Ocean biogeochemistry modeled with emergent trait-based genomics.

Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.

Multivariate characterization of white matter heterogeneity in autism spectrum disorder.

The complexity and heterogeneity of neuroimaging findings in individuals with autism spectrum disorder has suggested that many of the underlying alterations are subtle and involve many brain regions and networks. The ability to account for multivariate brain features and identify neuroimaging measures that can be used to characterize individual variation have thus become increasingly important for interpreting and understanding the neurobiological mechanisms of autism. In the present study, we utilize the Mahalanobis distance, a multidimensional counterpart of the Euclidean distance, as an informative index to characterize individual brain variation and deviation in autism. Longitudinal diffusion tensor imaging data from 149 participants (92 diagnosed with autism spectrum disorder and 57 typically developing controls) between 3.1 and 36.83 years of age were acquired over a roughly 10-year period and used to construct the Mahalanobis distance from regional measures of white matter microstructure. Mahalanobis distances were significantly greater and more variable in the autistic individuals as compared to control participants, demonstrating increased atypicalities and variation in the group of individuals diagnosed with autism spectrum disorder. Distributions of multivariate measures were also found to provide greater discrimination and more sensitive delineation between autistic and typically developing individuals than conventional univariate measures, while also being significantly associated with observed traits of the autism group. These results help substantiate autism as a truly heterogeneous neurodevelopmental disorder, while also suggesting that collectively considering neuroimaging measures from multiple brain regions provides improved insight into the diversity of brain measures in autism that is not observed when considering the same regions separately. Distinguishing multidimensional brain relationships may thus be informative for identifying neuroimaging-based phenotypes, as well as help elucidate underlying neural mechanisms of brain variation in autism spectrum disorders.

Influence of Al(2)O(3) nanoparticles on the isothermal cure of an epoxy resin.

The influence of Al(2)O(3) nanoparticles on the curing of an epoxy thermoset based on diglycidyl ether of bisphenol A was investigated using temperature-modulated differential scanning calorimetry (TMDSC) and rheology. Diethylene triamine was used as a hardener. TMDSC not only allows for a systematic study of the kinetics of cure but simultaneously gives access to the evolution of the specific heat capacities of the thermosets. The technique thus provides insight into the glass transition behaviour of the nanocomposites and hence makes it possible to shed some light on the interaction between the nanoparticles and the polymer matrix. The Al(2)O(3) fillers are shown to accelerate the growth of macromolecules upon isothermal curing. Several mechanisms which possibly could be responsible for the acceleration are described. As a result of the faster network growth chemical vitrification occurs at earlier times in the filled thermosets and the specific reaction heat decreases with increasing nanoparticle concentration. Rheologic measurements of the zero-shear viscosity confirm the faster growth of the macromolecules in the presence of the nanoparticles.

Photooxidative action in cancer and normal cells induced by the use of photofrin in photodynamic therapy.

Photofrin-mediated PDT was applied to malignant (A549 and MCF-7) and normal (HUV-EC-C) cells. The cells were incubated for different lengths of time after PDT. The cell responses to the therapy were examined by changes in SOD activity, phototoxicity, and mode of the cell death. PDT induced dynamic changes in SOD activity. Initially, an increase in SOD activity was observed, and after 6 hours of culture it decreased to the control level. Results obtained from MTT and the comet assay indicate that PDT caused immediate cell death via apoptosis in the A549, MCF-7, and HUV-EC-C cell lines. Our studies confirm that SOD is involved in the response of both cancer and normal cells to PDT.

Chemically induced transition phenomena in polyurethanes as seen from generalized mode Grüneisen parameters.

