A comparative radiation hybrid map of sheep chromosome 10

Comparative radiation hybrid (RH) maps of individual ovine chromosomes are essential to identify genes governing traits of economic importance in sheep, a livestock species for which whole genome sequence data are not yet available. The USUoRH5000 radiation hybrid panel was used to generate a RH map of sheep chromosome 10 (OAR10) with 59 markers that span 1,422 cR over an estimated 92 Mb of the chromosome, thus providing markers every 2 Mb (equivalent to every 24 cR). The markers were derived from 46 BAC end sequences (BESs), a single EST, and 12 microsatellites. Comparative analysis showed that OAR10 shares remarkable conservation of gene order along the entire length of cattle chromosome 12 and that OAR10 contains four major homologous synteny blocks, each related to segments of the homologous human chromosome 13. Extending the comparison to the horse, dog, mouse, and chicken genome showed that these blocks share conserved synteny across species.

Spanish America : or, A descriptive, historical, and geographical account of the dominions of Spain in the Western hemisphere, continental and insular; illustrated by a map of Spanish North America, and the West-India islands; a map of Spanish South America, and an engraving, representing the comparative altitudes of the mountains in those regions /

Includes index.

A comparative study of interactive rockclimbing guidebooks and conventional hardcopy guidebooks

Climbing guidebooks have been in existence ever since people started climbing cliffs for recreation. It has only been recently that these guidebooks have started to include photographs to help identification of climbs. To date, there are very few interactive guidebooks that are available online which include the ability to filter climbs and climbing areas based upon specific characteristics. Being able to interrogate a database of climbs and climbing areas by grade, style of climbing, quality of climbing,and length of climbs would be a significant addition to the guidebooks that are currently available. Integrating a fully illustrated database of climbs with open source mapping software such as Google Maps would extend the utility of current guidebooks significantly. As portable devices become more commonplace, the ability to further combine these guidebooks with GPS technology would make the location and identification of climbs much simpler. This study compares conventional hardcopy guidebooks with several online guidebooks. In addition, several Decision Support Systems are analysed to assess the ways in which Geographic Information Systems are integrated to assist in decision making. A prototype interactive guidebook was developed after presenting a survey to a group of climbers to assess what they would find useful in an online resource. This survey found that most climbers would like to see climbs represented on a map of the climbing site in order to aid in locating them. They also suggested that being able to filter climbs by various criteria would be useful. These features were subsequently integrated into the prototype. After review by several climbers it was found that this system has many benefits over conventional hardcopy guidebooks; however, it was also noted that to be even more useful further work needed to be done to improve the functionality of the prototypes. This work would include an ability to print a selection of climbs from those ranges searched.

Dimensions of the third sector : comparative perspectives on structure and change

Cross-nationally, the introduction of New Public Management coincides with a significant growth phase of the nonprofit or third sector. This growth has disproportionately been an expansion of the economic dimensions (employment, turnover) and basically involved the greater use of third sector organisations as service providers. Such provision uses complex contract regimes, and typically takes place in some form of public-private partnership with either public or private funding agencies. Other parts of the third sector such as membership, volunteering and giving have generally grown less. The paper suggests that the sector is becoming qualitatively different, although the nature and strength of this change depends on the nonprofit regime type in a given country. Generally, however, third sector growth has led to differentiation processes that involve new organisational forms, and changes in activities and overall composition. The paper explores the measurement aspects of the quantitative-qualitative jump in third sector development by trying to "map" changes in core facts or dimensions over time. In closing, the paper suggests to examine recombination and refunctionality processes in the third sector.

A comparative study of the semi-elastic and fully-elastic MapReduce models

MapReduce is a computation model for processing large data sets in parallel on large clusters of machines, in a reliable, fault-tolerant manner. A MapReduce computation is broken down into a number of map tasks and reduce tasks, which are performed by so called mappers and reducers, respectively. The placement of the mappers and reducers on the machines directly affects the performance and cost of the MapReduce computation in cloud computing. From the computational point of view, the mappers/reducers placement problem is a generation of the classical bin packing problem, which is NP-complete. Thus, in this paper we propose a new heuristic algorithm for the mappers/reducers placement problem in cloud computing and evaluate it by comparing with other several heuristics on solution quality and computation time by solving a set of test problems with various characteristics. The computational results show that our heuristic algorithm is much more efficient than the other heuristics and it can obtain a better solution in a reasonable time. Furthermore, we verify the effectiveness of our heuristic algorithm by comparing the mapper/reducer placement for a benchmark problem generated by our heuristic algorithm with a conventional mapper/reducer placement which puts a fixed number of mapper/reducer on each machine. The comparison results show that the computation using our mapper/reducer placement is much cheaper than the computation using the conventional placement while still satisfying the computation deadline.

