Applying uniqueness to the Java language

In this thesis we investigates the use of static guards to ensure that given variables will only contain a unique reference to a value. Unique references can help guard against race conditions and protect resources from simultaneous multiple uses. We analyze the interactions between the uniqueness property and several Java language features, defining additional weaker properties that are helpful in creating a usable system of uniqueness annotations. The system of annotations conforms to JSR (Java Specification Request) 308 (Annotations on Java Types). A post-processor based on the JSR 308 library statically checks that a program's uniqueness properties have been correctly annotated

Virtual Experts for Imagery Registration and Conflation

Abstract. The unique human expertise in imagery analysis should be preserved and shared with other imagery analysts to improve image analysis and decision-making. Such knowledge can serve as a corporate memory and be a base for an imagery virtual expert. The core problem in reaching this goal is constructing a methodology and tools that can assist in building the knowledge base of imagery analysis. This paper provides a framework for an imagery virtual expert system that supports imagery registration and conflation tasks. The approach involves two strategies: (1) recording expertise onthe-fly and (2) extracting information from the expert system in an optimized way. The second strategy is based on the theory of monotone Boolean functions

Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank

Deep sequencing technology has enabled the analysis of small RNA profiles of virus-infected plants and could provide insights into virus–host interactions. Potato virus Y is an economically important viral pathogen of potato worldwide. In this study, we investigated the nature and relative levels of virus-derived small interfering RNAs (vsiRNAs) in potato cv. Russet Burbank infected with three biologically distinct and economically important strains of PVY, the ordinary strain (PVY-O), tobacco veinal-necrotic strain (PVY-N) and tuber necrotic strain (PVY-NTN). The analysis showed an overall abundance of vsiRNAs of 20–24 nt in PVY-infected plants. Considerable differences were present in the distribution of vsiRNAs as well as total small RNAs. The 21 nt class was the most prevalent in PVY-infected plants irrespective of the virus strain, whereas in healthy potato plants, the 24 nt class was the most dominant. vsiRNAs were derived from every position in the PVY genome, though certain hotspots were identified for each of the PVY strains. Among the three strains used, the population of vsiRNAs of different size classes was relatively different with PVY-NTN accumulating the highest level of vsiRNAs, while PVY-N infected plants had the least population of vsiRNAs. Unique vsiRNAs mapping to PVY genome in PVY-infected plants amounted to 3.13, 1.93 and 1.70% for NTN, N and O, respectively. There was a bias in the generation of vsiRNAs from the plus strand of the genome in comparison to the negative strand. The highest number of total vsiRNAs was from the cytoplasmic inclusion protein gene (CI) in PVY-O and PVY-NTN strains, whereas from PVY-N, the NIb gene produced maximum total vsiRNAs. These findings indicate that the three PVY strains interact differently in the same host genetic background and provided insights into virus–host interactions in an important food crop

Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes

Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica) to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana) plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach), Malus × domestica (Apple), Populus trichocarpa (Black cottonwood), Fragaria vesca (Woodland Strawberry), Solanum lycopersicum (Tomato) and Vitis vinifera (Grapevine) also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of knowledge regarding plastid biology, preferentially based on model systems is deficient. New plant genomes are expected to enable the identification of potentially new plastid-targeted proteins that will aid in studying novel roles of plastids

Percentage of unique plastid proteome containing GO information.

<p>Plastid-targeted proteins were analyzed using Blast2GO to identify GO terms associated with each protein sequence. With the exception of <i>Arabidopsis,</i> significant proportions of chloroplast-targeted proteins datasets lack GO term information. This further increases in the datasets comprised of chloroplast-targeted proteins unique to each investigated species.</p><p>Percentage of unique plastid proteome containing GO information.</p

GO terms enriched in uniquely plastid-targeted proteins identified with UCLUST 50% method.

<p>Blast2GO was used to determine GO terms associated with all predicted plastid-targeted proteins. Enrichment analysis was performed with agriGO to identify significant enriched GO terms. Gene Ontology terms are provided for biological process (P), molecular function (F), and cellular component (C).</p><p>GO terms enriched in uniquely plastid-targeted proteins identified with UCLUST 50% method.</p

Results of putative plastid-targeted protein prediction.