Many phenomenological properties of reactive polymers like polyurethanes increase or decrease continuously in the course of the curing process before saturating at the end of the chemical reaction. This holds true for instance for the mass density, the refractive index, the chemical turnover and the hypersonic properties. The reason for this monotone behaviour is that the chemical reaction behaves like a continuous succession of irreversible phase transitions. These transitions are superposed by the sol-gel transition and possibly by the chemically induced glass transition, with the drawback that the latter two highlighted transitions are often hidden by the underlying curing process. In this work we propose generalized mode Grüneisen parameters as an alternative probe for elucidating the polymerization process itself and the closely related transition phenomena. As a model system we use polyurethane composed of a diisocyanate and varying ratios of difunctional and trifunctional alcohols.

Olfactory sensory neurons in the sea lamprey display polymorphisms.

The sea lamprey (Petromyzon marinus) is an ancient jawless fish phyletically removed from modern (teleost) fishes. It is an excellent organism in the study of olfaction due to its accessible olfactory pathway, which is susceptible to manipulation, and its important location in the evolution of vertebrates. There are many similarities in the olfactory systems of all fishes, and they also share characteristics with the olfactory system of mammals. Teleost fishes lack the distinctive vomeronasal organ of mammals; rather all odours are processed initially by olfactory sensory neurons (OSNs) of three morphotypes within the olfactory epithelium. We sought to identify olfactory sensory neuron polymorphisms in the sea lamprey. Using retrograde tracing with dyes injected into the olfactory bulb, we identified three morphotypes which are highly similar to those found in teleosts. This study provides the first evidence of morphotypes in the sea lamprey peripheral olfactory organ, and indicates that olfactory sensory neuron polymorphism may be a trait highly conserved throughout vertebrate evolution.

2-Chloroacetaldehyde induces epsilondA DNA adducts in DNA of Raji cells as demonstrated by an improved HPLC-fluorimetry method.

Etheno adducts in DNA are promutagenic lesions and are formed from vinyl chloride, urethane, and lipid peroxidation-derived products such as 4-hydroxynonenal. Such adducts were induced in a B-lymphoid cell line (Raji) by a metabolite of vinyl chloride, 2-chloroacetaldehyde. By modification of a method of Bedell et al., etheno dA was determined in 20 microg DNA by HPLC-fluorimetry. Our method has a detection limit of 5 fmol which is one two-hundredth that of the original method. By use of this method initial evidence was found that cigarette smoke can also induce etheno dA adducts in Raji cell DNA.

Effect of angiotensin II on protein phosphorylation in PC12 cell line.

Two subtypes of angiotensin II receptors have been characterised so far: AT1 and AT2. In PC12W pheochromocytoma cells, only AT2 receptors have been found (acting probably through G1 proteins or via G protein-independent mechanism). Here, dynamic changes in phosphorylation pattern in PC12W cells upon induction of angiotensin II and under influence of redox agents were investigated. PC12W pheochromocytoma cell line was preincubated with angiotensin II, then incubated with redox agents. After lysis the cells were subjected to Western-Blotting technique with antiphosphotyrosine and anti-ERK2 antibodies, as well as phosphotyrosine phosphatases and kinases activity was measured. Angiotensin II through its AT2 receptor induced dephosphorylation of tyrosines of the proteins in the range of 60 to 150 kD in PC12W cells. The obtained phosphorylation pattern suggests that AT2 receptors may act comparably to leukocyte CD45 receptor pathway. Treatment of PC12W cells with H2O2 resulted in significant decrease in phosphotyrosine phosphatases activity. It could be assumed that signal transduction based on protein phosphorylation might be controlled by cellular redox mechanisms.

Fluorescence studies on glyceraldehyde-3-phosphate dehydrogenase from bovine heart muscle.

Glyceraldehyde-3-phosphate dehydrogenase is a glycolytic enzyme that catalyses conversion of glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate. ATP has been found to have an inhibitory effect on this enzyme. To establish the interaction between the enzyme and ATP, a fluorescence technique was used. Fluorescence quenching in the presence of ATP suggests cooperative binding of ATP to the enzyme (the Hill obtained coefficient equals 2.78). The interaction between glyceraldehyde-3-phosphate dehydrogenase and ATP may control not only glycolysis but other activities of this enzyme, such as binding to the cytoskeleton.

