Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from anal...CIAT
This study aimed to clarify the phylogenetic relationships among wild Manihot species using DNA sequence data from chloroplast regions, a nuclear gene, and two nuclear sequences from cassava ESTs. Maximum parsimony and Bayesian analyses on the combined data supported some previously proposed species groupings but also showed inconsistencies with current taxonomic sections. Estimated divergence times placed the origin of the Manihot genus around 6.6 million years ago, coinciding with the origin of species in the Cerrado ecosystem of Brazil, where most Manihot species are found. The results support a recent and rapid diversification of the genus.
1) The researchers sequenced and analyzed the genomes of domesticated tomato and its wild relative Solanum pimpinellifolium.
2) They found the two tomato genomes show only 0.6% nucleotide divergence, indicating recent admixture, but more than 8% divergence from potato.
3) Comparative analysis revealed the Solanum lineage experienced two genome triplications, one ancient and shared with other plants and one more recent, providing material for genes controlling fruit traits like color and fleshiness to evolve.
Por primera vez, el genoma del tomate (Solanum lycopersicum) , ha sido descifrado completamente. Esto es en un paso importante hacia la mejora del rendimiento, la nutrición, la resistencia a las enfermedades, el sabor y el color del tomate y otros cultivos similares. La secuencia completa del genoma de la variedad Heinz 1706 así como la secuencia de un pariente silvestre, fue publicado en el último número de la revista Nature .
Los investigadores del Consorcio formado por investigadores de numerosos países informó que los tomates tienen unos 35.000 genes organizados en 12 cromosomas.
Las secuencias de estos genes y su disposición en los cromosomas se describen en el artículo de Nature. Esta información permitirá a los investigadores avanzar a un ritmo más rápido y a los criadores de plantas para producir nuevas variedades con determinadas características deseadas.
Ahora que la secuencia del genoma de esta variedad de tomate se conoce también será más fácil y mucho menos costoso conocer la secuencia de otras variantes de esta planta. Teniendo como molde la secuencia de esta variedad que costó millones de dólares permitirá conocer a muy bajo costo (10,000 dólares o menos) las secuencias de otras variedades.
Para facilitar el acceso a las secuencias de los genes del tomate y las especies afines han creado un sitio web interactivo ( www.solgenomics.net ).
La secuenciación del genoma del tomate tiene implicaciones para otras especies de plantas. Fresas, manzanas, melones, plátanos y otros muchos frutos carnosos, quienes comparten algunas características con los tomates, por lo que la información sobre los genes y las vías involucradas en la maduración del fruto potencialmente se puede aplicar a ellos, ayudando a mejorar la calidad de los alimentos, la seguridad alimentaria y reducir los costos de cultivo.
Comparative genome mapping involves comparing genetic maps between closely related species to study genome evolution and understand relationships at the genetic level. Genomes can be compared by looking at features like gene location and order, as well as sequence similarity. Many model systems have been used for comparative mapping, including plants like rice and maize, Arabidopsis and Brassica, tomato and potato. These studies have revealed things like conserved synteny between species, rates of rearrangement, and the effects of polyploidization. Comparative mapping is a useful tool for understanding genomes and their relationships across species.
This research article discusses the lateral transfer of group I introns between red and brown algae. The researchers found that a group I intron inserted at position 516 in the small subunit rRNA contained a unique helical insertion in the P5b helix in both bangiophyte red algae and the brown alga Aureoumbra lagunensis, though the host cells are evolutionarily distant. They analyzed the secondary structure and phylogeny of these introns to understand their origin. The highly conserved structure of the insertion suggests it is important functionally, though its specific role is unknown. Their analyses support the scenario that the intron was laterally transferred between red and brown algae after their divergence, rather than being present in
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from anal...CIAT
This study aimed to clarify the phylogenetic relationships among wild Manihot species using DNA sequence data from chloroplast regions, a nuclear gene, and two nuclear sequences from cassava ESTs. Maximum parsimony and Bayesian analyses on the combined data supported some previously proposed species groupings but also showed inconsistencies with current taxonomic sections. Estimated divergence times placed the origin of the Manihot genus around 6.6 million years ago, coinciding with the origin of species in the Cerrado ecosystem of Brazil, where most Manihot species are found. The results support a recent and rapid diversification of the genus.
1) The researchers sequenced and analyzed the genomes of domesticated tomato and its wild relative Solanum pimpinellifolium.
2) They found the two tomato genomes show only 0.6% nucleotide divergence, indicating recent admixture, but more than 8% divergence from potato.
3) Comparative analysis revealed the Solanum lineage experienced two genome triplications, one ancient and shared with other plants and one more recent, providing material for genes controlling fruit traits like color and fleshiness to evolve.
Por primera vez, el genoma del tomate (Solanum lycopersicum) , ha sido descifrado completamente. Esto es en un paso importante hacia la mejora del rendimiento, la nutrición, la resistencia a las enfermedades, el sabor y el color del tomate y otros cultivos similares. La secuencia completa del genoma de la variedad Heinz 1706 así como la secuencia de un pariente silvestre, fue publicado en el último número de la revista Nature .
Los investigadores del Consorcio formado por investigadores de numerosos países informó que los tomates tienen unos 35.000 genes organizados en 12 cromosomas.
Las secuencias de estos genes y su disposición en los cromosomas se describen en el artículo de Nature. Esta información permitirá a los investigadores avanzar a un ritmo más rápido y a los criadores de plantas para producir nuevas variedades con determinadas características deseadas.
