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1.
Capsule Woodpigeon Columba palumbus nest-tree selection is affected by human disturbance, grazing and tree characteristics. Aims To determine the characteristics of trees used for nesting by Woodpigeons under two levels of grazing and disturbance in a Holm oak Middle Atlas forest, Morocco. Methods Woodpigeon nest-tree selection was investigated in highly disturbed and less-disturbed sites over two years (2010 and 2011). The features of nest-tree characteristics were determined by comparing the characteristics of trees used for nesting to those of randomly selected trees. Results Tree physical characteristics, grazing intensity and level of human disturbance were the main factors determining selection for nest-trees. Woodpigeons chose nesting trees that were greater in height, larger in DBH, lower in base of the live crown, in denser stands and at greater distance from tracks. Conclusions Forest management for Woodpigeon nest habitat selection should focus on controlling the access of vehicles especially trucks, introducing a rotating system of forest utilization for grazing and maintaining (without extending) the cereal crops. These recommendations may assist land managers to plan for continued persistence of this species in Middle Atlas forests. 相似文献
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Schubert M Ginolhac A Lindgreen S Thompson JF Al-Rasheid KA Willerslev E Krogh A Orlando L 《BMC genomics》2012,13(1):178
ABSTRACT: BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material. 相似文献
3.
Donato Spoltore Wibren D. Oosterbaan Samira Khelifi John N. Clifford Aurelien Viterisi Emilio Palomares Marc Burgelman Laurence Lutsen Dirk Vanderzande Jean Manca 《Liver Transplantation》2013,3(4):466-471
The non‐geminate recombination of charge carriers in polymer‐fullerene solar cells has been modeled in the last few years with a trap‐assisted recombination model, which states that the apparent recombination order depends on the concentration of trapped charges tailing into the band gap. Higher concentrations of trapped charges lead to higher apparent recombination orders. In this work, the mass fraction f of highly crystalline nanofibrillar P3HT to the total P3HT content in P3HT:PCBM solar cells is consistently varied, controlling the temperature of a nanofibers‐P3HT casting dispersion. A systematic study of the apparent recombination order, measured with a transient photovoltage technique, as a function of f is presented. A correlation is shown between the apparent recombination order, the P3HT crystallinity, and the trap concentration in the band gap measured with an admittance spectroscopy technique. 相似文献
4.
Sébastien Fritz Aurelien Capitan Anis Djari Sabrina C. Rodriguez Anne Barbat Aurélia Baur Cécile Grohs Bernard Weiss Mekki Boussaha Diane Esquerré Christophe Klopp Dominique Rocha Didier Boichard 《PloS one》2013,8(6)
The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10−4) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle. 相似文献
5.
Nicola Vannini Vasco Campos Mukul Girotra Vincent Trachsel Shanti Rojas-Sutterlin Josefine Tratwal Simone Ragusa Evangelos Stefanidis Dongryeol Ryu Pernille Y. Rainer Gena Nikitin Sonja Giger Terytty Y. Li Aikaterini Semilietof Aurelien Oggier Yannick Yersin Loïc Tauzin Eija Pirinen Olaia Naveiras 《Cell Stem Cell》2019,24(3):405-418.e7
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Giulia Schiroli Anastasia Conti Samuele Ferrari Lucrezia della Volpe Aurelien Jacob Luisa Albano Stefano Beretta Andrea Calabria Valentina Vavassori Patrizia Gasparini Eralda Salataj Delphine Ndiaye-Lobry Chiara Brombin Julie Chaumeil Eugenio Montini Ivan Merelli Pietro Genovese Luigi Naldini Raffaella Di Micco 《Cell Stem Cell》2019,24(4):551-565.e8
7.
M phase phosphoprotein 1 is a human plus-end-directed kinesin-related protein required for cytokinesis 总被引:4,自引:0,他引:4
Abaza A Soleilhac JM Westendorf J Piel M Crevel I Roux A Pirollet F 《The Journal of biological chemistry》2003,278(30):27844-27852
The human M phase phosphoprotein 1 (MPP1), previously identified through a screening of a subset of proteins specifically phosphorylated at the G2/M transition (Matsumoto-Taniura, N., Pirollet, F., Monroe, R., Gerace, L., and Westendorf, J. M. (1996) Mol. Biol. Cell 7, 1455-1469), is characterized as a plus-end-directed kinesin-related protein. Recombinant MPP1 exhibits in vitro microtubule-binding and microtubule-bundling properties as well as microtubule-stimulated ATPase activity. In gliding experiments using polarity-marked microtubules, MPP1 is a slow molecular motor that moves toward the microtubule plus-end at a 0.07 microm/s speed. In cycling cells, MPP1 localizes mainly to the nuclei in interphase. During mitosis, MPP1 is diffuse throughout the cytoplasm in metaphase and subsequently localizes to the midzone to further concentrate on the midbody. MPP1 suppression by RNA interference induces failure of cell division late in cytokinesis. We conclude that MPP1 is a new mitotic molecular motor required for completion of cytokinesis. 相似文献
8.
To understand soil colonization by a root system, information is needed on the architecture of the root system. In monocotyledons, soil exploration is mainly due to the growth of adventitious primary roots. Primary root emergence in banana was quantified in relation to shoot and corm development. Root emergence kinetics were closely related to the development of aerial organs. Root position at emergence on the corm followed an asymptotic function of corm dry weight, so that the age of each root at a given time could be deduced from its position. Root diameter at emergence was related to the position of the roots on the corm, with younger roots being thicker than older ones. However, root diameters were not constant along a given root, but instead decreased with the distance to the base; roots appear to be conical in their basal and apical parts. Root growth directions at emergence were variable, but a high proportion of the primary roots emerged with a low angle to the horizontal. Further research is needed to evaluate whether these initial trajectories are conserved during root development. Results presented in this study are in good agreement with those reported for other monocotyledons such as maize and rice. They give quantitative information that will facilitate the development of models of root system architecture in banana. 相似文献
9.
de Vries SJ van Dijk AD Krzeminski M van Dijk M Thureau A Hsu V Wassenaar T Bonvin AM 《Proteins》2007,69(4):726-733
Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0. 相似文献
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