Mechanism of antinephritic effect of proteinase inhibitors in experimental anti-GBM glomerulopathy.

We have previously documented amelioration of rat autologous anti-GBM nephritis with the antiproteolytic drugs epsilon-aminocaproic acid (EACA) and aprotinin, given from the day of induction or later in the course of disease. In the present study we investigated potential mechanisms of this effect by assessing interactions of the drugs with proteinase-dependent generation of superoxide anion in glomeruli, and their influence on both GBM degradation in vitro and activity of glomerular proteolytic enzymes. Release of O2- by enzymatically disrupted glomeruli, isolated from nephritic control or EACA/aprotinin-treated rats, was measured with the ferricytochrome reduction method and its activity was correlated with proteinuria and glomerular cellularity at the early phase of the disease. The hydroxyproline release assay was used to quantitate degradation of rat GBM in vitro by leukocyte proteinases stimulated by phorbol myristate acetate (PMA), in the presence or absence of EACA and aprotinin. Finally, the activities of elastase, cathepsins B and L, and plasmin, together with collagenase-like activity, were assessed fluorimetrically in homogenates of glomeruli isolated from control and antiproteolytic-drug-treated nephritic rats. EACA and aprotinin notably inhibited production of superoxide by nephritic glomeruli (by 47% and 66%, respectively), and this effect was not significantly correlated with proteinuria or glomerular hypercellularity at the early stage of disease. On the other hand, generation of O2- by glomeruli of untreated nephritic rats was notably correlated with total glomerular cell counts and numbers of macrophages infiltrating glomeruli. PMA-stimulated neutrophils and macrophages caused degradation of isolated rat GBM in vitro, markedly attenuated in the presence of EACA (P<0.0005) and, to a lesser extent, by addition of aprotinin (P<0.01). The activity of elastase was significantly reduced in glomeruli of nephritic rats treated with EACA or aprotinin (both P<0.001), while activities of remaining proteinases were not appreciably affected. The beneficial influence of proteinase inhibitors on rat anti-GBM disease may be due, at least in part, to abrogation of superoxide generation in nephritic glomeruli. EACA and aprotinin also have potential to interfere with digestion of GBM, and both these effects may be related to suppression of glomerular elastase.

Serotonergic nerve fibers in the primary olfactory pathway of the larval sea lamprey, Petromyzon marinus.

In this study, serotonin (5-hydroxytryptamine; 5HT)-immunoreactive (5HT-IR) neuronal fibers were identified in the primary olfactory pathway of the sea lamprey. These neurons are likely part of a nonolfactory neural system that innervates the olfactory sac. Cell bodies with 5HT immunoreactivity predominated in the lamina propria of the rostral portion of the nasal cavity and were less prevalent adjacent to the olfactory epithelium. The 5HT-IR fibers were parallel to axons of the olfactory receptor neurons in the lamina propria of the olfactory mucosa and in the olfactory nerve. Serotonergic fibers crossed from the olfactory nerve into the olfactory bulb or branched in the caudal portion of the olfactory nerve and terminated at the junction of the olfactory nerve with the olfactory bulb. In the dorsal olfactory bulb, 5HT-IR fibers coursed along the layer of olfactory fibers. Throughout the layer with glomeruli and mitral cells, 5HT-IR fibers were seen along the border of glomerular units. Experimental lesion of the olfactory nerve was used to determine the origin of 5HT-IR fibers rostral to the olfactory bulb. The loss of these fibers and their reappearance during outgrowth of olfactory receptor neurons inferred that they emanate from the cell bodies in the olfactory sac. The results from this study suggest that axons of olfactory receptor neurons in larval lampreys receive modulation by 5HT from these neuronal fibers.

Evidence for iNOS-dependent peroxynitrite production in diabetic platelets.