Ahora que la secuencia del genoma de esta variedad de tomate se conoce también será más fácil y mucho menos costoso conocer la secuencia de otras variantes de esta planta. Teniendo como molde la secuencia de esta variedad que costó millones de dólares permitirá conocer a muy bajo costo (10,000 dólares o menos) las secuencias de otras variedades.
Para facilitar el acceso a las secuencias de los genes del tomate y las especies afines han creado un sitio web interactivo ( www.solgenomics.net ).
La secuenciación del genoma del tomate tiene implicaciones para otras especies de plantas. Fresas, manzanas, melones, plátanos y otros muchos frutos carnosos, quienes comparten algunas características con los tomates, por lo que la información sobre los genes y las vías involucradas en la maduración del fruto potencialmente se puede aplicar a ellos, ayudando a mejorar la calidad de los alimentos, la seguridad alimentaria y reducir los costos de cultivo.
Comparative genome mapping involves comparing genetic maps between closely related species to study genome evolution and understand relationships at the genetic level. Genomes can be compared by looking at features like gene location and order, as well as sequence similarity. Many model systems have been used for comparative mapping, including plants like rice and maize, Arabidopsis and Brassica, tomato and potato. These studies have revealed things like conserved synteny between species, rates of rearrangement, and the effects of polyploidization. Comparative mapping is a useful tool for understanding genomes and their relationships across species.
This research article discusses the lateral transfer of group I introns between red and brown algae. The researchers found that a group I intron inserted at position 516 in the small subunit rRNA contained a unique helical insertion in the P5b helix in both bangiophyte red algae and the brown alga Aureoumbra lagunensis, though the host cells are evolutionarily distant. They analyzed the secondary structure and phylogeny of these introns to understand their origin. The highly conserved structure of the insertion suggests it is important functionally, though its specific role is unknown. Their analyses support the scenario that the intron was laterally transferred between red and brown algae after their divergence, rather than being present in
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
The document discusses molecular biology research on the fungus Monascus spp. It provides details on:
1) Molecular markers that have been used to classify Monascus spp., including RAPD, D1/D2 regions of LSU rRNA, ITS, IGS, ISSR, and SRAP. These markers revealed genetic diversity and grouped species.
2) Genetic transformation techniques for Monascus spp., such as protoplast transformation, electroporation, bombardment, REMI, and ATMT. Protoplast transformation was successfully used to create mitotically stable transformants of M. aurantiacus and M. purpureus.
3) Cloning of some genes from Mon
This document reports on a study comparing the karyotypes and protein profiles of three Trifolium species: T. alexandrinum, T. refeigratum, and T. repens. The results found that T. refeigratum and T. repens both have 16 pairs of chromosomes with one pair containing satellites, while T. alexandrinum has 8 pairs of chromosomes. Analysis of the karyotypes showed differences in symmetry indices between the species. Protein profile analysis via SDS-PAGE revealed clustering of T. alexandrinum separately from the other two species, indicating polymorphic protein bands that differ. The study provides cytological and protein evidence to compare the three clover species
The document discusses the topic of phylogenetics. It begins with definitions of key terms like phylogeny, phylogenetic tree, clade, and orthologous genes. It then provides examples of how phylogenetic methods are used in fields like epidemiology, conservation biology, and pharmaceutical research. The document also discusses choosing appropriate genetic sequences to use in phylogenetic analysis and introduces molecular clock models.
This study analyzed the occurrence and diversity of integrons in bacteria isolated from an urban wastewater treatment plant. A total of 697 isolates of Enterobacteriaceae and Aeromonas were screened for integrons. Three new gene cassettes were identified, including a novel aadA variant and genes involved in cell signaling and unknown functions. Thirteen different gene cassette arrays were detected, with four representing novel integrons. Approximately 80% of isolates were resistant to at least 3 antibiotic classes. The presence of novel integron structures in treated effluent suggests wastewater treatment plants may facilitate the formation and spread of antibiotic resistance genes.
This document summarizes research on the mitochondrial large subunit rRNA gene sequence and microevolution in the ciliate Paramecium. Key findings include:
- The large subunit rRNA gene complex in Paramecium consists of a 283-base "5.8S-like" segment followed by the previously described 20S segment.
- The gene sequences from Paramecium primaurelia and Paramecium tetraurelia were 4% divergent.
- The genes lie adjacent to each other near the end of the linear mitochondrial genome and are transcribed from a common 23S precursor.
- Precise gene boundaries were determined using nuclease protection assays. The complex spans approximately 2654 base pairs.
This document outlines the schedule and requirements for a genomics course consisting of 9 sessions over March and May. Students are required to attend all sessions and give one 20-minute seminar and write one essay. Seminars will be 15% of the final grade and essays will also be 15%, with a final exam making up the remaining 70% of the grade. Topics for the seminars and essays will be assigned.
The ribosomal RNA gene unit of Tritrichomonas foetus was cloned and analyzed. Southern blot analysis showed the rDNA unit is organized as a tandem head to tail repeat of 6 kb, with 12 copies present. The small subunit rRNA is one of the shortest reported at 1571 bp, while the 5.8S rRNA is 159 bp. Northern blot analysis detected primary and precursor rRNA transcripts of 5.8 kb and 4 kb. Sequence analysis confirmed the secondary structure of the small subunit rRNA is similar to other eukaryotes, while being shorter in variable regions.
