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Kristoffersen SM Tourasse NJ Kolstø AB Økstad OA 《Molecular biology and evolution》2011,28(2):963-983
Many short (<400 bp) interspersed sequence repeats exist in bacteria, yet little is known about their origins, mode of generation, or possible function. Here, we present a comprehensive analysis of 18 different previously identified repeated DNA elements, bcr1-bcr18 (?kstad OA, Hegna I, Lindback T, Rishovd AL, Kolst? AB. 1999. Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiology. 145:621-631.; Tourasse NJ, Helgason E, ?kstad OA, Hegna IK, Kolst? AB. 2006. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol. 101:579-593.), in 36 sequenced genomes from the Bacillus cereus group of bacteria. This group consists of genetically closely related species with variable pathogenic specificity toward different hosts and includes among others B. anthracis, B. cereus, and B. thuringiensis. The B. cereus group repeat elements could be classified into three categories with different properties: Group A elements (bcr1-bcr3) exhibited highly variable copy numbers ranging from 4 to 116 copies per strain, showed a nonconserved chromosomal distribution pattern between strains, and displayed several features characteristic of mobile elements. Group B repeats (bcr4-bcr6) were present in 0-10 copies per strain and were associated with strain-specific genes and disruptions of genome synteny, implying a possible contribution to genome rearrangements and/or horizontal gene transfer events. bcr5, in particular, was associated with large gene clusters showing resemblance to integrons. In agreement with their potentially mobile nature or involvement in horizontal transfers, the sequences of the repeats from Groups A and B (bcr1-bcr6) followed a phylogeny different from that of the host strains. Conversely, repeats from Group C (bcr7-bcr18) had a conserved chromosomal location and orthologous gene neighbors in the investigated B. cereus group genomes, and their phylogeny matched that of the host chromosome. Several of the group C repeats exhibited a conserved secondary structure or had parts of the structure conserved, possibly indicating functional RNAs. Accordingly, five of the repeats in group C overlapped regions encoding previously characterized riboswitches. Similarly, other group C repeats could represent novel riboswitches, encode small RNAs, and/or constitute other types of regulatory elements with specific biological functions. The current analysis suggests that the multitude of repeat elements identified in the B. cereus group promote genome dynamics and plasticity and could contribute to the flexible and adaptive life style of these bacteria. 相似文献
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Simen Pedersen Karen M. Mathisen Lucrezia Gorini Harry P. Andreassen Eivin Røskaft Christina Skarpe 《European Journal of Wildlife Research》2014,60(3):527-534
Supplementary feeding of wild large herbivores is a widespread practice in North America and Europe. The presence of feeding stations may have ecological consequences through changes to animal distributions, patterns of herbivory and a net nutrient input into the ecosystem. In Fennoscandia, supplementary feeding of moose in winter (Alces alces) is increasing. Although it has been shown to affect bird communities, its effects on small mammal communities were unknown. Here, we studied the effects of moose supplementary feeding stations on plants and on abundance, reproduction, and biomass of small mammals in years with low and high vole abundance. We sampled small mammals with snap traps and conducted surveys of the field layer vegetation, at varying distances from moose supplemental feeding stations. Due to the vegetation changes induced by feeding stations, abundance of common shrews (Sorex araneus) and Microtus voles were positively affected by long-term moose winter feeding, while bank voles (Myodes glareolus) were not affected. Moose feeding stations did not affect reproduction, individual body mass, or the total biomass of small mammals. Moose winter-feeding stations have impacts on nontarget species, providing islands of preferred grass and forb habitat for Microtus spp. and common shrews, allowing them to penetrate into a matrix of less preferred forest habitat. 相似文献
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Simen Rød Sandve Heidi Rudi Guro Dørum Paul Ragnar Berg Odd Arne Rognli 《Molecular breeding : new strategies in plant improvement》2010,26(4):711-718
Novel high-throughput genotyping technologies have facilitated rapid genotyping of single nucleotide polymorphisms in non-model
organisms. Most plant species have complex genomes with a large proportion of their genes having one or more paralogous copies
due to single gene duplications and ancient or recent polyploidization events. These paralogous gene copies are potential
sources of genotyping errors, and hence genotyping of plant genomes is inherently difficult. Here we present a case study
that exemplifies paralog-related problems in high-throughput genotyping of plant genomes. We used the MassARRAY genotyping
platform to genotype the LpIRI locus in L. perenne populations; this gene is thought to be involved in low-temperature stress tolerance. The dissection of the molecular genetics