AIMS/HYPOTHESIS: The aim of the present study was twofold. Firstly, to determine whether diabetic platelets produce more peroxynitrite than normal platelets and secondly to correlate the peroxynitrite production with the intraplatelet induction of the inducible isoform of nitric oxide-synthase. METHODS: Intraplatelet peroxynitrite production was monitored with dichlorofluorescin acetate with a combination of confocal microscopy and steady-state fluorescence. The platelets were probed for the induction of the inducible-nitric oxide-synthase by western immunoblotting. RESULTS: In the presence of extracellular L-arginine (100 micromol/l), platelets from subjects with Type I (insulin-dependent) diabetes displayed about 5 times higher fluorescence than those from control subjects. To determine whether inducible-nitric oxide-synthase was the source of peroxynitrite, dichlorofluorescein production was quantified as a function of L-arginine as well as nitric oxide-synthase inhibitors, in platelets from control subjects, subjects with Type I diabetes and subjects with Type II (non-insulin-dependent) diabetes mellitus. Platelets from subjects with Type I yielded about sevenfold and those from Type II about threefold larger amounts of L-arginine/nitric oxide-synthase-dependent dichlorofluorescein fluorescence than those from control subjects. The platelets were then immunologically probed for inducible-nitric oxide-synthase, which has previously been implicated in peroxynitrite production and detected in megakaryocytes of subjects with coronary heart disease. Western immunoblots of intraplatelet proteins indicated that the inducible-nitric oxide-synthase was absent in control subjects. Platelets from both Type I and Type II diabetic subjects, however, contained inducible-nitric oxide-synthase. CONCLUSION/INTERPRETATION: Inducible-nitric oxide-synthase-derived peroxynitrite is a source of platelet damage in diabetes.

Tissue-engineered human bioartificial muscles expressing a foreign recombinant protein for gene therapy.

Murine skeletal muscle cells transduced with foreign genes and tissue engineered in vitro into bioartificial muscles (BAMs) are capable of long-term delivery of soluble growth factors when implanted into syngeneic mice (Vandenburgh et al., 1996b). With the goal of developing a therapeutic cell-based protein delivery system for humans, similar genetic tissue-engineering techniques were designed for human skeletal muscle stem cells. Stem cell myoblasts were isolated, cloned, and expanded in vitro from biopsied healthy adult (mean age, 42 +/- 2 years), and elderly congestive heart failure patient (mean age, 76 +/- 1 years) skeletal muscle. Total cell yield varied widely between biopsies (50 to 672 per 100 mg of tissue, N = 10), but was not significantly different between the two patient groups. Percent myoblasts per biopsy (73 +/- 6%), number of myoblast doublings prior to senescence in vitro (37 +/- 2), and myoblast doubling time (27 +/- 1 hr) were also not significantly different between the two patient groups. Fusion kinetics of the myoblasts were similar for the two groups after 20-22 doublings (74 +/- 2% myoblast fusion) when the biopsy samples had been expanded to 1 to 2 billion muscle cells, a number acceptable for human gene therapy use. The myoblasts from the two groups could be equally transduced ex vivo with replication-deficient retroviral expression vectors to secrete 0.5 to 2 microg of a foreign protein (recombinant human growth hormone, rhGH)/10(6) cells/day, and tissue engineered into human BAMs containing parallel arrays of differentiated, postmitotic myofibers. This work suggests that autologous human skeletal myoblasts from a potential patient population can be isolated, genetically modified to secrete foreign proteins, and tissue engineered into implantable living protein secretory devices for therapeutic use.

N-dansyl-S-nitrosohomocysteine a fluorescent probe for intracellular thiols and S-nitrosothiols.