Nature GeNetics VOLUME 46 NUMBER 10 OCTOBER 2014 1 0 8 9.docxgemaherd
Nature GeNetics VOLUME 46 | NUMBER 10 | OCTOBER 2014 1 0 8 9
A suite of forces and factors, including mutation, recombination,
selection, population history and gene duplication influence patterns
of intraspecific genetic variation. Distinguishing which factors have
shaped sequence variation across a genome requires extensive whole-
genome sequencing of multiple individuals, which has only recently
become tractable1. Most large-scale whole-genome resequencing
studies have focused on model and domesticated species1–5. However,
extensive sequencing of natural populations holds great promise for
advancing understanding of evolutionary biology, including identify-
ing functional variation and the molecular bases of adaptation. Recent
work in a number of species has identified genomic regions that show
signatures of positive selection, suggesting that such regions contain
loci that control adaptive traits4,6–8. Relatively few studies, however,
have combined genome-wide scans with phenotypic data to determine
whether computationally identified selected regions influence adap-
tive phenotypic variation5,9–13. Genome-wide studies of large natural
populations combined with phenotypic measurements are necessary
to determine which factors shape patterns of genetic variation within
species and, therefore, enhance understanding of adaptation.
With large geographic ranges spanning wide environmental gradi-
ents and a long history of research showing local adaptation14, forest
trees are ideal for examining the processes shaping genetic variation
in natural populations. Forest trees cover approximately 30% of ter-
restrial land area15, provide direct feedback to global climate15 and
are often foundation species that organize entire biotic communities
and biogeochemical systems16,17. Clearly, biotic and abiotic interac-
tions have influenced population sizes and distributions of forest
trees, leaving diagnostic signatures in the genomes of present-day
populations14,18,19. A deeper understanding of the evolutionary and
ecological forces that shaped these patterns will offer insights and
options for ecosystem management, applied tree improvement and
accelerated domestication efforts20.
Black cottonwood, Populus trichocarpa Torr. & Gray, is a dominant
riparian tree that has become a model for the advancement of genome-
level insights in forest trees21. The sequencing of 16 P. trichocarpa
genomes revealed widespread patterns of linkage disequilibrium (LD)
and population structure22 and extensive genecological studies have
revealed a high degree of adaptive phenotypic variation in growth,
vegetative phenology and physiological traits such as water-use effi-
ciency and photosynthesis23–25, suggesting that local adaptation is
prevalent. To date, candidate gene–association analyses have revealed
loci with significant effects on phenotypic traits26,27. However, thus
far there have been no publications describing whole-genome asso-
.
Nature GeNetics VOLUME 46 NUMBER 10 OCTOBER 2014 1 0 8 9.docxvannagoforth
Nature GeNetics VOLUME 46 | NUMBER 10 | OCTOBER 2014 1 0 8 9
A suite of forces and factors, including mutation, recombination,
selection, population history and gene duplication influence patterns
of intraspecific genetic variation. Distinguishing which factors have
shaped sequence variation across a genome requires extensive whole-
genome sequencing of multiple individuals, which has only recently
become tractable1. Most large-scale whole-genome resequencing
studies have focused on model and domesticated species1–5. However,
extensive sequencing of natural populations holds great promise for
advancing understanding of evolutionary biology, including identify-
ing functional variation and the molecular bases of adaptation. Recent
work in a number of species has identified genomic regions that show
signatures of positive selection, suggesting that such regions contain
loci that control adaptive traits4,6–8. Relatively few studies, however,
have combined genome-wide scans with phenotypic data to determine
whether computationally identified selected regions influence adap-
tive phenotypic variation5,9–13. Genome-wide studies of large natural
populations combined with phenotypic measurements are necessary
to determine which factors shape patterns of genetic variation within
species and, therefore, enhance understanding of adaptation.
With large geographic ranges spanning wide environmental gradi-
ents and a long history of research showing local adaptation14, forest
trees are ideal for examining the processes shaping genetic variation
in natural populations. Forest trees cover approximately 30% of ter-
restrial land area15, provide direct feedback to global climate15 and
are often foundation species that organize entire biotic communities
and biogeochemical systems16,17. Clearly, biotic and abiotic interac-
tions have influenced population sizes and distributions of forest
trees, leaving diagnostic signatures in the genomes of present-day
populations14,18,19. A deeper understanding of the evolutionary and
ecological forces that shaped these patterns will offer insights and
options for ecosystem management, applied tree improvement and
accelerated domestication efforts20.
Black cottonwood, Populus trichocarpa Torr. & Gray, is a dominant
riparian tree that has become a model for the advancement of genome-
level insights in forest trees21. The sequencing of 16 P. trichocarpa
genomes revealed widespread patterns of linkage disequilibrium (LD)
and population structure22 and extensive genecological studies have
revealed a high degree of adaptive phenotypic variation in growth,
vegetative phenology and physiological traits such as water-use effi-
ciency and photosynthesis23–25, suggesting that local adaptation is
prevalent. To date, candidate gene–association analyses have revealed
loci with significant effects on phenotypic traits26,27. However, thus
far there have been no publications describing whole-genome asso-
...
This document discusses constructing phylogenetic trees to analyze the evolutionary relationships between bacteria, archaea, and eukarya based on nuclear, membrane, and metabolic genes. 18 organisms were selected from each domain and their 16S rRNA, 18S rRNA, and gene sequences were obtained from databases. Multiple sequence alignments were performed and phylogenetic trees were constructed to compare the relationships depicted in the gene trees to the standard rRNA tree of life.
