Home About us Contact
|
Home About us Contact | ||
|
|
||
Isolated Fragments (isolated + fragment)
Selected AbstractsSpectroscopic and DNA-binding characterization of the isolated heme-bound basic helix,loop,helix-PAS-A domain of neuronal PAS protein 2 (NPAS2), a transcription activator protein associated with circadian rhythmsFEBS JOURNAL, Issue 11 2006Yuji Mukaiyama Neuronal PAS domain protein 2 (NPAS2) is a circadian rhythm-associated transcription factor with two heme-binding sites on two PAS domains. In the present study, we compared the optical absorption spectra, resonance Raman spectra, heme-binding kinetics and DNA-binding characteristics of the isolated fragment containing the N-terminal basic helix,loop,helix (bHLH) of the first PAS (PAS-A) domain of NPAS2 with those of the PAS-A domain alone. We found that the heme-bound bHLH-PAS-A domain mainly exists as a dimer in solution. The Soret absorption peak of the Fe(III) complex for bHLH-PAS-A (421 nm) was located at a wavelength 9 nm higher than for isolated PAS-A (412 nm). The axial ligand trans to CO in bHLH-PAS-A appears to be His, based on the resonance Raman spectra. In addition, the rate constant for heme association with apo-bHLH-PAS (3.3 × 107 mol,1·s,1) was more than two orders of magnitude higher than for association with apo-PAS-A (< 105 mol,1·s,1). These results suggest that the bHLH domain assists in stable heme binding to NPAS2. Both optical and resonance Raman spectra indicated that the Fe(II),NO heme complex is five-coordinated. Using the quartz-crystal microbalance method, we found that the bHLH-PAS-A domain binds specifically to the E-box DNA sequence in the presence, but not in the absence, of heme. On the basis of these results, we discuss the mode of heme binding by bHLH-PAS-A and its potential role in regulating DNA binding. [source] Connectivity, non-random extinction and ecosystem function in experimental metacommunitiesECOLOGY LETTERS, Issue 5 2010Philip Staddon Ecology Letters (2010) 13: 543,552 Abstract The spatial insurance hypothesis indicates that connectivity is an important attribute of natural ecosystems that sustains both biodiversity and ecosystem function. We tested the hypothesis by measuring the impact of manipulating connectivity in experimental metacommunties of a natural and diverse microecosystem. Isolation led to the extinction of large-bodied apex predators, subsequently followed by increases in prey species abundance. This trophic cascade was associated with significantly altered carbon and nitrogen fluxes in fragmented treatments. The ecosystem impacts were characteristic of a function debt because they persisted for several generations after the initial loss of connectivity. Local extinctions and disruption of ecosystem processes were mitigated, and even reversed, by the presence of corridors in the connected metacommunities, although these beneficial effects were unexpectedly delayed. We hypothesized that corridors maintained grazer movement between fragments, which enhanced microbial activity, and decomposition in comparison to isolated fragments. Our results indicate that knowledge of habitat connectivity and spatial processes is essential to understand the magnitude and timing of ecosystem perturbation in fragmented landscapes. [source] The effects of edge, fragment size and degree of isolation on avian species richness in highly fragmented forest in West AfricaIBIS, Issue 2 2007S. MANU Almost nothing is known of the effects of forest fragmentation on bird diversity within the heavily degraded and fragmented forest remnants in West Africa. We examined the effects of edge, fragment size and isolation on bird species richness in southwestern Nigeria where forest fragmentation is pronounced. In total, 122 km of line transects were used to survey birds and vegetation within 45 forest patches between January 2000 and March 2002: 197 species were recorded. Avian species number and total counts in forest patches were unrelated to fragment area (within the observed range of 14,445 ha), but were negatively influenced by degree of isolation and increasing distance from the edge. As the total area of forested land within 15 km of a patch fell from 4 to 0%, so 21% of species were lost. In total, six and zero species (of 154 recorded more than once) were consistently recorded in the larger and smaller forest fragments, respectively, and four and two bird species were consistently recorded in unisolated and isolated forest fragments, respectively, suggesting that the addition of ,edge' species did not compensate for loss of species sensitive to fragmentation. Diversity index was