Boxing for biodiversity: evaluation of an artificially created decaying wood habitat

Many saproxylic species are threatened in Europe because of habitat decline. Hollow trees represent an important habitat for saproxylic species. Artificial habitats may need to be created to maintain or increase the amount of habitat due to natural habitat decline. This study investigated the extent to which saproxylic beetles use artificial habitats in wooden boxes. The boxes were placed at various distances (0–1800 m) from known biodiversity hotspots with hollow oaks and studied over 10 years. Boxes were mainly filled with oak saw dust, oak leaves, hay and lucerne flour. In total, 2170 specimens of 91 saproxylic beetle species were sampled in 43 boxes. The abundance of species associated with tree hollows, wood rot and animal nests increased from the fourth to the final year, but species richness declined for all groups. This study shows that wooden boxes can function as saproxylic species habitats. The artificial habitats developed into a more hollow-like environment during the decade long experiment with fewer but more abundant tree hollow specialists.     

Karyotype analysis in Hyacinthella dalmatica (Hyacinthaceae) reveals vertebrate-type telomere repeats at the chromosome ends.

Chromosome analysis of three different populations of Hyacinthella dalmatica (Lallem.) Trinajsti?, an endemic species of the coastal region of southeastern Europe, showed a unique chromosome number, 2n = 2x = 20, and bimodal karyotype with one large and nine smaller pairs of chromosomes. Staining with fluorochromes CMA3 (chromomycin A3) and DAPI (4,6-diamidino-2-phenylindole) revealed heterochromatic regions associated with NORs, centromeres, and several interstitial heterochromatic bands on the longest chromosome pair. Double-target FISH with two ribosomal DNA probes revealed one locus of 5S rRNA genes in the pericentromeric region of chromosome pair 3 and one locus of 18S-5.8S-26S rRNA genes on the short arm of chromosome pair 4 in all plants and populations analyzed. Southern hybridization analysis and FISH experiments demonstrated that the distal ends of H. dalmatica chromosomes contain the vertebrate telomere (5'-TTAGGG-3') repeat type rather than the Arabidopsis (5'-TTTAGGG-3') heptamer, and so suggest that this Asparagales species along with Aloe and Othocallis contains the vertebrate-type telomere repeat.     

LINNAEUS: A species name identification system for biomedical literature

Background  

The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.     

Yeast glucoamylases: molecular-genetic and structural characterization

Glucoamylase is an extracellular enzyme produced mainly by microorganisms. It belongs to the commercially frequently exploited biocatalysts. The major application of glucoamylase is in the starch bioprocessing to produce glucose and in alcoholic fermentations of starchy materials. Filamentous fungi have been the source of glucoamylases for industrial purposes as well as an object of numerous research studies. Some yeasts also secrete a large amount of glucoamylase with biochemical characteristics slightly different from those of filamentous fungi. Modern biotechnological applications require glucoamylases of certain properties optimal for a given process. Novel biocatalysts can be prepared from already existing enzymes using techniques of protein engineering or directed evolution. Tailoring of a commercial glucoamylase requires knowledge, on a molecular level, of structure/function relationships of enzymes originating from various sources and having different catalytic properties. Sequences of the cloned genes, their recombinant expression and the tertiary structure determination of glucoamylase are prerequisite to obtain such information. The presented review focuses on molecular-genetic and structural aspects of yeast glucoamylases, supplemented with the basic biochemical characterization of the given enzymes.     

Biological and socio-economic effects of statewide limitation of deer licenses in Colorado

We evaluated the biological and socio-economic effects of statewide limitation of mule deer (Odocoileus hemionus) hunting licenses, which began in Colorado in 1999. We implemented a before-after-control-impact (BACI) analysis of annual helicopter sex and age class surveys, collected as part of the Colorado Division of Wildlife's routine monitoring, to assess changes in adult male/adult female ratios and fawn/adult female ratios in response to this change in harvest management. Following statewide limitation and reduction of license sales (1999–2006), we observed increases in adult male/adult female ratios of 7.39 (SE = 2.36) to 15.23 (SE = 1.22) adult males per 100 adult females in moderately limited areas and of 17.55 (SE = 3.27) to 21.86 (SE = 2.31) adult males per 100 adult females in highly limited areas. We simultaneously observed reductions in fawn/adult female ratios in newly limited areas by as much as 6.96 (SE = 2.19) fawns per 100 females, whereas in areas that had previously been limited we observed stabilization of fawn/adult female ratios at levels lower than levels observed under the unlimited harvest management structure. An immediate decline of $7.86 million in annual revenue stemmed from the change in harvest management, but revenue subsequently rebounded. This study provides preliminary evidence of potential effects that other state and provincial wildlife management agencies may face as they consider shifting mule deer harvest management towards limited license scenarios. © 2011 The Wildlife Society.     