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees...Jonathan Eisen
Lang JM, Darling AE, Eisen JA (2013) Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510
The document summarizes research on sequencing part of the ribosomal RNA coding region and determining the secondary structure of the 25S rRNA of Candida albicans. Key findings include:
- A rDNA cistron from C. albicans strain WO-1 was cloned and sequencing revealed the ITS1, ITS2, 5.8S rDNA and 25S rDNA coding regions.
- The C. albicans ITS regions are shorter than those of most other eukaryotes.
- The 5.8S and 25S rDNA sequences were used to model the secondary structure, which was compared to other species.
- Variable regions in the 25S r
The document summarizes a study that identified components of the BRL3 receptor complex in Arabidopsis thaliana plants through immunoprecipitation and mass spectrometry analysis. The study found that BAK1 and other known BR signaling proteins interact with BRL3. Genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that the BAK1, BRL1, and BRL3 signaling pathways regulate root growth and development by modulating the activities of provascular and quiescent center cells. This provides evidence that cell-specific BR receptor complexes assemble to direct different cellular activities during root development.
The document discusses H2A.Z, a histone variant. A recent study showed that the H2A.Z nucleosome structure was altered without changes to the H2A structure, avoiding clashes. As a result, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z nucleosome. The presence of H2A versus H2A.Z in the histone octamer affects nucleosome stability. H2A.Z accumulation around transcriptional start sites promotes transcriptional initiation, and it is required for activation of the Flowering Locus C gene in Arabidopsis.
Genetic diversity in wild and cultivated peanut_Khanal_2008Sameer Khanal
This document summarizes genetic diversity research on wild and cultivated peanut species. It describes mining genome survey sequences from diploid and tetraploid peanuts to develop simple sequence repeat (SSR) markers. Ninety-three polymorphic SSR markers were developed that showed high diversity among diploid species. Expressed sequence tags were also mined for SSRs, resulting in 19 polymorphic markers. The markers were used to analyze genetic diversity and population structure among peanut accessions. Dinucleotide repeats were found to be the most common and polymorphic repeat type. Studies on diploid peanut species with additional SSR markers aimed to estimate diversity and decipher population structure.
Development of a core set of single-locus SSR markers for allotetraploid rape...Eric Du
This document describes the development of a set of 230 single-locus SSR markers for Brassica napus (oilseed rape). The researchers collected existing SSR markers and developed new ones from genomic sequences of related Brassica species. They screened the markers on a set of rapeseed inbred lines and identified 2,701 that produced single amplicons, indicating they were putative single-locus markers. They then genetically mapped 230 high-quality single-locus SSR markers to the 19 linkage groups of B. napus using a segregating population. A subset of 78 markers was validated across 45 inbred lines and hybrids, demonstrating their stability. Most markers also showed single-locus behavior in other Brassica
This document describes the development of a set of 230 single-locus SSR markers for Brassica napus (oilseed rape). The researchers collected existing SSR markers and developed new ones from genomic sequences of related Brassica species. They screened the markers on a set of rapeseed inbred lines and identified 2,701 that produced single amplicons, indicating they were putative single-locus markers. They then genetically mapped 230 high-quality single-locus SSR markers to the 19 linkage groups of B. napus using a segregating population. A subset of 78 markers was validated across 45 inbred lines and hybrids, demonstrating their stability. Most markers also showed single-locus behavior in other Brassica
· Describe strategies to build rapport with inmates and offenders .docxgerardkortney
· Describe strategies to build rapport with inmates and offenders in a correctional treatment or supervision program.
· Describe the effect of group dynamics on facilitating programs.
· Describe techniques for establishing a therapeutic environment.
Generalist Case Management
Woodside and McClam
https://phoenix.vitalsource.com/books/9781483342047/pageid/44
https://phoenix.vitalsource.com/#/books/9781323128800
https://phoenix.vitalsource.com/#/books/9781483342047
https://phoenix.vitalsource.com/#/books/9781133795247
https://phoenix.vitalsource.com/#/books/1259760413
Use book and two outside sources.
At least 100 words per question
THANKS
1 The Role of the Correctional Counselor CHAPTER OBJECTIVES After reading this chapter, you will be able to: 1. Identify the functions and parameters of the counseling process. 2. Discuss the competing interests between security and counseling in the correctional counseling process. 3. Know common terms and concerns associated with custodial corrections. 4. Understand the role of the counselor as facilitator. 5. Identify the various personal characteristics associated with effective counselors. 6. Be aware of the impact that burnout can have on a counselor’s professional performance. 7. Identify the various means of training and supervision associated with counseling. PART ONE: A BRIEF INTRODUCTION TO COUNSELING AND CORRECTIONS There are many myths concerning the concept of counseling. Although the image of the counseling field has changed dramatically over the past two or three decades, much of society still views counseling and therapy as a mystic process reserved for those who lack the ability to handle life issues effectively. While the concept of counseling is often misunderstood, the problem is exacerbated when attempting to introduce the idea of correctional counseling. Therefore, the primary goal of this chapter is to provide a working definition of correctional counseling that includes descriptions of how and when it is carried out. In order to understand the concept of correctional counseling, however, the two words that derive the concept must first be defined: “corrections” and “counseling.” In addition, a concerted effort is made to identify the myriad of legal and ethical issues that pertain to counselors working with offenders. It is very difficult to identify a single starting point for the counseling profession. In essence, there were various movements occurring simultaneously that later evolved into what we now describe as counseling. One of the earliest connections to the origins of counseling took place in Europe during the Middle Ages (Brown & Srebalus, 2003). The primary objective was assisting individuals with career choices. This type of counseling service is usually described by the concept of “guidance.” In the late 1800s Wilhelm Wundt and G. Stanley Hall created two of the first known psychological laboratories aimed at studying and treating individuals with psychological and e.