The fluorescence emission spectrum of N-dansyl-S-nitrosohomocysteine was enhanced approximately 8-fold upon removal of the NO group either by photolysis or by transnitrosation with free thiols like glutathione. The fluorescence enhancement was reversible in that it could be quenched in the presence of excess S-nitrosoglutathione. Attempts were then made to utilize N-dansyl-S-nitrosohomocysteine as an intracellular probe of thiols/S-nitrosothiols. Fluorescence microscopy of fibroblasts in culture indicated that intracellular N-dansyl-S-nitrosohomocysteine levels reached a maximum within 5 min. N-Dansyl-S-nitrosohomocysteine fluorescence was directly proportional to intracellular GSH levels, directly determined with HPLC. N-Dansyl-S-nitrosohomocysteine preloaded cells were also sensitive to S-nitrosoglutathione uptake as the intracellular fluorescence decreased as a function of time upon exposure to extracellular S-nitrosoglutathione.

The expression of tenascin-C along the lamprey olfactory pathway during embryonic development and following axotomy-induced replacement of the olfactory receptor neurons.

Extracellular guidance molecules affect the pathway of growing axons by both attractive and repulsive interactions. Tenascin-C, a glycoprotein of the extracellular matrix, is localized along developing axonal pathways where it may function by repulsion, restricting axons within specific boundaries. The lamprey olfactory pathway offers an advantageous model for studying the role of extracellular matrix proteins in axon guidance because the entire pathway is readily seen in horizontal sections and because lesioning the olfactory nerve will induce the system into a new phase of coordinated neurogenesis and axon outgrowth. Although tenascin-C expression was absent during embryonic development, olfactory nerve fascicles contained tenascin-C-immunoreactivity (IR) during the larval stage. During retrograde degeneration, the fascicles lost tenascin-C-IR. Diffuse unfasciculated axonal processes extending from the olfactory epithelium did not express tenascin-C-IR; however, acetylated tubulin and GAP-43-IR was present, indicating axonal outgrowth. When the newly extended axons of olfactory receptor neurons converged to form fascicles, tenascin-C-IR was evident within the fascicular boundaries. The absence of tenascin-C expression when axonal process were short and diffuse, and its return when axons coalesced within fascicles, supports the view that tenascin-C functions as a boundary molecule in the olfactory pathway.

Glutathione and glutathione S-transferase in the rainbow trout olfactory mucosa during retrograde degeneration and regeneration of the olfactory nerve.

In the peripheral olfactory organ, continual olfactory receptor neuron (ORN) turnover exposes neighboring cells to potentially damaging cellular debris such as free radicals. These, in turn, may be inactivated by binding directly onto glutathione (GSH) or by enzymatic conjugation with glutathione S-transferase (GST). In this study, we have investigated GSH and GST during retrograde degeneration and regeneration of the olfactory nerve in rainbow trout. In these fish, prolonged ORN physiological activity and structural integrity following transection of the olfactory nerve may be mediated by GSH and GST. In the olfactory mucosa, early changes following nerve lesion and prior to ORN degeneration included a shift of intense GSH labeling from the dendrites and perikarya of a subpopulation of ORN, and from melanophores, to olfactory nerve fascicles. GSH levels were unchanged, but GST activity decreased by 33% and GST-immunoreactivity (GST-IR) in nerve fascicles diminished slightly. When the process of massive degeneration terminated and ORN were largely absent, GSH levels and GST activity decreased further, GSH labeling was confined to melanophores, and GST-IR was absent. As ORN repopulated the olfactory mucosa, GST-IR was widespread. The combination of increased GST activity (92% of preoperative values) and low GSH levels suggests GSH utilization for GST conjugation reactions. These changes imply that GSH provides protection from cellular debris associated with ORN degeneration. Recovery of GST activity and widespread GST-IR during regeneration indicates modulation of neuroprotective, developmental, and/or physiological processes by GST.

Nitric oxide synthase in the olfactory mucosa of the larval sea lamprey (Petromyzon marinus).