Reconstruction of the ancestral marsupial karyotype from comparative gene maps

BACKGROUND: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n=14 and 2n=22 ancestral marsupial karyotype. RESULTS: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n=14) and therian mammal (2n=19) karyotypes to be reconstructed. CONCLUSIONS: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n=14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Comparative analysis of the Metarhizium anisopliae secretome in response to exposure to the greyback cane grub and grub cuticles

Metarhizium anisopliae is a well-characterized biocontrol agent of a wide range of insects including cane grubs. In this study, a two-dimensional (2D) electrophoresis was used to display secreted proteins of M. anisopliae strain FI-1045 growing on the whole greyback cane grubs and their isolated cuticles. Hydrolytic enzymes secreted by M. anisopliae play a key role in insect cuticle-degradation and initiation of the infection process. We have identified all the 101 protein spots displayed by cross-species identification (CSI) from the fungal kingdom. Among the identified proteins were 64-kDa serine carboxypeptidase, 1,3 beta-exoglucanase, Dynamin GTPase, THZ kinase, calcineurin like phosphoesterase, and phosphatidylinositol kinase secreted by M. ansiopliae (FI-1045) in response to exposure to the greyback cane grubs and their isolated cuticles. These proteins have not been previously identified from the culture supernatant of M. anisopliae during infection. To our knowledge, this the first proteomic map established to study the extracellular proteins secreted by M. ansiopliae (FI-1045) during infection of greyback cane grubs and its cuticles.

Functionally associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.)

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important biological processes was used to detect polymorphic EST–RFLP loci in the F1(NA6 × AU6) population. A comprehensive set of EST–SSR markers was developed from the analysis of 14,767 unigenes, with 310 primer pairs showing efficient amplification and detecting 113 polymorphic loci. Two parental genetic maps were produced: the NA6 genetic map contains 88 EST–RFLP and 71 EST–SSR loci with a total map length of 963 cM, while the AU6 genetic map contains 67 EST–RFLP and 58 EST–SSR loci with a total map length of 757 cM. Bridging loci permitted the alignment of homologous chromosomes between the parental maps, and a sub-set of genomic DNA-derived SSRs was used to relate linkage groups to the perennial ryegrass reference map. Regions of segregation distortion were identified, in some instances in common with other perennial ryegrass maps. The EST-derived marker-based map provides the basis for in silico comparative genetic mapping, as well as the evaluation of co-location between QTLs and functionally associated genetic loci.

The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Using an established genetic map, a single gene conditioning covered smut resistance, Ruh.7H, was mapped to the telomere region of chromosome 7HS in an Alexis/Sloop doubled haploid barley population. The closest marker to Ruh.7H, abg704 was 7.5 cM away. Thirteen loci on the distal end of 7HS with potential to contain single nucleotide polymorphisms (SNPs) were identified by applying a comparative genomics approach using rice sequence data. Of these, one locus produced polymorphic co-dominant bands of different size while two further loci contained SNPs that were identified using the recently developed high resolution melting (HRM) technique. Two of these markers flanked Ruh.7H with the proximal marker located 3.8 cM and the distal marker 2.7 cM away. This is the first report on the application of the HRM technique to SNP detection and to rapid scoring of known cleaved amplified polymorphic sequence (CAPS) markers in plants. This simple, precise post-PCR technique should find widespread use in the fine-mapping of genetic regions of interest in complex cereal and other plant genomes.

DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS

A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (phi,psi and omega) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of alpha-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (phi-psi) are generally used to define secondary structure elements, the geometry of the C-alpha atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C-alpha trace and identify the deviations occurring both at mid-positions as well as at the terminii of alpha-helices, which often lead to occurrence of 3(10) and pi-helical fragments in both globular and membrane proteins.

Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

The Asian elephant Elephas maximus and the African elephant Loxodonta africana that diverged 5-7 million years ago exhibit differences in their physiology, behaviour and morphology. A comparative genomics approach would be useful and necessary for evolutionary and functional genetic studies of elephants. We performed sequencing of E. maximus and map to L. africana at similar to 15X coverage. Through comparative sequence analyses, we have identified Asian elephant specific homozygous, non-synonymous single nucleotide variants (SNVs) that map to 1514 protein coding genes, many of which are involved in olfaction. We also present the first report of a high-coverage transcriptome sequence in E. maximus from peripheral blood lymphocytes. We have identified 103 novel protein coding transcripts and 66-long non-coding (lnc)RNAs. We also report the presence of 181 protein domains unique to elephants when compared to other Afrotheria species. Each of these findings can be further investigated to gain a better understanding of functional differences unique to elephant species, as well as those unique to elephantids in comparison with other mammals. This work therefore provides a valuable resource to explore the immense research potential of comparative analyses of transcriptome and genome sequences in the Asian elephant.

