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Implications of Pyrosequencing Error Correction for Biological Data Interpretation
Matthew G. Bakker, Zheng J. Tu, James M. Bradeen, Linda L. Kinkel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0044357
Abstract: There has been a rapid proliferation of approaches for processing and manipulating second generation DNA sequence data. However, users are often left with uncertainties about how the choice of processing methods may impact biological interpretation of data. In this report, we probe differences in output between two different processing pipelines: a de-noising approach using the AmpliconNoise algorithm for error correction, and a standard approach using quality filtering and preclustering to reduce error. There was a large overlap in reads culled by each method, although AmpliconNoise removed a greater net number of reads. Most OTUs produced by one method had a clearly corresponding partner in the other. Although each method resulted in OTUs consisting entirely of reads that were culled by the other method, there were many more such OTUs formed in the standard pipeline. Total OTU richness was reduced by AmpliconNoise processing, but per-sample OTU richness, diversity and evenness were increased. Increases in per-sample richness and diversity may be a result of AmpliconNoise processing producing a more even OTU rank-abundance distribution. Because communities were randomly subsampled to equalize sample size across communities, and because rare sequence variants are less likely to be selected during subsampling, fewer OTUs were lost from individual communities when subsampling AmpliconNoise-processed data. In contrast to taxon-based diversity estimates, phylogenetic diversity was reduced even on a per-sample basis by de-noising, and samples switched widely in diversity rankings. This work illustrates the significant impacts of processing pipelines on the biological interpretations that can be made from pyrosequencing surveys. This study provides important cautions for analyses of contemporary data, for requisite data archiving (processed vs. non-processed data), and for drawing comparisons among studies performed using distinct data processing pipelines.
Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences
Alessandra Traini,Massimo Iorizzo,Harpartap Mann,James M. Bradeen,Domenico Carputo,Luigi Frusciante,Maria Luisa Chiusano
International Journal of Genomics , 2013, DOI: 10.1155/2013/257218
Abstract: Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches. 1. Background The subgenus Potatoe of the Solanaceae family includes approximately 188 tuber-bearing species [1]. They display large ecological adaptation encompassing several traits that are lacking in the commercial potato and useful for breeding [2]. Among wild potato species, Solanum bulbocastanum Dun. and S. commersonii Dun. ex Poir. have attracted the attention of researchers and breeders. S. bulbocastanum is a known source of resistance to late blight disease of potato, and four late blight resistance genes have been cloned from this species to date [3–7]. S. commersonii ranks first among Solanums in terms of cold tolerance and capacity to cold acclimate, and it is also a source of resistance to pathogens such as Ralstonia solanacearum and Pectobacterium carotovorum [8, 9]. S. bulbocastanum and S. commersonii are among approximately 20 diploid potato species classified as superseries Stellata by Hawkes [10]. Despite their importance as sources of genes for crop improvement, relatively few genetic and genomic resources are available for these species, and little is known on their genome organization, gene function, and regulatory networks. Recently, a Diversity Arrays Technology (DArT) array was constructed for potato [11]. The array contains markers derived from various Solanum species, including S. bulbocastanum and S. commersonii. DArT arrays offer the potential to simultaneously survey large numbers of anonymous loci
Apple skin patterning is associated with differential expression of MYB10
Adriana Telias, Kui Lin-Wang, David E Stevenson, Janine M Cooney, Roger P Hellens, Andrew C Allan, Emily E Hoover, James M Bradeen
BMC Plant Biology , 2011, DOI: 10.1186/1471-2229-11-93
Abstract: Here we show that striped areas of 'Honeycrisp' and 'Royal Gala' are due to sectorial increases in anthocyanin concentration. Transcript levels of the major biosynthetic genes and MYB10, a transcription factor that upregulates apple anthocyanin production, correlated with increased anthocyanin concentration in stripes. However, nucleotide changes in the promoter and coding sequence of MYB10 do not correlate with skin pattern in 'Honeycrisp' and other cultivars differing in peel pigmentation patterns. A survey of methylation levels throughout the coding region of MYB10 and a 2.5 Kb region 5' of the ATG translation start site indicated that an area 900 bp long, starting 1400 bp upstream of the translation start site, is highly methylated. Cytosine methylation was present in all three contexts, with higher methylation levels observed for CHH and CHG (where H is A, C or T) than for CG. Comparisons