Multiple facets of biodiversity are threatened by mining-induced land-use change in the Brazilian Amazon

Aim

Mining is increasingly pressuring areas of critical importance for biodiversity conservation, such as the Brazilian Amazon. Biodiversity data are limited in the tropics, restricting the scope for risks to be appropriately estimated before mineral licensing decisions are made. As the distributions and range sizes of other taxa differ markedly from those of vertebrates—the common proxy for analysis of risk to biodiversity from mining—whether mining threatens lesser-studied taxonomic groups differentially at a regional scale is unclear.

Location

Brazilian Amazon.

Methods

We assess risks to several facets of biodiversity from industrial mining by comparing mining areas (within 70 km of an active mining lease) and areas unaffected by mining, employing species richness, species endemism, phylogenetic diversity and phylogenetic endemism metrics calculated for angiosperms, arthropods and vertebrates.

Results

Mining areas contained higher densities of species occurrence records than the unaffected landscape, and we accounted for this sampling bias in our analyses. None of the four biodiversity metrics differed between mining and nonmining areas for vertebrates. For arthropods, species endemism was greater in mined areas. Mined areas also had greater angiosperm species richness, phylogenetic diversity and phylogenetic endemism, although less species endemism than unmined areas.

Main Conclusions

Unlike for vertebrates, facets of angiosperm and arthropod diversity are relatively higher in areas of mining activity, underscoring the need to consider multiple taxonomic groups and biodiversity facets when assessing risk and evaluating management options for mining threats. Particularly concerning is the proximity of mining to areas supporting deep evolutionary history, which may be impossible to recover or replace. As pressures to expand mining in the Amazon grow, impact assessments with broader taxonomic reach and metric focus will be vital to conserving biodiversity in mining regions.     

Osteohistological characterization of notosuchian osteoderms: Evidence for an overlying thick leathery layer of skin

Osteoderms are mineralized structures embedded in the dermis, known for nonavian archosaurs, squamates, xenarthrans, and amphibians. Herein, we compared the osteoderm histology of Brazilian Notosuchia of Cretaceous age using three neosuchians for comparative purposes. Microanatomical analyses showed that most of them present a diploe structure similar to those of other pseudosuchians, lizards, and turtles. This structure contains two cortices (the external cortex composed of an outer and an inner layers, and the basal cortex) and a core in-between them. Notosuchian osteoderms show high bone compactness (>0.85) with varying degrees of cancellous bone in the core. The neosuchian Guarinisuchus shows the lowest bone compactness with a well-developed cancellous layer. From an ontogenetic perspective, most tissues are formed through periosteal ossification, although the mineralized tissues observed in baurusuchid LPRP/USP 0634 suggest a late metaplastic development. Histology suggests that the ossification center of notosuchian osteoderm is located at the keel. Interestingly, we identified Sharpey's fibers running perpendicularly to the outer layer of the external cortex in Armadillosuchus arrudai, Itasuchus jesuinoi, and Baurusuchidae (LPRP/USP 0642). This feature indicates a tight attachment within the dermis, and it is evidence for the presence of an overlying thick leathery layer of skin over these osteoderms. These data allow a better understanding of the osteohistological structure of crocodylomorph dermal bones, and highlight their structural diversity. We suggest that the vascular canals present in some sampled osteoderms connecting the inner layer of the external cortex and the core with the external surface may increase osteoderm surface and the capacity of heat transfer in terrestrial notosuchians.     

Oleic Acid Blocks Epidermal Growth Factor-Activated Early Intracellular Signals without Altering the Ensuing Mitogenic Response

In EGFR-T17 cells, which express high levels of the epidermal growth factor (EGF) receptor, addition of a saturating dose of EGF (10 nM) leads to an increase in Ins(1,4,5)P₃/diacylglycerol and also to cytosolic calcium [Ca²⁺]_i due to both intracellular redistribution and influx from extracellular medium. Pretreatment of cells with cis -unsaturated nonesterified fatty acids such as oleic acid (1 to 100 μM) inhibited EGF-stimulated Ins(1,4,5)P₃ generation and Ca²⁺ release from intracellular stores. Furthermore, such a treatment completely suppress Ca²⁺ influx in a dose-dependent manner. At doses capable of suppressing such early signals, oleic acid did not alter the process of EGF-mediated internalization of the EGF/EGF-receptor complex, suggesting that [Ca²⁺]_i rise did not mediate receptor internalization. EGF-induced cell proliferation assessed by either thymidine incorporation into DNA, direct cell counting, and microscopic observation was not altered by oleic acid, at doses able to block EGF-mediated early signals. In conclusion, suppression of Ins(1,4,5)P₃ generation and [Ca²⁺]_i rises by oleic acid did not alter EGF-receptor internalization nor EGF-induced cell mitosis. Such results suggest that [Ca²⁺]_i rise is not instrumental for EGF-stimulated cell proliferation.     