· Debates continue regarding what constitutes an appropriate rol.docxgerardkortney
· Debates continue regarding what constitutes an appropriate role for the judiciary. Some argue that federal judges have become too powerful and that judges “legislate from the bench.”
1. What does it mean for a judge to be an activist?
2. What does it mean for a judge to be a restrainist?
· Although conservatives had long complained about the activism of liberal justices and judges, in recent years conservative judges and justices have been likely to overturn precedents and question the power of elected institutions of government.
3. When is judicial activism appropriate? Explain.
· To defenders of the right to privacy, it is implicitly embodied in the Constitution in the First, Fourth, Fifth, Ninth, and Fourteenth Amendments. To opponents, it is judge-made law because there is no explicit reference to it under the Constitution. The right to privacy dates back to at least 1890, when Boston attorneys Samuel Warren and Louis Brandeis equated it with the right to be left alone from journalists who engaged in yellow journalism.
4. In short, do you believe a right to privacy exists in the federal Constitution. Why or why not?
.
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
The document discusses molecular biology research on the fungus Monascus spp. It provides details on:
1) Molecular markers that have been used to classify Monascus spp., including RAPD, D1/D2 regions of LSU rRNA, ITS, IGS, ISSR, and SRAP. These markers revealed genetic diversity and grouped species.
2) Genetic transformation techniques for Monascus spp., such as protoplast transformation, electroporation, bombardment, REMI, and ATMT. Protoplast transformation was successfully used to create mitotically stable transformants of M. aurantiacus and M. purpureus.
3) Cloning of some genes from Mon
This document reports on a study comparing the karyotypes and protein profiles of three Trifolium species: T. alexandrinum, T. refeigratum, and T. repens. The results found that T. refeigratum and T. repens both have 16 pairs of chromosomes with one pair containing satellites, while T. alexandrinum has 8 pairs of chromosomes. Analysis of the karyotypes showed differences in symmetry indices between the species. Protein profile analysis via SDS-PAGE revealed clustering of T. alexandrinum separately from the other two species, indicating polymorphic protein bands that differ. The study provides cytological and protein evidence to compare the three clover species
The document discusses the topic of phylogenetics. It begins with definitions of key terms like phylogeny, phylogenetic tree, clade, and orthologous genes. It then provides examples of how phylogenetic methods are used in fields like epidemiology, conservation biology, and pharmaceutical research. The document also discusses choosing appropriate genetic sequences to use in phylogenetic analysis and introduces molecular clock models.
This study analyzed the occurrence and diversity of integrons in bacteria isolated from an urban wastewater treatment plant. A total of 697 isolates of Enterobacteriaceae and Aeromonas were screened for integrons. Three new gene cassettes were identified, including a novel aadA variant and genes involved in cell signaling and unknown functions. Thirteen different gene cassette arrays were detected, with four representing novel integrons. Approximately 80% of isolates were resistant to at least 3 antibiotic classes. The presence of novel integron structures in treated effluent suggests wastewater treatment plants may facilitate the formation and spread of antibiotic resistance genes.
This document summarizes research on the mitochondrial large subunit rRNA gene sequence and microevolution in the ciliate Paramecium. Key findings include:
- The large subunit rRNA gene complex in Paramecium consists of a 283-base "5.8S-like" segment followed by the previously described 20S segment.
- The gene sequences from Paramecium primaurelia and Paramecium tetraurelia were 4% divergent.
- The genes lie adjacent to each other near the end of the linear mitochondrial genome and are transcribed from a common 23S precursor.
- Precise gene boundaries were determined using nuclease protection assays. The complex spans approximately 2654 base pairs.
This document outlines the schedule and requirements for a genomics course consisting of 9 sessions over March and May. Students are required to attend all sessions and give one 20-minute seminar and write one essay. Seminars will be 15% of the final grade and essays will also be 15%, with a final exam making up the remaining 70% of the grade. Topics for the seminars and essays will be assigned.
The ribosomal RNA gene unit of Tritrichomonas foetus was cloned and analyzed. Southern blot analysis showed the rDNA unit is organized as a tandem head to tail repeat of 6 kb, with 12 copies present. The small subunit rRNA is one of the shortest reported at 1571 bp, while the 5.8S rRNA is 159 bp. Northern blot analysis detected primary and precursor rRNA transcripts of 5.8 kb and 4 kb. Sequence analysis confirmed the secondary structure of the small subunit rRNA is similar to other eukaryotes, while being shorter in variable regions.
Nature GeNetics VOLUME 46 NUMBER 10 OCTOBER 2014 1 0 8 9.docxgemaherd
Nature GeNetics VOLUME 46 | NUMBER 10 | OCTOBER 2014 1 0 8 9
A suite of forces and factors, including mutation, recombination,
selection, population history and gene duplication influence patterns
of intraspecific genetic variation. Distinguishing which factors have
shaped sequence variation across a genome requires extensive whole-
genome sequencing of multiple individuals, which has only recently
become tractable1. Most large-scale whole-genome resequencing
studies have focused on model and domesticated species1–5. However,
extensive sequencing of natural populations holds great promise for
advancing understanding of evolutionary biology, including identify-
ing functional variation and the molecular bases of adaptation. Recent
work in a number of species has identified genomic regions that show
signatures of positive selection, suggesting that such regions contain
loci that control adaptive traits4,6–8. Relatively few studies, however,
have combined genome-wide scans with phenotypic data to determine
whether computationally identified selected regions influence adap-
tive phenotypic variation5,9–13. Genome-wide studies of large natural
populations combined with phenotypic measurements are necessary
to determine which factors shape patterns of genetic variation within
species and, therefore, enhance understanding of adaptation.
