and in distinctive clusters in the hindbrain and spinal cord. This is the first report of a segmental pattern of expression of cadherin-4 in the hindbrain and spinal cord. Expression domains of cadherin-4 transcript and protein were compared with that of pax6.1. In the forebrain of zebrafish embryos, cad4 and pax6.1 expression domains overlapped extensively, although they were not completely coincident. Injection of pax6.1 mRNA resulted in an increase in cad4 expression, whereas overexpression of sonic hedgehog (shh), a midline signaling molecule that reduces pax6.1 expression, caused a reduction in cad4 expression throughout the brain. cad4 expression was increased in both forebrain and hindbrain in cyclops mutant embryos, which have a defect in midline signaling and an enlarged expression domain of pax6.1. These results suggest that zebrafish cadherin-4 may play a role in organization of neuronal architecture throughout the neural axis, and that its expression is regulated by a ventral midline signaling pathway that involves shh and pax6.1.

Cones regenerate from retinal stem cells sequestered in the inner nuclear layer of adult goldfish retina.

PURPOSE: To determine whether retinal progenitor cells in the inner nuclear layer give rise to regenerated cones after laser ablation of photoreceptors in adult goldfish retina. METHODS: Using a technique developed previously in this laboratory, photoreceptors in the retina of adult goldfish were ablated with an argon laser. The mitotic marker, bromodeoxyuridine, was used to label proliferating and regenerated cells, which were identified with cell-specific markers. RESULTS: Cells proliferating locally within lesion included microglia, Müller glia, and retinal progenitors in the inner nuclear layer (INL). The nuclei of both Müller glia and associated retinal progenitors migrated from the inner to the outer nuclear layer. The proliferating retinal progenitors, which express Notch-3 and N-cadherin, regenerated cone photoreceptors and then rod photoreceptors. CONCLUSIONS: Previous work has demonstrated that photoreceptors in the goldfish retina regenerate selectively after laser ablation, but the source of regenerated cones has not been identified. The results reported here provide support for the existence of retinal stem cells within the adult fish retina that are capable of regenerating cone photoreceptors. The data also support the involvement of Müller glia in the production of regenerated cones.

Zebrafish E-cadherin: expression during early embryogenesis and regulation during brain development.

Zebrafish E-cadherin (cdh1) cell adhesion molecule cDNAs were cloned. We investigated spatial and temporal expression of cdh1 during early embryogenesis. Expression was observed in blastomeres, the anterior mesoderm during gastrulation, and developing epithelial structures. In the developing nervous system, cdh1 was detected at the pharyngula stage (24 hpf) in the midbrain-hindbrain boundary (MHB). Developmental regulation of MHB formation involves wnt1 and pax2.1. wnt1 expression preceded cdh1 expression during MHB formation, and cdh1 expression in the MHB was dependent on normal development of this structure.

Riverine export of aged terrestrial organic matter to the North Atlantic Ocean.

Global riverine discharge of organic matter represents a substantial source of terrestrial dissolved and particulate organic carbon to the oceans. This input from rivers is, by itself, more than large enough to account for the apparent steady-state replacement times of 4,00-6,000 yr for oceanic dissolved organic carbon. But paradoxically, terrestrial organic matter, derived from land plants, is not detected in seawater and sediments in quantities that correspond to its inputs. Here we present natural 14C and 13C data from four rivers that discharge to the western North Atlantic Ocean and find that these rivers are sources of old (14C-depleted) and young (14C-enriched) terrestrial dissolved organic carbon, and of predominantly old terrestrial particulate organic carbon. These findings contrast with limited earlier data that suggested terrestrial organic matter transported by rivers might be generally enriched in 14C from nuclear testing, and hence newly produced. We also find that much of the young dissolved organic carbon can be selectively degraded over the residence times of river and coastal waters, leaving an even older and more refractory component for oceanic export. Thus, pre-ageing and degradation may alter significantly the structure, distributions and quantities of terrestrial organic matter before its delivery to the oceans.

Zebrafish genes rx1 and rx2 help define the region of forebrain that gives rise to retina.