not affected by either fragment area or degree of isolation, but decreased with distance from the edge. When individual species counts were considered, 68% of species (n = 62) showed no significant effect of distance to edge. Of those 20 species which showed an effect, 12 were less common close to the edge. Most species (65%) did not respond significantly to increasing isolation but of those 22 species that did, 20 were less common in more isolated fragments. Ninety-seven per cent of species showed no significant response to area. As avian diversity and species composition, but not species number, were apparently insensitive to forest fragmentation, our findings suggest that fragmentation reduces the probability of occurrence of a wide range of West African bird species, rather than a subset of fragmentation-sensitive species. The greater apparent sensitivity of present-day West African forest bird communities to fragmentation rather than patch size might reflect previous extinctions of area-sensitive species. Minimizing further forest fragmentation might be the most effective means of conserving avian diversity in current West African landscapes where most remaining forest patches are small (i.e. < 500 ha). [source] Genetic variation in the Desert Springsnail (Tryonia porrecta): implications for reproductive mode and dispersalMOLECULAR ECOLOGY, Issue 6 2005R. HERSHLER Abstract Allozymes and mitochondrial cytochrome c oxidase subunit I (mtCOI) sequences were analysed to determine whether populations of the western North American gastropod Tryonia porrecta (from California, Nevada, Utah, and northwest Mexico) are strongly differentiated in accordance with traditional interpretation of regional fauna as ancient relicts inhabiting isolated fragments of late Tertiary palaeodrainages. These data were also used to assess whether this species, for which males have not been recorded, is a rare example of a molluscan parthenogen. Both data sets strongly supported monophyly of T. porrecta populations. Five of the nine sampled populations consisted of a single monoallelic allozyme genotype while the others contained two to 10 distinct genotypes. Allozymic data for genetically diverse Utah populations provided evidence of clonal and sexual reproduction. mtCOI haplotypes of T. porrecta formed two subgroups which differed by 1.99,2.60%. The common haplotype was found in seven populations with rare haplotypes observed in single populations. Based on these results and an available mtCOI molecular clock for related hydrobiid snails, T. porrecta is interpreted as a primarily parthenogenetic species that undergoes occasional sexual reproduction and has accumulated substantial diversity following its mid-Pliocene to mid-Pleistocene origin. Our results also suggest that the distribution of present-day populations of these gill-breathing snails did not result from fragmentation of an ancient, well-integrated drainage but instead reflects overland colonization of habitats which only recently became available following desiccation of late Quaternary pluvial lakes. [source] Comparison by restriction fragment differential display RT‐PCR of gene expression pattern in bovine oocytes matured in the presence or absence of fetal calf serumMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 1 2001S. Jacek Rzucidlo Abstract A novel restriction fragment differential display (RFDD) RT‐PCR has been used to compare patterns of mRNA expression in bovine oocytes matured in vitro in the presence (10%) or absence of fetal calf serum (FCS). Total RNA extracted from matured and denuded oocytes was processed using display Profile kit (Display System Biotech). RFDD RT‐PCR products were separated on 6% polyacrylamide gel and analyzed using a Storm 860 scanner. Selected bands representing potentially differentially expressed fragments were excised from the gel and re‐amplified. Re‐amplified fragments with size matched to the original fragment were cloned into the TA vector and sequenced. Initially, 10 and 15 differentially expressed fragments were isolated from oocytes matured in the presence and absence of FCS, respectively. Eight out of 10 and 10 out of 15 fragments were re‐amplified successfully as evidenced bysize similarity to the original fragments. Finally, the size of six inserts sequenced from each group matched the size of corresponding original as well as re‐amplified fragments. Sequence comparison search revealed similarity of some isolated fragments to 18s ribosomal RNA, bovine apolipoprotein A‐I, bovine mitochondrion DNA, human CGI‐79 mRNA, human Ab1‐interactor protein, and bovine satellite DNA. The