With large geographic ranges spanning wide environmental gradi-
ents and a long history of research showing local adaptation14, forest
trees are ideal for examining the processes shaping genetic variation
in natural populations. Forest trees cover approximately 30% of ter-
restrial land area15, provide direct feedback to global climate15 and
are often foundation species that organize entire biotic communities
and biogeochemical systems16,17. Clearly, biotic and abiotic interac-
tions have influenced population sizes and distributions of forest
trees, leaving diagnostic signatures in the genomes of present-day
populations14,18,19. A deeper understanding of the evolutionary and
ecological forces that shaped these patterns will offer insights and
options for ecosystem management, applied tree improvement and
accelerated domestication efforts20.
Black cottonwood, Populus trichocarpa Torr. & Gray, is a dominant
riparian tree that has become a model for the advancement of genome-
level insights in forest trees21. The sequencing of 16 P. trichocarpa
genomes revealed widespread patterns of linkage disequilibrium (LD)
and population structure22 and extensive genecological studies have
revealed a high degree of adaptive phenotypic variation in growth,
vegetative phenology and physiological traits such as water-use effi-
ciency and photosynthesis23–25, suggesting that local adaptation is
prevalent. To date, candidate gene–association analyses have revealed
loci with significant effects on phenotypic traits26,27. However, thus
far there have been no publications describing whole-genome asso-
.
Nature GeNetics VOLUME 46 NUMBER 10 OCTOBER 2014 1 0 8 9.docxvannagoforth
Nature GeNetics VOLUME 46 | NUMBER 10 | OCTOBER 2014 1 0 8 9
A suite of forces and factors, including mutation, recombination,
selection, population history and gene duplication influence patterns
of intraspecific genetic variation. Distinguishing which factors have
shaped sequence variation across a genome requires extensive whole-
genome sequencing of multiple individuals, which has only recently
become tractable1. Most large-scale whole-genome resequencing
studies have focused on model and domesticated species1–5. However,
extensive sequencing of natural populations holds great promise for
advancing understanding of evolutionary biology, including identify-
ing functional variation and the molecular bases of adaptation. Recent
work in a number of species has identified genomic regions that show
signatures of positive selection, suggesting that such regions contain
loci that control adaptive traits4,6–8. Relatively few studies, however,
have combined genome-wide scans with phenotypic data to determine
whether computationally identified selected regions influence adap-
tive phenotypic variation5,9–13. Genome-wide studies of large natural
populations combined with phenotypic measurements are necessary
to determine which factors shape patterns of genetic variation within
species and, therefore, enhance understanding of adaptation.
With large geographic ranges spanning wide environmental gradi-
ents and a long history of research showing local adaptation14, forest
trees are ideal for examining the processes shaping genetic variation
in natural populations. Forest trees cover approximately 30% of ter-
restrial land area15, provide direct feedback to global climate15 and
are often foundation species that organize entire biotic communities
and biogeochemical systems16,17. Clearly, biotic and abiotic interac-
tions have influenced population sizes and distributions of forest
trees, leaving diagnostic signatures in the genomes of present-day
populations14,18,19. A deeper understanding of the evolutionary and
ecological forces that shaped these patterns will offer insights and
options for ecosystem management, applied tree improvement and
accelerated domestication efforts20.
Black cottonwood, Populus trichocarpa Torr. & Gray, is a dominant
riparian tree that has become a model for the advancement of genome-
level insights in forest trees21. The sequencing of 16 P. trichocarpa
genomes revealed widespread patterns of linkage disequilibrium (LD)
and population structure22 and extensive genecological studies have
revealed a high degree of adaptive phenotypic variation in growth,
vegetative phenology and physiological traits such as water-use effi-
ciency and photosynthesis23–25, suggesting that local adaptation is
prevalent. To date, candidate gene–association analyses have revealed
loci with significant effects on phenotypic traits26,27. However, thus
far there have been no publications describing whole-genome asso-
...
This document discusses constructing phylogenetic trees to analyze the evolutionary relationships between bacteria, archaea, and eukarya based on nuclear, membrane, and metabolic genes. 18 organisms were selected from each domain and their 16S rRNA, 18S rRNA, and gene sequences were obtained from databases. Multiple sequence alignments were performed and phylogenetic trees were constructed to compare the relationships depicted in the gene trees to the standard rRNA tree of life.
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees...Jonathan Eisen
Lang JM, Darling AE, Eisen JA (2013) Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE 8(4): e62510. doi:10.1371/journal.pone.0062510
The document summarizes research on sequencing part of the ribosomal RNA coding region and determining the secondary structure of the 25S rRNA of Candida albicans. Key findings include:
- A rDNA cistron from C. albicans strain WO-1 was cloned and sequencing revealed the ITS1, ITS2, 5.8S rDNA and 25S rDNA coding regions.
- The C. albicans ITS regions are shorter than those of most other eukaryotes.
- The 5.8S and 25S rDNA sequences were used to model the secondary structure, which was compared to other species.