of methylation levels of the MYB10 promoter in 'Honeycrisp' red and green stripes indicated that they correlate with peel phenotypes, with an enrichment of methylation observed in green stripes.Differences in anthocyanin levels between red and green stripes can be explained by differential transcript accumulation of MYB10. Different levels of MYB10 transcript in red versus green stripes are inversely associated with methylation levels in the promoter region. Although observed methylation differences are modest, trends are consistent across years and differences are statistically significant. Methylation may be associated with the presence of a TRIM retrotransposon within the promoter region, but the presence of the TRIM element alone cannot explain the phenotypic variability observed in 'Honeycrisp'. We suggest that methylation in the MYB10 promoter is more variable in 'Honeycrisp' than in 'Royal Gala', leading to more variable color patterns in the peel of this cultivar.Apple peel color is one of the most important factors determining apple market acceptance. In general, red
Sustainable Tourism and Management for Coral Reefs: Preserving Diversity and Plurality in a Time of Climate Change  [PDF]
M. James C. Crabbe
Journal of Service Science and Management (JSSM) , 2010, DOI: 10.4236/jssm.2010.32031
Abstract: Coral reefs throughout the world are under severe challenges from a variety of anthropogenic and environmental factors. In a period of climate change, where mobility and tourism are under threat, it is useful to demonstrate the value of eco- and research-tourism to individuals and to cultures, and how diversity and pluralism in sustainable environments may be preserved. Here we identify the ways in which organisations use research tourism to benefit ecosystem diversity and conservation, show how an Earthwatch project has produced scientific information on the fringing reefs of North Jamaica, and how a capacity-building programme in Belize developed specific action plans for ecotourism. We discuss how implementation of those plans can help research tourism and preserve ecosystem diversity in times of climate change.
Comparison of Two Reef Sites on the North Coast of Jamaica over a 15-Year Period  [PDF]
M. James C. Crabbe
American Journal of Climate Change (AJCC) , 2016, DOI: 10.4236/ajcc.2016.51002
Abstract: This paper compares two reef sites near Discovery Bay, Jamaica, Dairy Bull and Dancing Lady, from 2000 to 2015. At Dairy Bull reef, with low macroalgal cover (8% in 2002 falling to 1% in 2015) and significant number of Diadema antillarum urchins (c. 5 m-2), live coral cover increased from 13% ± 5% in 2006 after the bleaching event in 2005, to 31% ± 7% in 2008, while live Acropora cervicornis increased from 2% ± 2% in 2006 to 28% ± 5% in 2015. Coral cover levels were at least maintained until 2015, owing mostly to a slight increase in A. cervicornis. Dancing Lady reef however was dominated by macroalgae throughout this period (cover of c. 76% ± 7%), with no D. antillarum and showed little decrease in the already low (6% ± 1%) coral cover in 2005. Growth rates for Siderastrea siderea were similar for both sites (7 mm·yr-1), while growth rates of A. cervicornis and A. palmata were 120.0 ± 30 mm·yr-1 and 71.0 ± 29 mm·yr-1 respectively at Dairy Bull in 2015. At Dancing Lady reef, A. cervicornis colonies which were present from 2003 to 2005 had disappeared in 2006, possibly as a result of the mass bleaching event. It appears that A. cervicornis was the most impacted species during the 2005 bleaching event, but was also the species that recovered fastest after its decline at Dairy Bull.
Creating New Identities: Chinese American Women Professionals in Greater Baltimore  [PDF]
James M. Smith
Advances in Anthropology (AA) , 2016, DOI: 10.4236/aa.2016.62004
Abstract: This qualitative paper explores the attitudes, values and social practices of a small group of first generation Chinese American professional women in the Greater Baltimore Region. The research focuses on ethnic self-ascription, marriage, dating and interethnic social relations. To explore boundary persistence and acculturation, informants answered an online survey. After this stage, several informants were interviewed in a semi-structured format. Qualitative analysis suggests that Chinese immigrants selectively acculturate through situational interaction with co-ethnic and out-group actors. Informants interact with non-co ethnics at work, and increasingly in non-work settings. Some date and marry outside of the ethnic label, though most marry within group. In areas such as culinary habits and parenting, cultural attitudes and practices deemed “Chinese” prevail, but values identified as Chinese can vary by individual. Within the Chinese ethnic category, informants tend to prefer interaction with Chinese from the same region in China. Yet, interethnic dating and marriage do not necessarily weaken ethnic identity persistence. The central point is that Chinese American ethnic expression varies by individual, and is framed within place specific multi-scalar structures of regional culture, economy and attitudes toward immigrants and race.