other sequenced fragments may represent novel genes. We showed that RFDD RT‐PCR can be effectively applied to contrast gene expression pattern in bovine oocytes and that presence or absence of FCS during maturation interval affects gene expression pattern in matured bovine oocytes. Mol. Reprod. Dev. 59:90–96, 2001. © 2001 Wiley‐Liss, Inc. [source] Gap-crossing movements predict species occupancy in Amazonian forest fragmentsOIKOS, Issue 2 2009Alexander C. Lees In fragmented landscapes, species persistence within isolated habitat patches is governed by a myriad of species life-history, habitat patch and landscape characteristics. We investigated the inter-specific variation in non-forest gap-crossing abilities of an entire tropical forest-dependent avifauna. We then related this measure of dispersal ability to species life-history characteristics and occupancy data from 31 variable-sized forest patches sampled within the same fragmented forest landscape. A total of 5436 gap-crossing movements of 231 forest-dependent bird species were observed across ten linear forest gaps of varying widths, adjacent to large areas of undisturbed forest. Species persistence in isolated fragments was strongly linked to gap-crossing ability. The most capable gap-crossers were medium to large-bodied species in the large insectivore, frugivore and granivore guilds, matching the most prevalent subset of species in small forest patches. However, some competent gap-crossing species failed to occur in small patches, and minimum forest-patch area requirements were more important in determining patch occupancy for these species. Narrow forest gaps (4,70 m) created by roads and power-lines may become territory boundaries, thereby eliminating home-range gap-crossing movements for many forest species, but permit rarer dispersal events. Wider gaps (>70 m) may inhibit gap-crossing behaviour for all but the most vagile species. Although patch size and quality may be the most important factors in structuring species assemblages in forest fragments, our results show that the degree of patch isolation and permeability of the surrounding matrix also explain which species can persist in forest isolates. Reducing the number and width of forest-dividing gaps; maintaining and/or creating forest corridors and increasing matrix permeability through the creation and maintenance of ,stepping-stone' structures will maximise the species retention in fragmented tropical forest landscapes. [source] Investigating the distribution of prairie dogs in an urban landscapeANIMAL CONSERVATION, Issue 3 2009S. B. Magle Abstract Habitat fragmentation is a prevalent threat to biological diversity, and urbanization is a primary agent of fragmentation and a leading cause of species endangerment. Landscape biogeographic and local habitat characteristics can be important determinants of the distribution of species in habitat patches in urban landscapes. However, the specifics of which characteristics are most critical to maintaining biological diversity are not fully known for prairie ecosystems, especially in fragmented urban habitat. This study focuses on black-tailed prairie dogs along an urban gradient in Denver, CO. Prairie dogs have declined precipitously throughout the region and are an essential part of the prairie ecosystem, making them excellent study subjects. We identified a series of habitat fragments along a gradient of urbanization in the fully urbanized areas and south suburbs of Denver, CO, both containing and not containing prairie dogs. Local characteristics, including fragment slope and vegetative cover, and landscape characteristics, including fragment size, age and connectivity, were measured on each fragment. We used likelihood-based methods to explore which variables most accurately predicted prairie dog occurrence within our study area. Multiple factors influenced the distribution of prairie dogs in urban settings, with colony connectivity the strongest predictor of occupancy. Large and recently isolated fragments near other prairie dog colonies, flat areas and those with high graminoid cover were most likely to support prairie dog populations. Our study provides the first attempt to model prairie dog occurrence in highly fragmented urban habitat and has important implications for the management and conservation of prairie dogs. [source] Mating success of the endemic Des Murs' Wiretail (Sylviorthorhynchus desmursii, Furnariidae) in fragmented Chilean rainforestsAUSTRAL ECOLOGY, Issue 1 2006IVÁN A. DÍAZ Abstract: We studied the effects of fragment size, vegetation structure and presence of habitat corridors on the