Zebrafish retinal homeobox genes rx1 and rx2 are expressed exclusively in the optic primordia and then in cone photoreceptors of the differentiated neural retina. In this study, we show that the rx expression domain is coextensive with the region identified as the retinal field in published fate maps of the neural plate in zebrafish embryos. Analysis of the spatiotemporal relationships between retinal and forebrain precursors suggests that lateral movement of retinal precursors is responsible for evagination of the optic primordia. Overexpression of either rx1 or rx2 results in the loss of forebrain tissue and the ectopic formation of retinal tissue. We asked whether the deletion of forebrain and expansion of retinal tissue could be explained by the death of telencephalic precursors and enhanced proliferation of retinal precursors, and we found that it could not. Instead, our data are consistent with a change in cell fate of forebrain precursors associated with reduced expression of telencephalic markers (emx1 and BF-1) and ectopic expression of retinal markers (rx1/2/3, pax6, six6, and vsx2) at the neural keel stage. The rx homeodomain alone is sufficient to induce ectopic retinal tissue, although weakly so, and this observation, together with results from deletion constructs, suggests that interactions with unidentified transcriptional regulators are important for rx1 and rx2 function during early eye development. We conclude that regulated expression of zebrafish rx1 and rx2 helps to define the region of the forebrain fated to give rise to retinal tissue and may be involved in the cellular migrations that lead to splitting of the retinal field and formation of the optic primordia.

Isolation and characterization of a zebrafish homologue of the cone rod homeobox gene.

PURPOSE: To isolate and characterize a zebrafish CRX: homologue. Mammalian CRX: genes are expressed specifically in photoreceptors and pinealocytes, regulate photoreceptor gene expression, are necessary for normal photoreceptor differentiation, and when mutated cause a variety of photoreceptor degenerations. METHODS: A zebrafish retinal cDNA library was screened with a human CRX cDNA probe. Radiation hybrid mapping, Northern blot analysis, in situ hybridization, and transient transfection studies were performed using standard methods. RESULTS: Based on amino acid sequence comparisons, zebrafish crx shows 50% identity with human CRX, and 85% identity in the homeodomain. A phylogenetic analysis indicates that zebrafish crx is most closely related to the mammalian Crx proteins, and more distantly related to the Otx proteins. Zebrafish crx maps between 49.6 and 54.5 cm from the top of linkage group LG05C, a map position consistent with the location of the mouse and human CRX genes. Northern blot analysis and in situ hybridization indicate that zebrafish crx is expressed in the retina and pineal gland. In adult zebrafish, crx is expressed by both rods and cones in the outer nuclear layer, and in cells in the outer zone of the inner nuclear layer, in the region occupied by bipolar cells. Similar to mammalian Crx, zebrafish crx interacts with neural retinal leucine zipper (Nrl) to activate, although weakly, rhodopsin promoter activity. CONCLUSIONS: Based on molecular phylogeny, chromosomal location, expression pattern, and ability to activate rhodopsin promoter activity in transient transfection assays, zebrafish crx appears to be an orthologue and functional homologue of mammalian CRX:

Differential expression of cadherin-2 and cadherin-4 in the developing and adult zebrafish visual system.

Cadherins are homophilic cell adhesion molecules that control development of a variety of tissues and maintenance of adult structures. Although cadherins have been implicated in the development of the brain, including the visual system, in several vertebrate species, little is known of their role in zebrafish. In this study, we examined distribution of cadherin-2 (Cdh2, N-cadherin) in the visual system of developing and adult zebrafish using both immunocytochemical and in situ hybridization methods, and we compared Cdh2 distribution to that of the previously reported and closely related cadherin-4 (Cdh4, R-cadherin). As in other vertebrates, in zebrafish embryos Cdh2 was widely expressed in the early nervous system, but its expression became more restricted as development proceeded. Cdh4 was not detectable until later in development, at about the time when the first ganglion cells are generated. Cdh2 and Cdh4 were expressed in distinct regions of developing visual structures, including the lens. We hypothesize that the differential expression of these two cadherins in developing zebrafish visual structures reflects functionally different roles in the development of the vertebrate visual system.

Localization of cGMP-dependent protein kinase isoforms in mouse eye.