California’s Citizen Redistricting Commission, Electoral Competitiveness and Political Polarization  [PDF]
James M. De Vault
Open Journal of Political Science (OJPS) , 2016, DOI: 10.4236/ojps.2016.64036
Abstract: Passage of Proposition 20 in California in 2010 transferred the power to redistrict congressional seats from the state legislature to a new independent redistricting commission. The goals of this transfer were to increase electoral accountability, to reduce partisan bias, to promote greater transparency and to bolster public trust. In this paper, I analyze the impact of Proposition 20 on electoral accountability by examining its effect on electoral competitiveness and political polarization. The evidence in the paper demonstrates that Proposition 20 has enhanced competitiveness and reduced polarization but that these effects are modest to date.
Metapopulations and the Sinai Baton Blue (Pseudophilotes sinaicus Nakamura): an introduction
M James
Egyptian Journal of Biology , 2006,
Abstract:
Immigration and emigration in the Sinai Baton Blue butterfly: estimates from a single patch
M James
Egyptian Journal of Biology , 2006,
Abstract: The movement of individuals among patches of suitable habitat is a key process in metapopulation biology, but is very difficult to observe under natural conditions. Thus, many estimates of rates of movement are indirect and incomplete, and there is little empirical knowledge of the factors affecting immigration and emigration. I studied intensively a local population of Sinai Baton Blue butterflies in a discrete habitat patch. The study lasted the entire adult flight period, and involved almost every individual in the local population. Using these data I attempted to estimate the number of immigrants and emigrants, and identified an important factor affecting inter-patch movement. Early in the season, individuals were resident in the study patch for only a very short time; I assumed this was because they were emigrating, and thus estimated that at least 14% of the population emerging in the study patch emigrated. I assumed that butterflies not caught until they were relatively old, had immigrated to the patch (rather than being missed at a young age), and thus estimated that 13% of the population caught in the patch was composed of immigrants, most of which were females. Individuals assumed to be immigrants arrived in the patch throughout the adult flight period, but older individuals generally arrived later in the season. Timing of migration was almost certainly linked to phenology of the butterfly’s only hostplant, Sinai Thyme. Most butterflies remained in their natal patch. The degree of inter-patch movement estimated using this method was consistent with other metapopulation studies, and would suffice for this species to exist as a metapopulation.
Intra-patch movement in the Sinai Baton Blue butterfly: influence of micro-habitat and individual characteristics
M James
Egyptian Journal of Biology , 2006,
Abstract: Dispersal is a key process in metapopulation biology. The transfer of individuals among patches of suitable habitat has been widely studied, and rates of movement and the factors influencing these investigated. However, relatively few metapopulation studies have examined movement of individuals within a patch of habitat, and none of these have related intra-patch movement to inter-patch movement (dispersal). The intra-patch movement of a narrowly endemic butterfly Pseudophilotes sinaicus (Lycaenidae) that exists in a metapopulation structure was studied. It was found to be extremely sedentary, rarely moving more than 40 m in or between days, and occupying a very small area during its residency of the study patch. Its level of movement (distance between sightings) and the factors affecting this depended on its sex, and was primarily determined by the density of conspecifics in its immediate vicinity. Other factors also influenced movement, notably the phenology and size of hostplants in an individual’s immediate vicinity. Responding to these variables in a predictable way can be regarded as strategies enabling the butterfly to locate mates, food, and oviposition sites, and to escape resource depletion, and intraspecific competitors. These behavioural patterns are similar to mechanisms involved in dispersal of individuals among patches of habitat in fragmented landscapes.
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