Lignite mining and stream channelization influences on aquatic macroinvertebrate assemblages along the Natchez Trace Parkway,Mississippi, USA

The article describes the effects of channelization on selected water quality parameters and benthic macroinvertebrate assemblages in four Big Black River (Mississippi, USA) tributaries crossing the Natchez Trace Parkway [U.S. National Park Service (NPS)]. Two of the streams were unchannelized (Little Bywy Creek and McCurtain Creek), and two were channelized (Big Bywy Creek and Middle Bywy Creek). Lignite mining occurs in the headwaters of Little Bywy Creek and Middle Bywy Creek. During this 3-year study, benthic macroinvertebrates were collected monthly from all four streams using Hester-Dendy Multiple plate samplers, and enumerated taxonomically and functionally. Hypotheses were tested using analyses of variance. Relationships were determined using multivariate analyses. Relative abundances of mayflies (Ephemeroptera), stoneflies (Plecoptera), caddisflies (Trichoptera) and aquatic beetles (Coleoptera) were associated with moderate to high conductivity, alkalinity, pH, and dissolved oxygen. Hellgrammites (Megaloptera), midges, blackflies, and mosquitoes (Diptera), crayfish (Crustacea: Decapoda) and leeches (Annelida: Hirudinea) were associated with lower values for these parameters. These patterns reflected seasonal rather than spatial variation (i.e., among the streams). Invertebrate assemblage composition was similar among the four streams with respect to functional groups. Invertebrate relative abundances in the two channelized streams were approximately half those of the unchannelized streams. Macroinvertebrate species richness was greater in unchannelized streams. Environmental indices categorized all four streams as having fair to good condition. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

2D gene expression parameters of wing imaginal disc of Drosophila for developmental analysis

 By using high resolution two-dimensional (2D) gel electrophoresis coupled with computer-analysis we have established a quantitative Drosophila wing imaginal disc protein database of third instar larvae as a reference to be used for comparative purposes in genetic studies. A general catalogue integrated by 1,184 ³⁵S-methionine-labelled polypeptides from wing imaginal disc has been obtained. The level of expression for all the proteins has been quantitatively determined. The quantitative reproducibility of the analysis system has been estimated and all the controls studied as database reference to interpret the results of experiments with mutant discs. One example, corresponding to iro ¹ mutation, has been used to show how some of the changes observed with mutant discs clearly extend out of the limits defined by the controls. This enables us to generate comparative parameters for the study of proliferation, morphogenesis and differentiation of Drosophila and opens the possibility of rapidly defining the nature and quantity of changes in patterns of gene expression in developmental genetic studies. Received: 21 June 1996 / Accepted: 27 September 1996     

Diversity of endemic rhizobia on Christmas Island: Implications for agriculture following phosphate mining

Given that phosphate supplies may diminish and become uneconomic to mine after 2020, there is a compelling need to develop alternative industries to support the population on Christmas Island. Former mine sites could be turned into productive agricultural land, however, large-scale commercial agriculture has never been attempted, and, given the uniqueness of the island, the diversity of rhizobia prior to introducing legumes needed evaluation. Therefore, 84 rhizobia isolates were obtained from nine different hosts, both crop and introduced legumes, located at seven sites across the island. Based on 16S rRNA and recA gene sequence analysis, the isolates grouped into 13 clades clustering within the genus Bradyrhizobium, Ensifer, Cupriavidus and Rhizobium. According to the sequences of their symbiosis genes nodC and nifH, the isolates were classified into 12 and 11 clades, respectively, and clustered closest to tropical or crop legume isolates. Moreover, the symbiosis gene phylogeny and Multi Locus Sequence Analysis gene phylogeny suggested vertical transmission in the Alpha-rhizobia but horizontal transmission within the Beta-rhizobia. Furthermore, this study provides evidence of a large diversity of endemic rhizobia associated with both crop and introduced legumes, and highlights the necessity of inoculation for common bean, chickpea and soybean on the Island.     

THERPA: A small molecule database related to prion protein regulation and prion diseases progression

Prion diseases are fatal neurodegenerative disorders that affect humans and animals. Although various small molecules have been evaluated for application in the treatment of prion diseases, none have been shown to be efficacious. Expanding our knowledge of these molecules is important for understanding of the complex mechanisms of prion diseases. To improve access to the scattered information on small molecules related to prion diseases, we built a database of therapeutic molecules associated with prion diseases (THERPA, therpa.pythonanywhere.com). THERPA includes 119 small molecules and their 283 relationships with prion diseases. THERPA is an interactive visual database and useful for improving search efficiency which can help researchers identify intrinsic small molecules that can be used for developing therapeutics for prion diseases.     

