NeXML: rich, extensible, and verifiable representation of comparative data and metadata

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.     

Nitric oxide synthase in photoreceptive pineal organs of fish

Photoreceptor cells in the fish pineal gland transduce light-dark information differentially into a neuroendocrine melatonin message; distinguishing features are the presence or absence of endogenous oscillators that drive these rhythms. In the present study, we have analysed the presence and distribution of nitric oxide (NO) synthase in both pineal types by NADPH-diaphorase (NADPHd) histochemistry and determined the effects of NO donors on cGMP formation and melatonin production. NADPHd staining was confined to photoreceptor cells in clock-driven pineal organs of zebrafish and goldfish as evidenced by a codistribution with S-antigen-immunoreactivity (-ir) or cyclic GMP-ir and, in the pineal of the trout, to cells that are S-antigen negative. In the trout pineal, but not in the other species, NADPHd staining was clearly codistributed with growth associated protein-43 (GAP-43) immunoreactivity, an antibody that recognizes developing and regenerating neurons in the fish brain. The presence of a functional NO system in photosensory pineal organs is supported by the fact that NO donors like S-nitroso N-acetylpenicillamine (SNAP) elevate intracellular cGMP levels. However, despite the significant rise in cGMP levels nitric oxide donors did neither affect acute light-dependent melatonin formation in the trout pineal nor the rhythmic production of melatonin in the zebrafish pineal.     

Impacts of climate warming on lake fish community structure and potential effects on ecosystem function

Fish play a key role in the trophic dynamics of lakes, not least in shallow systems. With climate warming, complex changes in fish community structure may be expected owing to the direct and indirect effects of temperature, and indirect effects of eutrophication, water-level changes and salinisation on fish metabolism, biotic interactions and geographical distribution. We review published and new data supporting the hypotheses that, with a warming climate, there will be changes in: fish community structure (e.g. higher or lower richness depending on local conditions); life history traits (e.g. smaller body size, shorter life span, earlier and less synchronised reproduction); feeding mode (i.e. increased omnivory and herbivory); behaviour (i.e. stronger association with littoral areas and a greater proportion of benthivores); and winter survival. All these changes imply higher predation on zooplankton and macroinvertebrates with increasing temperatures, suggesting that the changes in the fish communities partly resemble, and may intensify, the effects triggered by eutrophication. Modulating factors identified in cold and temperate systems, such as the presence of submerged plants and winter ice cover, seem to be weaker or non-existent in warm(ing) lakes. Consequently, in the future lower nutrient thresholds may be needed to obtain clear-water conditions and good ecological status in the future in currently cold or temperate lakes. Although examples are still scarce and more research is needed, we foresee biomanipulation to be a less successful restoration tool in warm(ing) lakes without a strong reduction of the nutrient load.     

Intrinsic Photosensitive Retinal Ganglion Cells in the Diurnal Rodent,Arvicanthis ansorgei

Intrinsically photosensitive retinal ganglion cells (ipRGCs) represent a new class of photoreceptors which support a variety of non-image forming physiological functions, such as circadian photoentrainment, pupillary light reflex and masking responses to light. In view of the recently proposed role of retinal inputs for the regulation of diurnal and nocturnal behavior, we performed the first deep analysis of the ipRGC system in a diurnal rodent model, Arvicanthis ansorgei , and compared the anatomical and physiological properties of ipRGCs with those of nocturnal mice. Based on somata location, stratification pattern and melanopsin expression, we identified two main ipRGC types in the retina of Arvicanthis : M1, constituting 74% of all ipRGCs and non-M1 (consisting mainly of the M2 type) constituting the following 25%. The displaced ipRGCs were rarely encountered. Phenotypical staining patterns of ganglion cell markers showed a preferential expression of Brn3 and neurofilaments in non-M1 ipRGCs. In general, the anatomical properties and molecular phenotyping of ipRGCs in Arvicanthis resemble ipRGCs of the mouse retina, however the percentage of M1 cells is considerably higher in the diurnal animal. Multi-electrode array recordings (MEA) identified in newborn retinas of Arvicanthis three response types of ipRGCs (type I, II and III) which are distinguished by their light sensitivity, response strength, latency and duration. Type I ipRGCs exhibited a high sensitivity to short light flashes and showed, contrary to mouse type I ipRGCs, robust light responses to 10 ms flashes. The morphological, molecular and physiological analysis reveals very few differences between mouse and Arvicanthis ipRGCs. These data imply that the influence of retinal inputs in defining the temporal niche could be related to a stronger cone input into ipRGCs in the cone-rich Arvicanthis retina, and to the higher sensitivity of type I ipRGCs and elevated proportion of M1 cells.     