<p>Predicted transcripts were selected from 7 sequenced genomes representing both model organisms as well as agriculturally important fruit-producing crops. Translated sequences were analyzed using TargetP to predict cellular localization. Sequences were clustered with 40% coverage and 40% identity to predict proteins unique to the plastid proteome of each species. *Represents sequences from Chloroplast 2010 project and sequences associated with predicted plastid-targeted embryo lethal mutant.</p><p>Results of putative plastid-targeted protein prediction.</p

GO terms enriched in <i>Arabidopsis thaliana</i> members of the 289 plastid-targeted protein clusters shared between all species investigated.

<p>GO terms from the 497 <i>Arabidopsis thaliana</i> proteins present within the 289 shared clusters were analyzed by agriGO to identify enriched GO terms. Chi-square test was performed with a p-value cutoff of 0.01.</p><p>GO terms enriched in <i>Arabidopsis thaliana</i> members of the 289 plastid-targeted protein clusters shared between all species investigated.</p

Uniquely targeted plastid-targeted protein sequences.

<p>A USEARCH comparison of plastid-targeted protein datasets was performed at 40% identity and 40% coverage against a database containing the chloroplast protein sequences from all six other species investigated in this study. A second comparison was performed against a database containing the entire protein set from the other species. An increase in matching suggests the presence of differentially localized homologues in other systems. Additionally, these results suggest a sizeable number of plastid-targeted proteins may be unique to each species.</p><p>Uniquely targeted plastid-targeted protein sequences.</p

Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing

BACKGROUND: Sweet cherry (Prunus avium L.), a non-model crop with narrow genetic diversity, is an important member of sub-family Amygdoloideae within Rosaceae. Compared to other important members like peach and apple, sweet cherry lacks in genetic and genomic information, impeding understanding of important biological processes and development of efficient breeding approaches. Availability of single nucleotide polymorphism (SNP)-based molecular markers can greatly benefit breeding efforts in such non-model species. RNA-seq approaches employing second generation sequencing platforms offer a unique avenue to rapidly identify gene-based SNPs. Additionally, haplotype markers can be rapidly generated from transcript-based SNPs since they have been found to be extremely utile in identification of genetic variants related to health, disease and response to environment as highlighted by the human HapMap project. RESULTS: RNA-seq was performed on two sweet cherry cultivars, Bing and Rainier using a 3' untranslated region (UTR) sequencing method yielding 43,396 assembled contigs. In order to test our approach of rapid identification of SNPs without any reference genome information, over 25% (10,100) of the contigs were screened for the SNPs. A total of 207 contigs from this set were identified to contain high quality SNPs. A set of 223 primer pairs were designed to amplify SNP containing regions from these contigs and high resolution melting (HRM) analysis was performed with eight important parental sweet cherry cultivars. Six of the parent cultivars were distantly related to Bing and Rainier, the cultivars used for initial SNP discovery. Further, HRM analysis was also performed on 13 seedlings derived from a cross between two of the parents. Our analysis resulted in the identification of 84 (38.7%) primer sets that demonstrated variation among the tested germplasm. Reassembly of the raw 3'UTR sequences using upgraded transcriptome assembly software yielded 34,620 contigs containing 2243 putative SNPs in 887 contigs after stringent filtering. Contigs with multiple SNPs were visually parsed to identify 685 putative haplotypes at 335 loci in 301 contigs. CONCLUSIONS: This approach, which leverages the advantages of RNA-seq approaches, enabled rapid generation of gene-linked SNP and haplotype markers. The general approach presented in this study can be easily applied to other non-model eukaryotes irrespective of the ploidy level to identify gene-linked polymorphisms that are expected to facilitate efficient Gene Assisted Breeding (GAB), genotyping and population genetics studies. The identified SNP haplotypes reveal some of the allelic differences in the two sweet cherry cultivars analyzed. The identification of these SNP and haplotype markers is expected to significantly improve the genomic resources for sweet cherry and facilitate efficient GAB in this non-model crop