Identification of major histocompatibility complex genes in the guppy,Poecilia reticulata

The guppy, Poecilia reticulata, a teleostean fish of the order Cyprinodontiformes, has been used extensively in studies of host-parasite interactions, courtship behavior, and mating preference, as well as in ecological and evolutionary genetics. A related species was among the first poikilotherm vertebrates to be used in the study of histocompatibility genes. All these studies could benefit from the identification and characterization of the guppy major histocompatibility complex (Mhc) genes. Here, both class I and class II genes of the guppy are described. The number of expressed loci, as determined by representation of clones in a cDNA library, sequencing, and Southern blot analysis, may be low in both Mhc classes: combined evidence suggests that there may be one expressed class II locus only and one or two expressed class I loci. The variability of aquaristic guppy stocks is very low: only three and two genes have been detected at the class I and class II loci, respectively, in the stocks examined. This genetic paucity is most likely the consequence of breeding practices employed by aquarists and commercial establishments. Limited sampling of wild guppy populations revealed extensive Mhc polymorphism at loci of both classes in nature. Comparison of guppy Mhc sequences with those of other vertebrates has revealed the existence of a set of insertions/deletions which can be used as characters in cladistic analysis to infer phylogenetic relationships among vertebrate taxa and the Mhc genes themselves. These indels are particularly frequent in the regions coding for the loops of 1 and 2 domains of class I proteins.The nucleotide sequence data reported in this publication have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers Z54076-Z54095     

Formulation of 3D pharmacophore models for bradykinin B2-receptor antagonists

In order to make a further contribution to the elucidation of the essential structural features for bradykinin (BK) antagonism, we extracted 3D pharmacophore models from a training set consisting of nine relatively rigid, small organic, non-peptide molecules, reported to be more or less active, competitive BK B₂-receptor antagonists. This was accomplished by means of the expert system Catalyst. The information contained in one of these models was then used to identify relevant structural features and perform consensus molecular dynamics simulations including, in addition to the non-peptide antagonist set, four prototypical linear and cyclic peptide antagonists, and BK itself. This combined approach allowed us to identify regions of the conformational space shared by this series of compounds, which includes highly flexible, and, hence, otherwise almost inaccessible for conventional conformational sampling techniques, peptide molecules. As a result, we obtained a relatively small number of extended pharmacophore models, whose average, together with the original Catalyst model, could be used to search proprietary 3D databases for potential candidates. The results of such a search are also reported.     

Formulation of 3D pharmacophore models for bradykinin B2-receptor antagonists

Summary In order to make a further contribution to the elucidation of the essential structural features for bradykinin (BK) antagonism, we extracted 3D pharmacophore models from a training set consisting of nine relatively rigid, small organic, non-peptide molecules, reported to be more or less active, competitive BK B₂-receptor antagonists. This was accomplished by means of the expert system Catalyst^TM. The information contained in one of these models was then used to identify relevant structural features and perform consensus molecular dynamics simulations including, in addition to the non-peptide antagonist set, four prototypical linear and cyclic peptide antagonists, and BK itself. this combined approach allowed us to identify regions of the conformational space shared by this series of compounds, which includes highly flexible, and, hence, otherwise almost inaccessible for conventional conformational sampling techniques, peptide molecules. As a result, we obtained a relatively small number of extended pharmacophore models, whose average, together with the original Catalyst model, could be used to search proprietary 3D databases for potential candidates. The results of such a search are also reported.     

Effect of stimulating maize germination on cell cycle proteins

The germination process can be accelerated if seeds are stimulated either by adding cytokinins or by osmopriming. Under these conditions, cells in maize ( Zea mays ) embryo axes shorten the time at which the first round of DNA replication and mitosis takes place, thus advancing the cell cycle. Using heterologous antibodies against different cell cycle proteins, we have followed the behaviour of several markers for G1 phase (cyclin D, E2F and p53) and a marker of G2 phase (cyclin B) under either control or "accelerated" germination conditions. The results showed two classes of behaviour: either there was no variation in the amount of the protein present under control or accelerated germination conditions, represented by cyclin Band E2F‐type proteins, or the amount of the proteins was drastically reduced, more rapidly under accelerated germination, as was the case for cyclin D‐ and p53‐type proteins. Although the cyclin D‐type protein was synthesized de novo during germination, the balance was towards degradation so that there was no cyclin D detected 15 h after germination in benzyladenine‐treated and osmoprimed seeds. A Cdk4‐type protein seemed to be present in cyclin D immunoprecipitates and its kinase activity paralleled the fluctuations of the cyclin amount during germination. These data are discussed in the context of early seed germination.     