PURPOSE: To examine the expression of the major isoforms of cyclic guanosine monophosphate (cGMP)-dependent protein kinase (cGK) in mouse eye. METHODS: Immunohistochemical localization of cGMP in mouse eye cryosections was performed using an anti-cGMP antibody, followed by visualization with indirect fluorescence microscopy. The presence of types Ialpha, Ibeta, and II cGK mRNAs in mouse eye extracts was determined initially by RNase protection analysis. Further localization of cGK I and II mRNAs on cryosections was accomplished by in situ hybridization using digoxigenin-labeled cRNA probes and an alkaline phosphatase-conjugated anti-digoxigenin antibody. Finally, cGK I protein was localized to subcellular areas within the retina using an anti-cGK I-specific primary antibody. RESULTS: In initial immunohistochemical experiments cGMP was present in numerous regions and layers within the eye and retina. Subsequent RNase protection studies demonstrated that cGK Ialpha, Ibeta, and II mRNAs were present in mouse eye and that type Ibeta mRNA were 6.6 and 30 times more abundant than type Ialpha and type II, respectively. By in situ hybridization, cGK I mRNA was localized to photoreceptor inner segments and the ganglion cell and inner nuclear layers of the retina, and lesser amounts were found in the ciliary epithelium, lens, and cornea. The cGK II mRNA expression pattern was similar but not identical with that of cGK I. Finally, within the retina, cGK I protein was most abundant in the inner plexiform layer, with significant amounts in ganglion cells and photoreceptor inner segments as well. CONCLUSIONS: The presence of these cGK isoforms in discrete areas throughout the eye suggests multiple roles for the cGMP-dependent signal transduction system in the regulation of physiologic and pathologic ocular processes.

Function for Hedgehog genes in zebrafish retinal development.

The hedgehog (hh) genes encode secreted signaling proteins that have important developmental functions in vertebrates and invertebrates. In Drosophila, expression of hh coordinates retinal development by propagating a wave of photoreceptor differentiation across the eye primordium. Here we report that two vertebrate hh genes, sonic hedgehog (shh) and tiggy-winkle hedgehog (twhh), may perform similar functions in the developing zebrafish. Both shh and twhh are expressed in the embryonic zebrafish retinal pigmented epithelium (RPE), initially in a discrete ventral patch which then expands outward in advance of an expanding wave of photoreceptor recruitment in the subjacent neural retina. A gene encoding a receptor for the hedgehog protein, ptc-2, is expressed by retinal neuroepithelial cells. Injection of a cocktail of antisense (alphashh/alphatwhh) oligonucleotides reduces expression of both hh genes in the RPE and slows or arrests the progression of rod and cone photoreceptor differentiation. Zebrafish strains known to have mutations in Hh signaling pathway genes similarly exhibit retardation of photoreceptor differentiation. We propose that hedgehog genes may play a role in propagating photoreceptor differentiation across the developing eye of the zebrafish.

Expression of three Rx homeobox genes in embryonic and adult zebrafish.

The paired-class homeobox gene, Rx, is important in eye development. In this study we analyze expression patterns of three zebrafish Rx genes (Zrx1, 2, 3) in embryos and adults. All three genes show dynamic spatiotemporal patterns of expression. Zrx3 is expressed earliest, in the anteriormost region of the neural plate, in regions that give rise to ventral diencephalon and retinae. As development proceeds, Zrx3 expression is reduced in the lateral optic primordia, and is absent in the optic cup, but is retained at the ventral midline of the diencephalon, and is expressed in hypothalamus in the adult. As the neural retina begins to differentiate, Zrx3 is re-expressed in a subset of cells in the inner nuclear layer, presumably bipolar cells, and this expression is retained in the adult. In contrast, Zrx1/2 have a slightly later onset of expression, are initially coincident with Zrx3, but then become complementary, remaining on in the optic primordia but disappearing from the ventral midline of the diencephalon. Zrx1/2 are down-regulated as the retina differentiates, except in the outer nuclear layer where they continue to be expressed at high levels in cone, but not rod, photoreceptors. This is the first transcription factor described that distinguishes between cone and rod photoreceptors.

Spatial correspondence between R-cadherin expression domains and retinal ganglion cell axons in developing zebrafish.