Presence of a sodium-dependentd-glucose transport system in the kidney of the atlantic hagfish (Myxine glutinosa)

Summary A membrane fraction, rich in brushborder membranes, was prepared from the archinephric duct of the atlantic hagfish (Myxine glutinosa) and the uptake ofd-glucose and other sugars into the membrane vesicles was investigated by a rapid filtration technique. Uptake ofd-glucose was found to be sodium-dependent, phloridzin-inhibitable and osmotically sensitive. A sodium gradient dependent overshoot was demonstrated at 25° C as well as at the more physiological temperature of 4°C. The sodium dependentd-glucose transport was inhibited by -methyl-d-glucoside, but not by 2-deoxy-d-glucose. Furthermore at the same concentration of sugars the initial uptake ofd-glucose was 7.2-fold higher thanl-glucose uptake.d-glucose transport across the membrane in the presence of a sodium gradient was stimulated when SCN^– replaced Cl^– and inhibited when gluconate replaced Cl^–.d-glucose uptake in the presence of a sodium- and potassium gradient was decreased by the addition of valinomycin. In addition, the presence of ad-glucose gradient enhanced sodium uptake into the vesicles as compared to a mannitolgradient. Phloridzin inhibited thed-glucose dependent sodium flux. Thus an electrogenic stereospecific sodium glucose co-transport system, with properties similar to that found in the kidney of higher vertebrates is present in this primitive vertebrate and might participate in secondary-active sugar reabsorption in the archinephric duct.     

Circadian variation in cell proliferation and maturation

The rat corneal epithelium has been chosen as a model for studying growth regulation. In this epithelium a large single cohort of cells enters the S phase during a fairly short time period once a day. The factor responsible for this wave of cell proliferation is unknown, but it may be a chemical signal from the central nervous system (the suprachiasmatic nucleus or the corpus pineale). The mature cell compartment of the corneal epithelium is assumed to produce a negative feedback factor (chalone), counteracting the effect of the circadian proliferative factor on the local cell proliferation. When no circadian factor is being produced, during most of the 24 h, the chalone seems to enhance the maturation process. During diminished chalone production (e.g. after cell injury and subsequent regeneration), we will get a more or less unrestricted cell proliferation in the tissue with a delayed maturation process prolonging the chalone depletion. This interaction between the circadian proliferative factor and the negative feedback factor for regulation of proliferation with its accompanying stimulatory effect on maturation, may represent a general mechanism in the regulation of cell proliferation in any tissue. Since in at least some organs virtually all cells entering the S phase do this as a single wave once a day, this mechanism may be enough to explain the regulation of cell proliferation during both normal and regenerative conditions.     

Habitat use of arctic charrSalvelinus alpinus in Thingvallavatn,Iceland

Synopsis Habitat use by four morphs of arctic charr,Salvelinus alpinus, was investigated in Thingvallavatn, Iceland, by sampling with pelagic and benthic gill nets. Sampling was done in May/June and August/September. Greatest abundance of fish was recorded in the littoral and epipelagic zone in early autumn. Catches were low in early summer. The four morphs are partly segregated in habitat. Small (SB-) and large benthivorous (LB-) charr have a more restricted spatial distribution than piscivorous (PI-), and especially planktivorous (PL-) charr. Both benthivorous morphs are mainly found in the littoral zone, and occur in largest numbers in stony shallows at depths between 0 and 10 m. PL-charr usually dominates in numbers in all habitats. PI-charr is most abundant in epibenthic habitats, although numbers are always low. All morphs are caught in higher numbers at night than during the day, but the diurnal activity difference is highest among SB-charr. The habitat use by different morphs is as may be expected from their morphology and diets. Within the population of PL-charr, young and small fish are more abundant on the bottom than in the pelagic zone, and there is a surplus of females in the pelagic zone. Along the benthic profile, young, small and immature PL-charr are more abundant in deep than in shallow waters. The results are discussed in relation to food supply, competition and predation. Possible reasons for the occurrence of four arctic charr morphs are also discussed.Contribution from the Thingvallavatn project.     

Adaptation of renal function to hypotonic medium in the winter flounder (Pseudopleuronectes americanus)

Summary The kidneys of winter flounders transferred to hypotonic medium were investigated for glomerular and tubular handling of fluid and electrolytes and for the urinary excretion of proteins. Media were sea water (925 mosm·kg^–1) and brackish water (70 mosm·kg^–1).In sea water, the urine was hypertonic to the plasma in 7 fish of this study. Urine flow rate was correlated with the GFR. After adaptation to brackish water a delay of 1 to 3 days was observed until the kidneys switched from fluid retention to the excretion of large amounts of dilute urine. GFR and urine flow rate were increased from 0.61±0.08 to 1.58±0.29 ml·h^–1·kg^–1 and from 0.14±0.02 to 0.68±0.08 ml·h^–1·kg^–1, respectively . With increased filtered load the tubular reabsorption of fluid decreased from 74±2.4% to 45±11.2%. The excretion rates of sodium and potassium were increased due to decreased fractional sodium and potassium reabsorption. The urinary excretion of divalent cations, however, was reduced because the net tubular reabsorption of calcium was increased and the net secretion of magnesium was diminished.Both the urinary total protein concentration and the protein pattern showed no significant change, but the rate of protein excretion was increased from 0.21±0.04 to 0.60±0.05 mg·h^–1·kg^–1. The comparison of protein patterns obtained from urine and serum samples revealed that high molecular weight (HMW) proteins prevail in the serum whereas low molecular weight (LMW) proteins dominate in the urine. The diminished quantity of the HMW-protein fraction in the urine thus may reflect size selectivity of the glomerular filtration barrier for serum proteins also in the winter flounder.Abbreviations BW brackish water - SW sea water - GFR glomerular filtration rate - HMW heigh molecular weight - LMW low molecular weight