Preparation of Giant Myelin Vesicles and Proteoliposomes to Register Ionic Channels

Abstract: Myelin vesicles, reconstituted liposomes with proteolipid protein (PLP), the main protein component of myelin, and electrophysiological patch-clamp are potentially powerful tools to study the role of myelin in functional ionic channels. However, technical difficulties in the vesiculation of myelin and the small size of the vesicles obtained do not permit the application of micropipettes for current recordings. From a suspension of purified myelin we have prepared oligolamellar vesicles (mean diameter of 144 nm) using the so-called French pressure system. From this preparation we obtained giant myelin vesicles ∼10 µm in mean diameter, using a dehydration-rehydration procedure. Qualitative analysis of proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed no significant loss of any component in these vesicles due to pressure, in comparison with non-vesiculated myelin. A way of preparing giant liposomes of ∼80–100 µm and proteoliposomes of ∼30 µm in mean diameter, using the same dehydration-rehydration procedure, is also reported. Reconstitution of purified PLP in giant liposomes was confirmed by fluorescent labeling of PLP and by fluorescence microscopy. The current recordings from these vesicles prove the validity of these methods and provide significant evidence of the existence of ionic channels in myelin membranes and the possibility that PLP functions as a channel. The physiological significance and characterization of these channels remain yet unresolved. These results have a special significance for elucidating the molecular role of myelin in the regulation of neural activity and in the brain ion microenvironment.     

Effects of cations on Methanosarcina thermophila TM-1 growing on moderate concentrations of acetate: production of single cells

Summary The effects of different concentrations of Mg²⁺, Ca²⁺, or Na⁺ on the morphology and growth of Methanosarcina thermophila TM-1 growing on acetate at concentrations comparable with those found in anaerobic digestors was studied. At 30 mm Mg²⁺ or less, M. thermophila grew as large aggregates that settled rapidly. At 100 mm Mg²⁺ or more, the bacteria grew as single cells or a mixture of single cells and small aggregates is suspended culture. Mg²⁺ was necessary for growth and could not be substituted by addition of either Ca²⁺ or Na⁺. The optimal Mg²⁺ concentration was 30 mm and no growth was observed at 400 mm Mg²⁺. Cultures could be adapted to 300 mm Mg²⁺ without a change in growth rate. Added Ca²⁺ was not required for growth and had no effect on cell morphology. Inhibition by Na⁺ was directly related to the Mg²⁺ concentration. When the Mg²⁺ was 0.05 mm or less, 0.35 m Na⁺ completely inhibited growth. However, more Na⁺ was required for inhibition at higher Mg²⁺ concentrations. The same inhibitory effect of Na⁺ was observed when the temperature was 52°C or 45°C. The potential for disaggregation of Methanosarcina aggregates in anaerobic digestor environments was discussed. Offprint requests to: B. K. Ahring     

Primate DRB6 pseudogenes: clue to the evolutionary origin of the HLA-DR2 haplotype

The HLA-DR2 haplotype contains three \-chain encoding DRB genes and one -chain encoding DRA gene. Of the three DRB genes, two are presumably functional (HLA-DRB1 and HLA-DRB5), whereas the third (HLA-DRBV1) is a pseudogene. A pseudogene closely related to HLA-DRBVI is present in the chimpanzee (Patr-DRB6) and in the gorilla (Gogo-DRB6). We sequenced the HLA-DRBVI and Patr-DRB6 pseudogenes (all exons and most of the introns), and compared the sequence to that of the Gogo-DRB6 gene (of which only the exon sequence is available). All three pseudogenes seem to lack exon 1 and contain other deletions responsible for shifts in the translational reading frame. At least the HLA-DRBVI pseudogene, however, seems to be transcribed nevertheless. The chimpanzee pseudogene contains two inserts in intron 2, one of which is an Alu repeat belonging to the Sb subfamily, while the other remains unidentified. These inserts are lacking in the human gene. A comparison with sequences published by other investigators revealed the presence of the HLA-DRBVI pseudogene also in the DRI and DRw10 haplotypes. Measurements of genetic distances indicate DRB6 to be closely related to the DRB2 pseudogene and to the HLA-DRB4 functional gene. In humans, gorillas, and chimpanzees, the DRB6 pseudogene is associated with the same functional gene (DRB5) indicating that this linkage disequilibrium is at least six million years old and that DR2 is one of the oldest DR haplotypes in higher primates.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M77284-M77295. Address correspondence and offprint requests to: J. Klein.