Using stressor gradients to determine reference expectations for great river fish assemblages

We describe a simple empirical modeling approach for determining least-disturbed conditions for the great rivers of the Upper Mississippi River basin: Missouri, Upper Mississippi, and Ohio Rivers. We used multivariate analysis to identify reference strata (reaches for which a single reference expectation was appropriate) on each river. Strata included the Upper Missouri, Lower Missouri, impounded Upper Mississippi, unimpounded Upper Mississippi, and the Ohio River. We created a multimetric stressor gradient for each stratum using a suite of site- and landscape-scale metrics. Site-scale metrics included water chemistry, aquatic and riparian habitat, and human disturbance metrics. Landscape-scale metrics included land use, land cover, and proximity to human disturbance. The gradient was scaled from 0 (least stressed) to 1 (most stressed). Multimetric indices of condition based on fish assemblages for the Lower Missouri and Upper Mississippi River were responsive to stressor gradients based on 18–24 abiotic stressor metrics. Ohio River fish assemblages were responsive to a hand-picked three-metric gradient. We used the y-intercept of quantile regression to predict the fish index value for a stressor gradient value of 0 (the fish index value at a site with the lowest mean stressor gradient score in the reference stratum) which we designated as least-disturbed condition for the fish index for that stratum. We trisected the difference between predicted least-disturbed condition (ceiling value) and a floor value set at the 5th percentile of the sample to create thresholds for three condition classes: least-disturbed, intermediate, and most-disturbed. Based on the derived condition class thresholds for the fish index, 10% (by length) of the Lower Missouri was in least-disturbed condition, compared to 14% of the Ohio River and 19% of the impounded Upper Mississippi River. The index of condition exhibited longitudinal variation that was associated with the location of major urban areas along each river. We conclude that empirical modeling based on an abiotic stressor gradient can provide an alternative approach for deriving internal reference expectations for great rivers with few, if any, minimally disturbed sites.     

Application of morphometric techniques to postnatal rat testes in organ culture: insights into testis growth

The extent of Sertoli cell proliferation during fetal and neonatal development determines the final adult testis size and potential for sperm output. To gain further knowledge of the factors that regulate Sertoli cell proliferation, the present study used a new approach to analyse changes in morphology and proliferation in the postnatal testis by combining organ culture with morphometric analysis. Fragments of rat testes from days 0 to 10 postpartum were cultured in contact with DMEM for 6 h or 72 h and fixed. The effects of ovine follicle-stimulating hormone (FSH) and activin were studied in an additional 72-h organ culture experiment using day 9 testes. Bromodeoxyuridine (BrdU) was added for the last 6 h of culture to mark proliferating cells. Two-microm sections of the fragments were analysed for morphological changes of the seminiferous cords, and the proportion of BrdU-labelled Sertoli and germ cells was determined. Assessment of 6-h samples revealed growth characteristics consistent with those observed in vivo during days 1-10 of postnatal development. From day 2 onwards, the volume fraction of seminiferous cords began to increase, while significant growth in cross-sectional area of the cords occurred only after day 6. In these culture conditions, germ cell proliferation and testicular architecture was consistent with that expected for the age of the tissue at time of explant. The proportion of dividing Sertoli cells declined from 15-20% at days 0-4 postpartum to below % at day 10 postpartum in the 6-h culture, and it was low or abolished in the 3-day culture at all time points. Activin and FSH together, but not singly, stimulated Sertoli cell proliferation in the 72-h culture. This paper presents a new approach to analysis of in vitro testis development. The combination of fragment culture and stereological analysis permits rigorous and detailed assessment of developmental changes in the postnatal testis.     