reproductive success of the Des Murs' Wiretail (Sylviorthorhynchus desmursii Des Murs, Furnariidae), a small (10 g) understorey bird, endemic to South American forests. In a rural landscape of Chiloé Island, southern Chile (42°S; 70°W), we determined the mating and nesting success of wiretails in 28 territories distributed in seven small (1,20 ha) and two large (>300 ha) forest fragments during the 1997,1998 breeding season. Wiretails inhabited dense bamboo thickets in the understorey of forest patches, dense shrublands covering old fields, and dense early successional forest vegetation. Wiretails avoided open pastures. Reproductive success depended solely on the probability of finding mates, and the main factor affecting mating success was the presence of corridors. Mated individuals occupied 72% of the territories in forest patches <20 ha connected by corridors, 73% of the territories in large (>300 ha) fragments, but only 20% of territories in isolated fragments surrounded by pastures. Because of the rapid expansion of pastures in southern Chile, the conservation of wiretails and other understorey birds will depend on the maintenance of travel corridors with dense understorey vegetation between forest fragments. [source] Bat Mobility and Roosts in a Fragmented Landscape in Central Amazonia, BrazilBIOTROPICA, Issue 2 2003Enrico Bernard ABSTRACT In spite of the important role played by bats in tropical ecosystems, little is known about how they are affected by habitat fragmentation. By using a mark/recapture protocol and radiotelemetry techniques in a naturally fragmented landscape composed of primary forests and forest fragments surrounded by savannas in Alter do Chao, Para State, Brazil, we were able to track the movements of various species of bats, calculate the size of the area used, locate roosts and potential feeding areas, and determine preferred flight routes. We marked 3440 bats belonging to 44 species and recaptured 151 belonging to 14 species. The average distance between extra-site recaptures was 2.2 km. With the exception of bats marked in fragments and recaptured in forests, all other possible inter-habitat recaptures were observed. We selected 23 bats of 8 species for radiotelemetry and the areas used by them varied from 65 to 530 ha. Some species restricted their activity to the vicinity of their roosts, rarely moving more than 500 m away, but others traveled greater distances between roosts and foraging areas. All tracked bats flew over savannas, crossing distances from 0.5 to 2.5 km. Roost location and type varied among species, from individuals roosting alone in the foliage to colonies in buildings. Bats were highly mobile and savannas did not appear to inhibit the movements of some species, suggesting that a persistent biological flow may be maintained among isolated fragments, with bats acting as pollinators and seed dispersers. RESUMO Apesar da importa,ncia dos morcegos nos ecossistemas tropicais, pouco se sabe a respeito de como estes animais interagem com uma paisagem fragmentada. Apresentamos aqui dados sobre a mobilidade de morcegos em uma paisagem naturalmente fragmentada, composta por florestas e fragmentos florestais circundados por savanas em Alter do Chão, Estado do Pará, Brasil. Através de marcação/recaptura e de rádio-telemetria conseguimos rastrear os movi-mentos de espécies selecionadas, calcular o tamanho da área usada, localizar abrigos e áreas potenciais de forrageio e apontar rotas preferidas de vo,o. Marcamos 3440 morcegos de 44 espécies e recapturamos 151 individuos de 14 espécies. A dista,ncia média entre recapturas em sítios diferentes foi de 2.2 km. Com exceção dos morcegos que foram marcados em fragmentos e recapturados em florestas, todas as outras combinações de recapturas entre habitats foram observadas. Selecionamos 23 morcegos de oito espécies para radio-telemetria e as áreas usadas por eles variaram entre 65 e 530 ha. Algumas espécies restringiram suas atividades ao redor dos abrigos, raramente afastando-se mais do que 500 m destes, enquanto outras deslocaram-se por dista,ncias maiores entre os ábrigos e as areas de forrageio. Todos os morcegos rastreados cruzaram as savanas, cobrindo dista,ncias de 0.5 a 2.5 km. O tipo e a localização dos abrigos variou entre as espécies, desde individuos abrigando-se sozinhos na folhagem até colo,nias em edificações. Os morcegos apresentaram alta mobilidade e as savanas aparentemente não inibiram a movimentação de algumas espécies, sugerindo que um fluxo boilógico entre fragmentos pode persistir, tendo os morcegos como agentes polinizadores e dispersores de sementes. [source] | ||||||||||