Avaliação Econômica do Biodiesel no Brasil: Investigando a Competitividade e Eficiência do Sistema Produtivo a partir da MAP.

O presente trabalho tem por finalidade realizar uma análise econômica dos possíveis impactos gerados na economia brasileira pelo Programa Nacional de Produção e Uso do Biodiesel (PNPB) e pela Lei N 11.097, que define percentuais mínimos obrigatórios de adição de biodiesel ao óleo diesel. Para atingir tal objetivo, apresenta-se uma avaliação econômica por meio do método de investigação conhecido como Matriz de Análise de Política (MAP). O emprego deste instrumental proporciona uma avaliação em termos de competitividade e eficiência do sistema de produção com base em um estudo comparativo da cadeia produtiva de biodiesel selecionando duas matérias-primas a soja e a mamona. Neste sentido, inicialmente investiga-se a cadeia produtiva do biodiesel no Brasil para diagnosticar as vantagens no que tange a escala de produção, a escolha de matérias-primas, bem como o custo de oportunidade, método de comercialização e distribuição e também a questão tributária. Os resultados da analise econômica revelaram que o emprego do óleo de soja para geração do biodiesel apresenta maior rentabilidade privada e social indicando ser mais competitivo e eficiente frente ao sistema produtivo que emprega o óleo de mamona. Os resultados da pesquisa evidenciando não apenas os aspectos econômicos como os sócio-ambientais favoráveis ao PNPB mostrando que o Brasil tem todas as condições para tornar-se um grande produtor de biodiesel.

Avaliação econômica do biodiesel no Brasil: investigando a competitividade e eficiência do sistema produtivo a partir da MAP

O presente trabalho realiza uma análise econômica dos possíveis impactos gerados na economia brasileira pelo Programa Nacional de Produção e Uso do Biodiesel (PNPB) e pela Lei N 11.097/2005, que define percentuais mínimos obrigatórios de adição de biodiesel ao óleo diesel. Para atingir tal objetivo, apresenta-se uma avaliação econômica por meio de um método de investigação conhecido como Matriz de Análise de Política (MAP). Este instrumental permite uma avaliação em termos de competitividade e eficiência do sistema produtivo de biodiesel com base em um estudo comparativo da cadeia produtiva de biodiesel selecionando duas matérias-primas a soja e a mamona. Neste sentido, inicialmente investiga-se a cadeia produtiva do biodiesel no Brasil para diagnosticar as vantagens no que tange a escala de produção, a escolha de matérias-primas, bem como o custo de oportunidade, método de comercialização e distribuição e também a questão tributária. Por fim são apresentados os resultados da pesquisa evidenciando que os dois sistemas são rentáveis, competitivos e eficientes, no entanto, maiores ganhos, em termos de uso dos recursos disponíveis e de custos de produção podem ser obtidos no sistema de produção do biodiesel a partir da soja. O lucro maior apresentado para a produção de biodiesel da soja permite confirmar a preferência por este sistema de produção dada sua maior rentabilidade.

Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates

Pacific white shrimp (Litopenaeus vannamei) is the leading species farmed in the Western Hemisphere and an economically important aquaculture species in China. In this project, a genetic linkage map was constructed using amplified fragment length polymorphism (AFLP) and microsatellite markers. One hundred and eight select AFLP primer combinations and 30 polymorphic microsatellite markers produced 2071 markers that were polymorphic in either of the parents and segregated in the progeny. Of these segregating markers, 319 were mapped to 45 linkage groups of the female framework map, covering a total of 4134.4 cM; and 267 markers were assigned to 45 linkage groups of the male map, covering a total of 3220.9 cM. High recombination rates were found in both parental maps. A sex-linked microsatellite marker was mapped on the female map with 6.6 cM to sex and a LOD of 17.8, two other microsatellite markers were also linked with both 8.6 cM to sex and LOD score of 14.3 and 16.4. The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map, quantitative trait loci (QTLs) detection, marker-assisted selection (MAS) and comparative genome mapping.