underlying the genotyping results provides a good example of how unknown paralogs can mask the true genotype of the locus,
instructive to the non-specialist plant researcher and breeder. 相似文献
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Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod 下载免费PDF全文
Tina Graceline Kirubakaran Harald Grove Matthew P. Kent Simen R. Sandve Matthew Baranski Torfinn Nome Maria Cristina De Rosa Benedetta Righino Torild Johansen Håkon Otterå Anna Sonesson Sigbjørn Lien Øivind Andersen 《Molecular ecology》2016,25(10):2130-2143
Atlantic cod is composed of multiple migratory and stationary populations widely distributed in the North Atlantic Ocean. The Northeast Arctic cod (NEAC) population in the Barents Sea undertakes annual spawning migrations to the northern Norwegian coast. Although spawning occurs sympatrically with the stationary Norwegian coastal cod (NCC), phenotypic and genetic differences between NEAC and NCC are maintained. In this study, we resolve the enigma by revealing the mechanisms underlying these differences. Extended linkage disequilibrium (LD) and population divergence were demonstrated in a 17.4‐Mb region on linkage group 1 (LG1) based on genotypes of 494 SNPs from 192 parents of farmed families of NEAC, NCC or NEACxNCC crosses. Linkage analyses revealed two adjacent inversions within this region that repress meiotic recombination in NEACxNCC crosses. We identified a NEAC‐specific haplotype consisting of 186 SNPs that was fixed in NEAC sampled from the Barents Sea, but segregating under Hardy–Weinberg equilibrium in eight NCC stocks. Comparative genomic analyses determine the NEAC configuration of the inversions to be the derived state and date it to ~1.6–2.0 Mya. The haplotype block harbours 763 genes, including candidates regulating swim bladder pressure, haem synthesis and skeletal muscle organization conferring adaptation to long‐distance migrations and vertical movements down to large depths. Our results suggest that the migratory ecotype experiences strong directional selection for the two adjacent inversions on LG1. Despite interbreeding between NEAC and NCC, the inversions are maintaining genetic differentiation, and we hypothesize the co‐occurrence of multiple adaptive alleles forming a ‘supergene’ in the NEAC population. 相似文献
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The coastal heathlands of the Royal National Park are impacted by both fire and herbivory by introduced deer, and to date these two factors have been dealt with independently in the management of natural areas. In recent years, there has been increasing recognition for a more integrated approach to manage these two disturbance agents. Fire and its role in Australian heathlands are well known, while impacts from introduced deer and the combined effects of fire and introduced deer are still poorly understood. In this study, we investigated the effects of fire and Javan rusa deer (Cervus timorensis) on both vegetation cover and floristics. The percentage cover of plants at different height layers and the presence/absence of individual species were recorded at sites representing two different burn histories (1993/1994 and 2000/2001) and deer presence or absence. Fire significantly reduced vegetation cover at low (<50 cm) and intermediate heights (50–100 cm), while deer presence affected grasses and sedges, and low vegetation at more recently burnt sites. Rusa deer also affected composition of the plant species assemblages, but no such effect was found for fire. Understanding the influence of each disturbance factor independently and together in the heathlands will be critical for implementing a more robust framework for future management. 相似文献
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Yasuhiro Onoue Toshiharu Suzuki Max Davidson Owe Orwar Kazuhiko Kinosita Jr. 《生物化学与生物物理学报:生物膜》2009,1788(6):1332-865
We present an experimental system that allows visualization of conformational changes in membrane proteins at the single-molecule level. The target membrane protein is reconstituted in a giant liposome for independent control of the aqueous environments on the two sides of the membrane. For direct observation of conformational changes, an extra-liposomal site(s) of the target protein is bound to a glass surface, and a probe that is easily visible under a microscope, such as a micron-sized plastic bead, is attached to another site on the intra-liposomal side. A conformational change, or an angular motion in the tiny protein molecule, would manifest as a visible motion of the probe. The attachment of the protein on the glass surface also immobilizes the liposome, greatly facilitating its manipulation such as the probe injection. As a model system, we reconstituted ATP synthase (FOF1) in liposomes tens of μm in size, attached the protein specifically to a glass surface, and demonstrated its ATP-driven rotation in the membrane through the motion of a submicron bead. 相似文献
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Max Lataillade Jennifer Chiarella Rong Yang Steven Schnittman Victoria Wirtz Jonathan Uy Daniel Seekins Mark Krystal Marco Mancini Donnie McGrath Birgitte Simen Michael Egholm Michael Kozal 《PloS one》2010,5(6)