Complete genome sequencing of sixteen Francisella noatunensis subsp. orientalis isolates: A genomic approach for molecular characterization and spread dynamics of this clonal population

Francisella noatunensis subsp. orientalis (FNO) is an important emerging pathogen associated with disease outbreaks in farm-raised Nile tilapia. FNO genetic diversity using PCR-based typing, no intra-species discrimination was achieved among isolates/strains from different countries, thus demonstrating a clonal behaviour pattern. In this study, we aimed to evaluate the population structure of FNO isolates by comparing whole-genome sequencing data. The analysis of recombination showed that Brazilian isolates group formed a clonal population; whereas other lineages are also supported by this analysis for isolates from foreign countries. The whole-genome multilocus sequence typing (wgMLST) analysis showed varying numbers of dissimilar alleles, suggesting that the Brazilian clonal population are in expansion. Each Brazilian isolate could be identified as a single node by high-resolution gene-by-gene approach, presenting slight genetic differences associated to mutational events. The common ancestry node suggests a single entry into the country before 2012, and the rapid dissemination of this infectious agent may be linked to market sales of infected fingerlings.     

Molecular genetics of the transcription factor GLIS3 identifies its dual function in beta cells and neurons

The GLIS family zinc finger 3 isoform (GLIS3) is a risk gene for Type 1 and Type 2 diabetes, glaucoma and Alzheimer's disease endophenotype. We identified GLIS3 binding sites in insulin secreting cells (INS1) (FDR q < 0.05; enrichment range 1.40–9.11 fold) sharing the motif wrGTTCCCArTAGs, which were enriched in genes involved in neuronal function and autophagy and in risk genes for metabolic and neuro-behavioural diseases. We confirmed experimentally Glis3-mediated regulation of the expression of genes involved in autophagy and neuron function in INS1 and neuronal PC12 cells. Naturally-occurring coding polymorphisms in Glis3 in the Goto-Kakizaki rat model of type 2 diabetes were associated with increased insulin production in vitro and in vivo, suggestive alteration of autophagy in PC12 and INS1 and abnormal neurogenesis in hippocampus neurons. Our results support biological pleiotropy of GLIS3 in pathologies affecting β-cells and neurons and underline the existence of trans?nosology pathways in diabetes and its co-morbidities.     

Public informatics resources for rice and other grasses

As an emerging model system, rice will benefit from an informatics infrastructure which organizes genome data and makes it available worldwide. RiceGenes and other Internet-accessible resources are evolving to meet these goals. Grass crops such as rice, maize, millet, sorghum and wheat are closely related but are represented by independent database projects; interlinking these resources would create a broad view of grass genetics and make it easier to compare data across genomes. The future success of grass informatics depends on the development of new comparative mapping displays as well as the participation of the research community in assembling and curating comparative map data.     

Pattern of tree species diversity in riparian forest fragments of different widths (SE Brazil)

Width is an essential element of the spatial configuration of riparian forests and may be fundamental in determining their corridor function. In the present study we tested the effect of forest width on floristic structure (tree species composition and diversity) in 15 fragments of riparian forest in an agricultural fragmented landscape of SE Brazil. All these fragments were chosen in a geomorphological homogeneous river reach under similar soil, topographic and human disturbance conditions in order to minimize the influence of these factors. The forest widths considered ranged from 30 to 650 m. The results showed that total species richness and climax species richness were significantly greater when we consider larger fragments, as has been observed in other studies. Nevertheless, species diversity and evenness were not significantly correlated with forest width. The analysis of species composition showed that the narrowest fragments were characterized by species well adapted to temporary flood conditions, while medium and wide fragments showed a composition typical of drier upland areas. Therefore, the effect of forest width on floristic structure appears to be more strongly linked to the effect of river floods in the case of the fragments studied. The existence in riparian corridors of a drier forest, in general richer and more diversified than the annually flooded forest, seems to favor the maintenance of regional species diversity in fragmented landscapes.     

Stimulation of fibrinogen synthesis in cultured rat hepatocytes by fibrinogen fragment E

Because of the inherent difficulties of experimentation in intact animals, we used primary monolayer cultures of non-proliferating adult rat hepatocytes to study the effects of fibrinogen degradation products on fibrinogen biosynthesis. The freshly isolated hepatocytes obtained by collagenase perfusion of the liver in situ were cultured in a chemically defined serum-free medium. The rate of fibrinogen synthesis in control cultures was $\text{40–50}\text{pmol}\text{2.5·10}{}^6$ cells per 24 h. Additions of 20, 60 or 100 μg of homologous stage I fibrinogen degradation products had no effect on fibrinogen synthesis. In contrast, addition of the same amounts of homologous or heterologous (human) stage III fibrinogen degradation products resulted in a concentration-dependent increase in fibrinogen biosynthesis without affecting the rate of synthesis of albumin. When purified stage III fibrinogen degradation products D and E (human) were tested in 10, 30 or 50 μg/3 ml medium only fragment E showed a significant increase in fibrinogen biosynthesis (1.9-, 2.8- and 5.6-fold, respectively, over the control cultures). The presence of excess fibrinogen had no effect. These results suggest that fibrinogen fragment E may be a specific stimulator of fibrinogen biosynthesis which may play an important role in maintaining normal levels of plasma fibrinogen.