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71.
Sehgal RN Buermann W Harrigan RJ Bonneaud C Loiseau C Chasar A Sepil I Valkiūnas G Iezhova T Saatchi S Smith TB 《Proceedings. Biological sciences / The Royal Society》2011,278(1708):1025-1033
Critical to the mitigation of parasitic vector-borne diseases is the development of accurate spatial predictions that integrate environmental conditions conducive to pathogen proliferation. Species of Plasmodium and Trypanosoma readily infect humans, and are also common in birds. Here, we develop predictive spatial models for the prevalence of these blood parasites in the olive sunbird (Cyanomitra olivacea). Since this species exhibits high natural parasite prevalence and occupies diverse habitats in tropical Africa, it represents a distinctive ecological model system for studying vector-borne pathogens. We used PCR and microscopy to screen for haematozoa from 28 sites in Central and West Africa. Species distribution models were constructed to associate ground-based and remotely sensed environmental variables with parasite presence. We then used machine-learning algorithm models to identify relationships between parasite prevalence and environmental predictors. Finally, predictive maps were generated by projecting model outputs to geographically unsampled areas. Results indicate that for Plasmodium spp., the maximum temperature of the warmest month was most important in predicting prevalence. For Trypanosoma spp., seasonal canopy moisture variability was the most important predictor. The models presented here visualize gradients of disease prevalence, identify pathogen hotspots and will be instrumental in studying the effects of ecological change on these and other pathogens. 相似文献
72.
Zea ribosomal repeat evolution and substitution patterns 总被引:1,自引:1,他引:1
Zea and Tripsacum nuclear ribosomal internal transcribed spacer (ITS)
sequences were used to evaluate patterns of concerted evolution, rates of
substitutions, patterns of methylation-induced deamination, and structural
constraints of the ITS. ITS pseudogenes were identified by their
phylogenetic position, differences in nucleotide composition, extensive
deamination at ancestral methylation sites, and substitutions resulting in
low-stability secondary RNA structures. Selection was important in shaping
the kinds of polymorphisms and substitutions observed in the ITS. ITS
substitution rates were significantly different among the Zea taxa.
Deamination of cytosines at methylation sites was a potent mutation source,
but selection appeared to maintain high methylation site density throughout
the ribosomal repeat except for the gene promoter. Nucleotide divergence
statistics identified selectively constrained regions at the 5' ends of the
ITS1 and ITS2.
相似文献
73.
74.
Brockman MA Chopera DR Olvera A Brumme CJ Sela J Markle TJ Martin E Carlson JM Le AQ McGovern R Cheung PK Kelleher AD Jessen H Markowitz M Rosenberg E Frahm N Sanchez J Mallal S John M Harrigan PR Heckerman D Brander C Walker BD Brumme ZL 《Journal of virology》2012,86(12):6913-6923
An attenuation of the HIV-1 replication capacity (RC) has been observed for immune-mediated escape mutations in Gag restricted by protective HLA alleles. However, the extent to which escape mutations affect other viral proteins during natural infection is not well understood. We generated recombinant viruses encoding plasma HIV-1 RNA integrase sequences from antiretroviral-naïve individuals with early (n = 88) and chronic (n = 304) infections and measured the in vitro RC of each. In contrast to data from previous studies of Gag, we observed little evidence that host HLA allele expression was associated with integrase RC. A modest negative correlation was observed between the number of HLA-B-associated integrase polymorphisms and RC in chronic infection (R = −0.2; P = 0.003); however, this effect was not driven by mutations restricted by protective HLA alleles. Notably, the integrase variants S119R, G163E, and I220L, which represent uncommon polymorphisms associated with HLA-C*05, -A*33, and -B*52, respectively, correlated with lower RC (all q < 0.2). We identified a novel C*05-restricted epitope (HTDNGSNF114–121) that likely contributes to the selection of the S119R variant, the polymorphism most significantly associated with lower RC in patient sequences. An NL4-3 mutant encoding the S119R polymorphism displayed a ∼35%-reduced function that was rescued by a single compensatory mutation of A91E. Together, these data indicate that substantial HLA-driven attenuation of integrase is not a general phenomenon during HIV-1 adaptation to host immunity. However, uncommon polymorphisms selected by HLA alleles that are not conventionally regarded to be protective may be associated with impaired protein function. Vulnerable epitopes in integrase might therefore be considered for future vaccine strategies. 相似文献
75.