Antagonism of CD95 signaling blocks butyrate induction of apoptosis in young adult mouse colonic cells

There is greatinterest in utilizing butyrate as a chemopreventive agent for colontumorigenesis because of its ability to promote apoptosis in colontumor cell lines. Because CD95 (APO-1/Fas) transduces signals resultingin apoptosis, we tested the hypothesis that butyrate-dependentcolonocyte apoptosis is mediated by this death receptor. Butyrate (1 mM) exposure for 24 h upregulated expression of Fas andits ligand in young adult mouse colon (YAMC) cells. To delineate theproapoptotic effect of butyrate and to avoid the confounding effects ofdetachment from the extracellular matrix, adherent cell apoptosis wasmonitored as loss of plasma membrane asymmetry and dissipation ofmitochondrial membrane potential (_mt) by lasercytometry. Soluble Fas receptor protein (Fas:Fc chimera) and caspaseinhibitors (z-VAD-fmk and z-IETD-fmk) blocked butyrate induction ofapoptosis. Treatment with Fas agonistic antibody (clone Jo-2)significantly induced cell death, indicating that Fas in colonocytes isfunctional. In addition, butyrate promoted apoptosis by inducing lossof _mt and phospholipidasymmetry of the plasma membrane after 12 and 24 h of exposure,respectively, before cell detachment. Therefore, Fas receptor-dependentsignal transduction is involved in butyrate induction of apoptosis in colonocytes.

     

Neuroproteomics: Expression Profiling of the Brain's Proteomes in Health and Disease

The term "proteome" describes the protein complement of a genome. Proteomes of cells are dynamic and are directly affected by environmental factors, such as stress and/or drug treatment, or as a result of aging and disease. One of the distinct advantages of proteomic analysis, not attainable with RNA expression data, is the ability to fractionate the cell's proteins into various subpopulations. In neuroscience, "neuromics" (proteomics in the central nervous system) is in its infancy, with a paucity of studies in the context of the brain. One of the objectives of this review is to illustrate the potential of neuromics to profile differences in the distribution of thousands of proteins as a function of disease markers. We have previously used this approach to determine the effects of varied postmortem interval in examining human brain tissue and to identify biomarkers. Here we review proteomic studies of schizophrenia, Alzheimer's disease, and Parkinson's disease. Experimental results regarding Parkinson's disease are presented to illustrate the potential of neuromics to identify pathways of pathogenesis and novel therapeutic targets.     

The PRINTS database: a resource for identification of protein families

The PRINTS database houses a collection of protein fingerprints, which may be used to assign family and functional attributes to uncharacterised sequences, such as those currently emanating from the various genome-sequencing projects. The April 2002 release includes 1,700 family fingerprints, encoding approximately 10,500 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. Fingerprints are groups of conserved motifs that, taken together, provide diagnostic protein family signatures. They derive much of their potency from the biological context afforded by matching motif neighbours; this makes them at once more flexible and powerful than single-motif approaches. The technique further departs from other pattern-matching methods by readily allowing the creation of fingerprints at superfamily-, family- and subfamily-specific levels, thereby allowing more fine-grained diagnoses. Here, we provide an overview of the method of protein fingerprinting and how the results of fingerprint analyses are used to build PRINTS and its relational cousin, PRINTS-S.     

Drosophila necrotic mutations mirror disease-associated variants of human serpins

Polymerization of members of the serpin superfamily underlies diseases as diverse as cirrhosis, angioedema, thrombosis and dementia. The Drosophila serpin Necrotic controls the innate immune response and is homologous to human alpha(1)-antitrypsin. We show that necrotic mutations that are identical to the Z-deficiency variant of alpha(1)-antitrypsin form urea-stable polymers in vivo. These necrotic mutations are temperature sensitive, which is in keeping with the temperature-dependent polymerization of serpins in vitro and the role of childhood fevers in exacerbating liver disease in Z alpha-antitrypsin deficiency. In addition, we identify two nec mutations homologous to an antithrombin point mutation that is responsible for neonatal thrombosis. Transgenic flies carrying an S>F amino-acid substitution equivalent to that found in Siiyama-variant antitrypsin (nec(S>F.UAS)) fail to complement nec-null mutations and demonstrate a dominant temperature-dependent inactivation of the wild-type nec allele. Taken together, these data establish Drosophila as a powerful system to study serpin polymerization in vivo.