Genome-wide association and functional follow-up reveals new loci for kidney function

Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.     

Interactions among invaders: community and ecosystem effects of multiple invasive species in an experimental aquatic system

With ecosystems increasingly supporting multiple invasive species, interactions among invaders could magnify or ameliorate the undesired consequences for native communities and ecosystems. We evaluated the individual and combined effects of rusty crayfish (Orconectes rusticus) and Chinese mystery snails [Bellamya (=Cipangopaludina) chinensis] on native snail communities (Physa, Helisoma and Lymnaea sp.) and ecosystem attributes (algal chlorophyll a and nutrient concentrations). Both invaders are widespread in the USA and commonly co-occur within northern temperate lakes, underscoring the importance of understanding their singular and joint effects. An outdoor mesocosm experiment revealed that while the two invaders had only weakly negative effects upon one another, both negatively affected the abundance and biomass of native snails, and their combined presence drove one native species to extinction and reduced a second by >95%. Owing to its larger size and thicker shell, adult Bellamya were protected from crayfish attack relative to native species (especially Physa and Lymnaea), suggesting the co-occurrence of these invaders in nature could have elevated consequences for native communities. The per capita impacts of Orconectes (a snail predator) on native snails were substantially greater than those of Bellamya (a snail competitor). Crayfish predation also had a cascading effect by reducing native snail biomass, leading to increased periphyton growth. Bellamya, in contrast, reduced periphyton biomass, likely causing a reduction in growth by native lymnaeid snails. Bellamya also increased water column N:P ratio, possibly because of a low P excretion rate relative to native snail species. Together, these findings highlight the importance of understanding interactions among invasive species, which can have significant community- and ecosystem-level effects.     

Freshwater fish introductions in mediterranean‐climate regions: are there commonalities in the conservation problem?

Aim To compare patterns and drivers of freshwater fish introductions across five climatically similar regions and evaluate similarities and differences in the non‐native species introduced. Location Five mediterranean‐climate regions: California (USA), central Chile, south‐western Australia, the Iberian peninsula (Spain and Portugal) and the south‐western Cape (South Africa). Methods Species presence–absence for native and non‐native fishes were collated across the regions, and patterns of faunal change were examined using univariate and multivariate statistical approaches. Taxonomic patterns in freshwater fish introductions were evaluated by comparing the number of species introduced by order to the numbers expected from binomial probabilities. Factors influencing multiple introductions of freshwater fish species in mediterranean regions were determined using generalized linear modelling. Results High levels of endemism (70–90%) were revealed for south‐western Cape, south‐western Australia and Chile. Despite their high rates of endemism, all regions currently have more non‐native species than endemic species. Taxonomic selection was found for five orders, although this was only significant for Salmoniformes across regions. The average increase in regional compositional similarity of fish faunas resulting from non‐native fish introductions was 8.0%. Important factors predicting multiple introductions of a species include previous introduction success and mean latitude of its distribution Main conclusions The mediterranean‐climate regions of the world, separated by vast distances, originally had a few fish species in common but are now more similar, owing to species introductions, illustrating the extent and importance of taxonomic homogenization. Introductions are largely driven by taxonomically biased human interests in recreational fisheries, aquaculture and ornamental pet species.     

Distribution of acid hydrolases in subcellular fractions of proliferating vs non-proliferating fibroblasts