The Werner syndrome protein operates in base excision repair and cooperates with DNA polymerase beta 下载免费PDF全文
Harrigan JA Wilson DM Prasad R Opresko PL Beck G May A Wilson SH Bohr VA 《Nucleic acids research》2006,34(2):745-754
Genome instability is a characteristic of cancer and aging, and is a hallmark of the premature aging disorder Werner syndrome (WS). Evidence suggests that the Werner syndrome protein (WRN) contributes to the maintenance of genome integrity through its involvement in DNA repair. In particular, biochemical evidence indicates a role for WRN in base excision repair (BER). We have previously reported that WRN helicase activity stimulates DNA polymerase beta (pol β) strand displacement synthesis in vitro. In this report we demonstrate that WRN exonuclease activity can act cooperatively with pol β, a polymerase lacking 3′–5′ proofreading activity. Furthermore, using small interference RNA technology, we demonstrate that WRN knockdown cells are hypersensitive to the alkylating agent methyl methanesulfonate, which creates DNA damage that is primarily repaired by the BER pathway. In addition, repair assays using whole cell extracts from WRN knockdown cells indicate a defect in long patch (LP) BER. These findings demonstrate that WRN plays a direct role in the repair of methylation-induced DNA damage, and suggest a role for both WRN helicase and exonuclease activities together with pol β during LP BER. 相似文献
76.
77.
Ingrid Parmentier Ryan J. Harrigan Wolfgang Buermann Edward T. A. Mitchard Sassan Saatchi Yadvinder Malhi Frans Bongers William D. Hawthorne Miguel E. Leal Simon L. Lewis Louis Nusbaumer Douglas Sheil Marc S. M. Sosef Kofi Affum‐Baffoe Adama Bakayoko George B. Chuyong Cyrille Chatelain James A. Comiskey Gilles Dauby Jean‐Louis Doucet Sophie Fauset Laurent Gautier Jean‐François Gillet David Kenfack François N. Kouamé Edouard K. Kouassi Lazare A. Kouka Marc P. E. Parren Kelvin S.‐H. Peh Jan M. Reitsma Bruno Senterre Bonaventure Sonké Terry C. H. Sunderland Mike D. Swaine Mbatchou G. P. Tchouto Duncan Thomas Johan L. C. H. Van Valkenburg Olivier J. Hardy 《Journal of Biogeography》2011,38(6):1164-1176
Aim Our aim was to evaluate the extent to which we can predict and map tree alpha diversity across broad spatial scales either by using climate and remote sensing data or by exploiting spatial autocorrelation patterns. Location Tropical rain forest, West Africa and Atlantic Central Africa. Methods Alpha diversity estimates were compiled for trees with diameter at breast height ≥ 10 cm in 573 inventory plots. Linear regression (ordinary least squares, OLS) and random forest (RF) statistical techniques were used to project alpha diversity estimates at unsampled locations using climate data and remote sensing data [Moderate Resolution Imaging Spectroradiometer (MODIS), normalized difference vegetation index (NDVI), Quick Scatterometer (QSCAT), tree cover, elevation]. The prediction reliabilities of OLS and RF models were evaluated using a novel approach and compared to that of a kriging model based on geographic location alone. Results The predictive power of the kriging model was comparable to that of OLS and RF models based on climatic and remote sensing data. The three models provided congruent predictions of alpha diversity in well‐sampled areas but not in poorly inventoried locations. The reliability of the predictions of all three models declined markedly with distance from points with inventory data, becoming very low at distances > 50 km. According to inventory data, Atlantic Central African forests display a higher mean alpha diversity than do West African forests. Main conclusions The lower tree alpha diversity in West Africa than in Atlantic Central Africa may reflect a richer regional species pool in the latter. Our results emphasize and illustrate the need to test model predictions in a spatially explicit manner. Good OLS or RF model predictions from inventory data at short distance largely result from the strong spatial autocorrelation displayed by both the alpha diversity and the predictive variables rather than necessarily from causal relationships. Our results suggest that alpha diversity is driven by history rather than by the contemporary environment. Given the low predictive power of models, we call for a major effort to broaden the geographical extent and intensity of forest assessments to expand our knowledge of African rain forest diversity. 相似文献
78.
79.
Stacking transgenic event DAS‐Ø15Ø7‐1 alters maize composition less than traditional breeding 下载免费PDF全文
Rod A. Herman Brandon J. Fast Peter N. Scherer Alyssa M. Brune Denise T. de Cerqueira Barry W. Schafer Ricardo D. Ekmay George G. Harrigan Greg A. Bradfisch 《Plant biotechnology journal》2017,15(10):1264-1272
The impact of crossing (‘stacking’) genetically modified (GM) events on maize‐grain biochemical composition was compared with the impact of generating nonGM hybrids. The compositional similarity of seven GM stacks containing event DAS‐Ø15Ø7‐1, and their matched nonGM near‐isogenic hybrids (iso‐hybrids) was compared with the compositional similarity of concurrently grown nonGM hybrids and these same iso‐hybrids. Scatter plots were used to visualize comparisons among hybrids and a coefficient of identity (per cent of variation explained by line of identity) was calculated to quantify the relationships within analyte profiles. The composition of GM breeding stacks was more similar to the composition of iso‐hybrids than was the composition of nonGM hybrids. NonGM breeding more strongly influenced crop composition than did transgenesis or stacking of GM events. These findings call into question the value of uniquely requiring composition studies for GM crops, especially for breeding stacks composed of GM events previously found to be compositionally normal. 相似文献
80.
The effect of exercise on body composition and bone mineral density in breast cancer survivors taking aromatase inhibitors 下载免费PDF全文