The use of nitric oxide, a product of enzymatic reduction of L-arginine by nitric oxide synthase, as a modulator of processes within the olfactory mucosa was investigated in larval sea lampreys, extant fish of ancient vertebrate origin. In the present study, we demonstrated that the sea lamprey olfactory mucosa is specifically sensitive to L-arginine, that the L-arginine responses are inhibited by an inhibitor of nitric oxide synthase, N omega-nitro-L-arginine, and that nitric oxide synthase is present in olfactory receptor cells, sustentacular cells, and basal cells. Electron microscopic examination using NADPH-diaphorase histochemistry revealed intense labeling within secretory vesicles of sustentacular cells and in proximity to mitochondria within olfactory receptor cell dendrites and sustentacular cells. At the base of the olfactory epithelium, NADPH-diaphorase staining was intense in the perinuclear cytoplasm of a subpopulation of basal cells, moderate in sustentacular cell foot processes, and scattered in olfactory receptor cell axons. Throughout axons in the olfactory epithelium and the lamina propria, labeling predominated in axonal profiles with mitochondria. These physiological and ultrastructural studies imply that in sea lamprey larvae, nitric oxide modulates peri-receptor events of L-arginine chemostimulation, olfactory receptor cell axonal activity, and developmental processes.

Potential role in development of the major cysteine protease in larvae of the brine shrimp Artemia franciscana.

Encysted embryos and larvae of the brine shrimp Artemia franciscana contain a cysteine protease which represents over 90% of the protease activity in these organisms. We have used immunocytochemical methods to determine the localization and potential role of the cysteine protease in development of young larvae. In prenauplius larvae, there is intense staining for the protease on the basal side of the epidermal layer in the posterior region and diffuse staining for the protease throughout the embryo. In first instar larvae, cysteine-protease staining becomes intense in the midgut-forming area where a reticulum-like pattern emerges in cells with an abundance of yolk platelets. Cysteine-protease staining in second instar larvae becomes intense in the apical side of epidermal cells and in the basal and apical zones of midgut cells. Subcellular localization of the protease in the epidermis and midgut of young larvae using immunogold electron microscopy suggests that most is located in the cytosol and extracellular matrix adjacent to these cells. Addition of cysteine-protease inhibitors to the growth medium, especially the fluoromethyl ketone Z-Phe-Ala-CH2F, inhibits growth and segmentation of the thorax. Collectively, these observations suggest that the major cysteine protease in embryos and larvae functions in yolk utilization, as a hatching enzyme, in apolysis during the molt cycle, and as a digestive enzyme when the swimming larvae begin to feed.

The morphology of the olfactory epithelium in larval, juvenile and upstream migrant stages of the sea lamprey, Petromyzon marinus.

The structure of the olfactory epithelium in the larval, juvenile and upstream migrant stages of the sea lamprey, Petromyzon marinus, was investigated by light microscopy and by scanning and transmission electron microscopy. Ciliated olfactory receptor cells (ORC) were present in all stages. In larval specimens, the number of ORC was 20 +/- 8 ORC per 100 microns length of olfactory epithelial surface. In juveniles and in upstream migrants the ORC density dropped to 9 +/- 2 and 6 +/- 2 ORC/100 microns, respectively. Sustentacular cells were microvillar in the smallest larval stage (with a body length of 15 mm) and ciliated in larger larvae and later life stages. The morphological characteristics of the olfactory mucosa suggest that the sea lamprey's capacity for use of the olfactory system extends into the larval stage, and that there are specific changes associated with metamorphosis.

Immunohistochemical localization of glutathione S-transferase pi in rainbow trout olfactory receptor neurons.

In the fish olfactory system, glutathione S-transferases (GST) which detoxify electrophilic substances and participate in reactions of lipophilic compounds, may be active in the biotransformation of odorants and xenobiotics. In this study GST activity in the rainbow trout olfactory mucosa was high (477.6 +/- 218 nmol/min per mg protein). The GST pi class was demonstrated by Western immunoblot analysis and localized by immunofluorescence to the dendritic and perinuclear regions of olfactory receptor neurons; areas previously shown to contain elevated glutathione. The presence of GST and glutathione in fish olfactory receptor neurons suggests that these cells utilize the glutathione pathway.