We have employed colloidal silica (Percoll) density-gradient subcellular fractionation technique to examine the distribution of lysosomal hydrolases between intermediate vesicles (primary lysosomes) and secondary lysosomes in contact-inhibited non-proliferating vs proliferating chicken embryo fibroblasts. We find that the activities of lysosomal specific enzymes from both phases of growth are distributed within two peaks; however, the relative amounts differ markedly. In normal, non-proliferating cells approx. 60% of the total activities of cathepsin B, beta-mannosidase, alpha-fucosidase, beta-galactosidase and hexosaminidase is recovered in the heavier density fraction corresponding to secondary lysosomes, while less than 9% of the enzyme activities are recovered in the light-density peak. With transformed cells, between 16 and 22% of activity for these enzymes are recovered in the lighter density intermediate vesicle fraction, when less than 40% of the enzyme activities recovered in the heavy density fraction. beta-Glucuronidase distribution was different from that of the above enzymes. First, a more even distribution between the two lysosomal fractions was found with non-proliferating normal cells (33% in heavy-density fraction and 21% in light-density fraction), whereas more than 40% of the total enzyme activity was recovered in the lighter density fraction from transformed cells. Also, the amount of cathepsin B contained in the vesicle fractions is increased severalfold relative to that of contact-inhibited normal cells. However, the apparent differences in enzyme distribution between confluent normal and transformed cells are not found when vesicles are prepared from subconfluent, actively proliferating cultures. We have also compared the Percoll density gradient patterns of membrane vesicles from proliferating and non-proliferating human fibroblasts, since most earlier studies utilized this system. Again, we find that the majority of beta-hexosaminidase activity (41%) of contact-inhibited, confluent cells is recovered in the heavier density fraction with less than 15% in the lighter density fraction. Also, the distribution of beta-hexosaminidase between the heavy density and light density vesicle fractions is altered in homogenates from exponentially growing cells, being 22% and 26% respectively. We conclude that the distribution of lysosomal hydrolases between the two vesicle populations is growth-phase dependent and is markedly heterogeneous in proliferating cells.     

Role of carbohydrate in glycoprotein secretion by human hepatoma cells

We have previously shown that export of nine proteins by human hepatoma cells falls into three discrete kinetic classes with intracellular retention half-times of approximately 35 min, 77 min and 115 min. To determine if carbohydrate on secretory glycoproteins determines the secretory class we have measured the kinetics of export of the nine proteins after tunicamycin-treatment of cultures. We found no apparent correlation between the kinetic class of a secretory protein and sensitivity of secretion to tunicamycin-treatment. For example, three glycoproteins are exported with rapid kinetics and secretion of only one, alpha 1-protease inhibitor, is inhibited by tunicamycin treatment. In addition, three glycoproteins are secreted with intermediate kinetics and tunicamycin-treatment inhibits the secretion of two of these proteins, alpha 2-macroglobulin and ceruloplasmin but not the third, plasminogen.     

Variability in transport rates of secretory glycoproteins through the endoplasmic reticulum and Golgi in human hepatoma cells

We have previously shown that newly synthesized liver secretory proteins are exported at three distinct characteristic rates, with intracellular retention half-times of 110-120 min (e.g. transferrin), 75-80 min (e.g. ceruloplasmin), and 30-40 min (e.g. alpha 1-protease inhibitor) (J. B. Parent, H. Bauer, and K. Olden (1985) Biochim. Biophys. Acta, in press). In the present study we have determined the average time required for specific glycoproteins to move through the various compartments of the intracellular transport pathway, consisting of endoplasmic reticulum and Golgi complex. Localization in particular compartments was monitored by the use of the following complementary approaches: (i) Percoll density gradient fractionation of the subcellular organelles, (ii) sensitivity of the glycan moiety of N-linked glycosylation to endo-beta-N-acetylglucosaminidase H, and (iii) by the lectin-binding characteristics. The cell fractionation studies revealed that alpha 1-protease inhibitor, ceruloplasmin, and transferrin were transported from the rough endoplasmic reticulum with a retention half-time of 10, 30, or 45 min, respectively. Measurements of the rate at which newly synthesized glycoprotein became endo H-resistant (an event localized near the medial region of Golgi) demonstrated that it took 60-70, 30, and 18 min for 50% of transferrin, ceruloplasmin, and alpha 1-protease inhibitor, respectively, to reach the medial Golgi. Consistent with this finding, maximal binding of transferrin to wheat germ agglutinin (also a medial Golgi event) and Ricinus communis agglutinin I (a trans Golgi event) required 75 and 90 min, respectively, and maximal binding of ceruloplasmin to both lectins occurred in approximately 30 min. Maximal binding of alpha 1-protease inhibitor to wheat germ agglutinin and Ricinus communis agglutinin I required 15 and 30 min, respectively. The results presented here clearly indicate that (i) the time required for protein secretion cannot be entirely accounted for by lag in transport from the rough endoplasmic reticulum to the Golgi since the glycoproteins examined are retained in the former organelle for no more than two-fifths of the total intracellular retention half-time, and (ii) the variability in rates of protein secretion is not due solely to differences in rates of transport from the rough endoplasmic reticulum to the Golgi as variability in retention within the Golgi is also demonstrated. The results are discussed in terms of their compatibility with receptor-mediated transport of glycoproteins in both the endoplasmic reticulum and Golgi.     