- Variable regions in the 25S r
The document summarizes a study that identified components of the BRL3 receptor complex in Arabidopsis thaliana plants through immunoprecipitation and mass spectrometry analysis. The study found that BAK1 and other known BR signaling proteins interact with BRL3. Genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that the BAK1, BRL1, and BRL3 signaling pathways regulate root growth and development by modulating the activities of provascular and quiescent center cells. This provides evidence that cell-specific BR receptor complexes assemble to direct different cellular activities during root development.
The document discusses H2A.Z, a histone variant. A recent study showed that the H2A.Z nucleosome structure was altered without changes to the H2A structure, avoiding clashes. As a result, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z nucleosome. The presence of H2A versus H2A.Z in the histone octamer affects nucleosome stability. H2A.Z accumulation around transcriptional start sites promotes transcriptional initiation, and it is required for activation of the Flowering Locus C gene in Arabidopsis.
Genetic diversity in wild and cultivated peanut_Khanal_2008Sameer Khanal
This document summarizes genetic diversity research on wild and cultivated peanut species. It describes mining genome survey sequences from diploid and tetraploid peanuts to develop simple sequence repeat (SSR) markers. Ninety-three polymorphic SSR markers were developed that showed high diversity among diploid species. Expressed sequence tags were also mined for SSRs, resulting in 19 polymorphic markers. The markers were used to analyze genetic diversity and population structure among peanut accessions. Dinucleotide repeats were found to be the most common and polymorphic repeat type. Studies on diploid peanut species with additional SSR markers aimed to estimate diversity and decipher population structure.
Development of a core set of single-locus SSR markers for allotetraploid rape...Eric Du
This document describes the development of a set of 230 single-locus SSR markers for Brassica napus (oilseed rape). The researchers collected existing SSR markers and developed new ones from genomic sequences of related Brassica species. They screened the markers on a set of rapeseed inbred lines and identified 2,701 that produced single amplicons, indicating they were putative single-locus markers. They then genetically mapped 230 high-quality single-locus SSR markers to the 19 linkage groups of B. napus using a segregating population. A subset of 78 markers was validated across 45 inbred lines and hybrids, demonstrating their stability. Most markers also showed single-locus behavior in other Brassica
This document describes the development of a set of 230 single-locus SSR markers for Brassica napus (oilseed rape). The researchers collected existing SSR markers and developed new ones from genomic sequences of related Brassica species. They screened the markers on a set of rapeseed inbred lines and identified 2,701 that produced single amplicons, indicating they were putative single-locus markers. They then genetically mapped 230 high-quality single-locus SSR markers to the 19 linkage groups of B. napus using a segregating population. A subset of 78 markers was validated across 45 inbred lines and hybrids, demonstrating their stability. Most markers also showed single-locus behavior in other Brassica
· Describe strategies to build rapport with inmates and offenders .docxgerardkortney
· Describe strategies to build rapport with inmates and offenders in a correctional treatment or supervision program.
· Describe the effect of group dynamics on facilitating programs.
· Describe techniques for establishing a therapeutic environment.
Generalist Case Management
Woodside and McClam
https://phoenix.vitalsource.com/books/9781483342047/pageid/44
https://phoenix.vitalsource.com/#/books/9781323128800
https://phoenix.vitalsource.com/#/books/9781483342047
https://phoenix.vitalsource.com/#/books/9781133795247
https://phoenix.vitalsource.com/#/books/1259760413
Use book and two outside sources.
At least 100 words per question
THANKS
1 The Role of the Correctional Counselor CHAPTER OBJECTIVES After reading this chapter, you will be able to: 1. Identify the functions and parameters of the counseling process. 2. Discuss the competing interests between security and counseling in the correctional counseling process. 3. Know common terms and concerns associated with custodial corrections. 4. Understand the role of the counselor as facilitator. 5. Identify the various personal characteristics associated with effective counselors. 6. Be aware of the impact that burnout can have on a counselor’s professional performance. 7. Identify the various means of training and supervision associated with counseling. PART ONE: A BRIEF INTRODUCTION TO COUNSELING AND CORRECTIONS There are many myths concerning the concept of counseling. Although the image of the counseling field has changed dramatically over the past two or three decades, much of society still views counseling and therapy as a mystic process reserved for those who lack the ability to handle life issues effectively. While the concept of counseling is often misunderstood, the problem is exacerbated when attempting to introduce the idea of correctional counseling. Therefore, the primary goal of this chapter is to provide a working definition of correctional counseling that includes descriptions of how and when it is carried out. In order to understand the concept of correctional counseling, however, the two words that derive the concept must first be defined: “corrections” and “counseling.” In addition, a concerted effort is made to identify the myriad of legal and ethical issues that pertain to counselors working with offenders. It is very difficult to identify a single starting point for the counseling profession. In essence, there were various movements occurring simultaneously that later evolved into what we now describe as counseling. One of the earliest connections to the origins of counseling took place in Europe during the Middle Ages (Brown & Srebalus, 2003). The primary objective was assisting individuals with career choices. This type of counseling service is usually described by the concept of “guidance.” In the late 1800s Wilhelm Wundt and G. Stanley Hall created two of the first known psychological laboratories aimed at studying and treating individuals with psychological and e.
· Debates continue regarding what constitutes an appropriate rol.docxgerardkortney
· Debates continue regarding what constitutes an appropriate role for the judiciary. Some argue that federal judges have become too powerful and that judges “legislate from the bench.”
1. What does it mean for a judge to be an activist?
2. What does it mean for a judge to be a restrainist?
· Although conservatives had long complained about the activism of liberal justices and judges, in recent years conservative judges and justices have been likely to overturn precedents and question the power of elected institutions of government.