Mechanisms underlying axonal pathfinding have been investigated for decades, and numerous molecules have been shown to play roles in this process, including members of the cadherin family of cell adhesion molecules. We showed in the companion paper that a member of the cadherin family (zebrafish R-cadherin) is expressed in retinal ganglion cells, and in presumptive visual structures in zebrafish brain, during periods when the axons were actively extending toward their targets. The present study extends the earlier work by using 1,1'-dioctadecyl-3,3,3',3', tetramethylindocarbocyanine perchlorate (DiI) anterograde tracing techniques to label retinal ganglion cell axons combined with R-cadherin in situ hybridization to explicitly examine the association ofretinal axons and brain regions expressing R-cadherin message. We found that in zebrafish embryos at 46-54 hours postfertilization, DiI-labeled retinal axons were closely associated with cells expressing R-cadherin message in the hypothalamus, the pretectum, and the anterolateral optic tectum. These results demonstrate that R-cadherin is appropriately distributed to play a role in regulating development of the zebrafish visual system, and in particular, pathfinding and synaptogenesis of retinal ganglion cell axons.

R-cadherin expression in the developing and adult zebrafish visual system.

Cell adhesion molecules in the cadherin family have been implicated in histogenesis and maintenance of cellular structure and function in several organs. Zebrafish have emerged as an important new developmental model, but only three zebrafish cadherin molecules have been identified to date (N-cadherin, paraxial protocadherin, and VN-cadherin). We began a systematic study to identify other zebrafish cadherins by screening zebrafish cDNA libraries using an antibody raised to the cytoplasmic domain of mouse E-cadherin. Here, we report a partial cDNA with extensive sequence homology to R-cadherin. Spatial and temporal expression of this putative zebrafish R-cadherin was examined in embryos and adults by Northern analysis, RNase protection, and in situ hybridization. R-cadherin message increased during embryogenesis up to 80 hours postfertilization (hpf) and persisted in adults. In the embryonic brain, R-cadherin was first expressed in groups of cells in the diencephalon and pretectum. In adult zebrafish brain, R-cadherin continued to be expressed in several specific regions including primary visual targets. In the retina, R-cadherin was first detected at about 33 hours postfertilization in the retinal ganglion cell layer and the inner part of the inner nuclear layer. Expression levels were highest during periods of axon outgrowth and synaptogenesis. Retrograde labeling of the optic nerve with 1,1'-dioctadecyl-3,3,3',3', tetramethylindocarbocyanine perchlorate (DiI) followed by in situ hybridization confirmed that a subset of retinal ganglion cells in the embryo expressed R-cadherin message. In the adult, R-cadherin expression continued in a subpopulation of retinal ganglion cells. These results suggest that R-cadherin-mediated adhesion plays a role in development and maintenance of neuronal connections in zebrafish visual system.

Novel expression pattern of interphotoreceptor retinoid-binding protein (IRBP) in the adult and developing zebrafish retina and RPE.

PURPOSE: Interactions between the neural retina and retinal pigment epithelium (RPE) are mediated by the interphotoreceptor matrix (IPM). The transport of retinoids across the IPM is mediated by interphotoreceptor retinoid-binding protein (IRBP). To explore the possibility that IRBP is important during retinal development, we examined its spatiotemporal expression pattern in embryonic zebrafish. METHODS: IRBP mRNA expression was examined using RT-PCR and in situ hybridization. IRBP was localized using antiserum against recombinant zebrafish IRBP. IRBP synthesis and secretion were studied by in vitro metabolic labeling of retinas and RPE-eyecups. RESULTS: IRBP mRNA was first observed in the pineal at 24 hours post-fertilization (hpf) and in the ventral retina at 50 hpf. Immunoreactive IRBP was first observed at 72 hpf. Remarkably, IRBP was expressed not only by photoreceptors but also by the adult and embryonic RPE. In embryos, expression in both retina and RPE began in a ventronasal patch and spread to involve the entire eye. In general, early IRBP expression was dominated by photoreceptors, but then RPE expression spread beyond the limit of photoreceptor expression. Double in situ hybridizations suggests that cones express IRBP mRNA before they express a specific opsin, while rods may express rod opsin prior to IRBP. CONCLUSIONS: The temporal and spatial patterns of IRBP expression by the RPE and retina are consistent with a role in retinal development and suggest coordination of RPE and photoreceptor differentiation.