Estimates of niche position and breadth vary across spatial scales for native and alien inland fishes

Aim

We estimate and compare niche position, marginality and breadth of Iberian inland fishes at three geographical extents (regional, restricted to the species’ range and global) to understand the effect of spatial scale on niche metrics. Furthermore, we investigate differences in niche metrics between native and alien fish, and test for associations with introduction date of alien species and niche characterization to better understand their invasion process.

Location

Iberian Peninsula and global.

Time period

2000–2020.

Major taxa studied

Fifty-one native and 17 alien inland fish species from the Iberian Peninsula.

Methods

Outlying mean index (OMI) analyses were used to estimate the niche position, marginality and breadth of Iberian inland fishes. Climatic OMI analyses were computed at three different scales (regional, restricted to the species’ range and global). Permutational analyses of variance (PERMANOVAs) were used to test for differences in niche position, marginality and breath among native and alien species.

Results

Niche metrics differed depending on the geographical extent of the investigation, as well as with respect to species origin (native versus alien). Differences in climatic niche position between native and alien species observed at the global scale were non-existent at the regional scale. The niche breadth of widely distributed alien species was highly underestimated when only considering the invaded region, and further influenced by the first date of of species introduction.

Main conclusions

Estimating niches of freshwater species, especially of alien invaders, should carefully consider the geographical extent of the investigation. We suggest that analyses that jointly consider regional and global scales will improve the estimation of niche metrics of widely distributed organisms, particularly regarding species climatic niche, and the assessment of the invasive potential of species.     

Phosphorylation of filamin and other proteins in cultured fibroblasts.

Incubation of subcellular fractions of fibroblasts with [³²P]ATP demonstrated 10 phosphoproteins whose phosphorylation can be increased by cyclic AMP or cyclic AMP-dependent protein kinase. One of these phosphoproteins, MW 240,000, resembles the actin binding protein, filamin, and can be selectively precipitated by antibodies to chicken gizzard filamin. Furthermore chicken gizzard filamin can be phosphorylated by skeletal muscle protein kinase and cyclic AMP stimulates this reaction.     

Toxicogenomic approach for assessing toxicant-related disease

The problems of identifying environmental factors involved in the etiology of human disease and performing safety and risk assessments of drugs and chemicals have long been formidable issues. Three principal components for predicting potential human health risks are: (1) the diverse structure and properties of thousands of chemicals and other stressors in the environment; (2) the time and dose parameters that define the relationship between exposure and disease; and (3) the genetic diversity of organisms used as surrogates to determine adverse chemical effects. The global techniques evolving from successful genomics efforts are providing new exciting tools with which to address these intractable problems of environmental health and toxicology. In order to exploit the scientific opportunities, the National Institute of Environmental Health Sciences has created the National Center for Toxicogenomics (NCT). The primary mission of the NCT is to use gene expression technology, proteomics and metabolite profiling to create a reference knowledge base that will allow scientists to understand mechanisms of toxicity and to be able to predict the potential toxicity of new chemical entities and drugs. A principal scientific objective underpinning the use of microarray analysis of chemical exposures is to demonstrate the utility of signature profiling of the action of drugs or chemicals and to utilize microarray methodologies to determine biomarkers of exposure and potential adverse effects. The initial approach of the NCT is to utilize proof-of-principle experiments in an effort to "phenotypically anchor" the altered patterns of gene expression to conventional parameters of toxicity and to define dose and time relationships in which the expression of such signature genes may precede the development of overt toxicity. The microarray approach is used in conjunction with proteomic techniques to identify specific proteins that may serve as signature biomarkers. The longer-range goal of these efforts is to develop a reference relational database of chemical effects in biological systems (CEBS) that can be used to define common mechanisms of toxicity, chemical and drug actions, to define cellular pathways of response, injury and, ultimately, disease. In order to implement this strategy, the NCT has created a consortium of research organizations and private sector companies to actively collaborative in populating the database with high quality primary data. The evolution of discrete databases to a knowledge base of toxicogenomics will be accomplished through establishing relational interfaces with other sources of information on the structure and activity of chemicals such as that of the National Toxicology Program (NTP) and with databases annotating gene identity, sequence, and function.