Effects of willow nutrition and morphology on calving success of moose

Across much of North America, populations of moose (Alces alces) are declining because of disease, predation, climate change, and anthropogenic-driven habitat loss. Contrary to this trend, populations of moose in Colorado, USA, have continued to grow. Studying successful (i.e., persistent or growing) populations of moose can facilitate continued conservation by identifying habitat features critical to persistence of moose. We hypothesized that moose using habitat with higher quality willow (Salix spp.) would have a higher probability of having a calf-at-heel (i.e., calving success). We evaluated moose calving success using repeated ground observations of collared individuals with calves in an occupancy model framework to account for detection probability. We then evaluated the impact of willow habitat quality and nutrition on moose calving success by studying 2 spatially segregated populations of moose in Colorado. Last, we evaluated correlations between willow characteristics (browse intensity, height, cover, leaf length, and species) and willow nutrition (dry matter digestibility [DMD]) to assess the utility of using those characteristics to assess willow nutrition. We found willow height and cover had a high probability of being positively associated with higher individual-level calving success. Willow DMD, browse intensity, and leaf length were not predictive of individual moose calving success; however, the site with higher mean DMD consistently had higher mean estimates of calving success for the same year. Our results suggest surveying DMD is likely not a useful metric for assessing differences in calving success of individual moose but may be of use at population levels. Further, the assessment of willow morphology and density may be used to identify areas that support higher levels of moose calving success.     

Phylogenetic and molecular clock inferences of cyanobacterial strains within Rivulariaceae from distant environments

Heterocyst-forming cyanobacteria are important players at both evolutionary and ecological scales, but to date it has been difficult to establish their phylogenetic affiliations. We present data from a phylogenetic and molecular clock analysis of heterocystous cyanobacteria within the family Rivulariaceae, including the genera Calothrix, Rivularia, Gloeotrichia and Tolypothrix. The strains were isolated from distant geographic regions including fresh and brackish water bodies, microbial mats from beach rock, microbialites, pebble beaches, plus PCC strains 7103 and 7504. Phylogenetic inferences (distance, likelihood and Bayesian) suggested the monophyly of genera Calothrix and Rivularia. Molecular clock estimates indicate that Calothrix and Rivularia originated ～1500 million years ago (MYA) ago and species date back to 400-300 MYA while Tolypothrix and Gloeotrichia are younger genera (600-400 MYA).     

Newly established in vitro system with fluorescent proteins shows that abnormal expression of downstream prion protein-like protein in mice is probably due to functional disconnection between splicing and 3' formation of prion protein pre-mRNA

We and others previously showed that, in some lines of prion protein (PrP)-knockout mice, the downstream PrP-like protein (PrPLP/Dpl) was abnormally expressed in brains partly due to impaired cleavage/polyadenylation of the residual PrP promoter-driven pre-mRNA despite the presence of a poly(A) signal. In this study, we newly established an in vitro transient transfection system in which abnormal expression of PrPLP/Dpl can be visualized by expression of the green fluorescence protein, EGFP, in cultured cells. No EGFP was detected in cells transfected by a vector carrying a PrP genomic fragment including the region targeted in the knockout mice intact upstream of the PrPLP/Dpl gene. In contrast, deletion of the targeted region from the vector caused expression of EGFP. By employing this system with other vectors carrying various deletions or point mutations in the targeted region, we identified that disruption of the splicing elements in the PrP terminal intron caused the expression of EGFP. Recent lines of evidence indicate that terminal intron splicing and cleavage/polyadenylation of pre-mRNA are functionally linked to each other. Taken together, our newly established system shows that the abnormal expression of PrPLP/Dpl in PrP-knockout mice caused by the impaired cleavage/polyadenylation of the PrP promoter-driven pre-mRNA is due to the functional dissociation between the pre-mRNA machineries, in particular those of cleavage/polyadenylation and splicing. Our newly established in vitro system, in which the functional dissociation between the pre-mRNA machineries can be visualized by EGFP green fluorescence, may be useful for studies of the functional connection of pre-mRNA machineries.