3. When is judicial activism appropriate? Explain.
· To defenders of the right to privacy, it is implicitly embodied in the Constitution in the First, Fourth, Fifth, Ninth, and Fourteenth Amendments. To opponents, it is judge-made law because there is no explicit reference to it under the Constitution. The right to privacy dates back to at least 1890, when Boston attorneys Samuel Warren and Louis Brandeis equated it with the right to be left alone from journalists who engaged in yellow journalism.
4. In short, do you believe a right to privacy exists in the federal Constitution. Why or why not?
.
· Critical thinking paper · · · 1. A case study..docxgerardkortney
· Critical thinking paper
·
·
· 1.
A case study.
Deborah Shore, aged 45, works for a small corporation in the Research and Development department.
When she first became a member of the department 15 years ago, Deborah was an unusually creative and productive researcher; her efforts quickly resulted in raises and promotions within the department and earned her the respect of her colleagues. Now, Deborah finds herself less interested in doing research; she is no longer making creative contributions to her department, although she is making contributions to its administration.
She is still respected by the coworkers who have known her since she joined the firm, but not by her younger coworkers.
Analyze the case study from the psychoanalytic, learning, and contextual perspectives: how would a theorist from each perspective explain Deborah's development? Which perspective do you believe provides the most adequate explanation, and why?
2. Interview your mother (and grandmothers, if possible), asking about experiences with childbirth. Include your own experiences if you have had children. Write a paper summarizing these childbirth experiences and comparing them with the contemporary experiences described in the text.
3. Identify a "type" of parent (e.g., single parent, teenage parent, low-income parent, dual-career couple) who is most likely to be distressed because an infant has a "difficult" temperament. Explain why you believe that this type of parent would have particular problems with a difficult infant. Write an informational brochure for the selected type of parent. The brochure should include an explanation of temperament in general and of the difficult temperament in particular, and give suggestions for parents of difficult infants.
4. Plan an educational unit covering nutrition, health, and safety for use with preschoolers and kindergartners. Take into account young children's cognitive and linguistic characteristics. The project should include (1) an outline of the content of the unit; and (2) a description of how the content would be presented, given the intellectual abilities of preschoolers. For example, how long would each lesson be? What kinds of pictures or other audiovisual materials would be used? How would this content be integrated with the children's other activities in preschool or kindergarten?
5. Visit two day care centers and evaluate each center using the information from the text as a guide. Request a fee schedule from each center. Write a paper summarizing your evaluation of each center.
Note:
Unless you are an actual potential client of the center, contact the director beforehand to explain the actual purpose of the visit, obtain permission to visit, and schedule your visit so as to minimize disruption to the center's schedule.
6. Watch some children's television programs and advertising, examine some children's toys and their packaging, read some children's books, and listen to some children's recor.
· Coronel & Morris Chapter 7, Problems 1, 2 and 3
· Coronel & Morris Chapter 8, Problems 1 and 2
A People’s History of Modern Europe
“A fascinating journey across centuries towards the world as we experience it today. ... It is
the voice of the ordinary people, and women in particular, their ideas and actions, protests
and sufferings that have gone into the making of this alternative narrative.”
——Sobhanlal Datta Gupta, former Surendra Nath Banerjee
Professor of Political Science, University of Calcutta
“A history of Europe that doesn’t remove the Europeans. Here there are not only kings,
presidents and institutions but the pulse of the people and social organizations that shaped
Europe. A must-read.”
——Raquel Varela, Universidade Nova de Lisboa
“Lively and engaging. William A Pelz takes the reader through a thousand years of
European history from below. This is the not the story of lords, kings and rulers. It is the
story of the ordinary people of Europe and their struggles against those lords, kings and
rulers, from the Middle Ages to the present day. A fine introduction.”
——Francis King, editor, Socialist History
“This book is an exception to the rule that the winner takes all. It highlights the importance
of the commoners which often is only shown in the dark corners of mainstream history
books. From Hussites, Levellers and sans-culottes to the women who defended the Paris
Commune and the workers who occupied the shipyards during the Carnation revolution in
Portugal. The author gives them their deserved place in history just like Howard Zinn did
for the American people.”
——Sjaak van der Velden, International Institute of Social History, Amsterdam
“The author puts his focus on the lives and historical impact of those excluded from
power and wealth: peasants and serfs of the Middle Ages, workers during the Industrial
Revolution, women in a patriarchic order that transcended different eras. This focus not
only makes history relevant for contemporary debates on social justice, it also urges the
reader to develop a critical approach.”
——Ralf Hoffrogge, Ruhr-Universität Bochum
“An exciting story of generations of people struggling for better living conditions, and for
social and political rights. ... This story has to be considered now, when the very notions of
enlightenment, progress and social change are being questioned.”
——Boris Kagarlitsky, director of Institute for globalization studies and social
movements, Moscow, and author of From Empires to Imperialism
“A splendid antidote to the many European histories dominated by kings, businessmen
and generals. It should be on the shelves of both academics and activists ... A lively and
informative intellectual tour-de-force.”
——Marcel van der Linden, International Institute of Social History, Amsterdam
A People’s History
of Modern Europe
William A. Pelz
First published 2016 by Pluto Press
345 Archway Road, London N6 5AA
www.pluto.
· Complete the following problems from your textbook· Pages 378.docxgerardkortney
· Complete the following problems from your textbook:
· Pages 378–381: 10-1, 10-2, 10-16, and 10-20.
· Pages 443–444: 12-7 and 12-9.
· Page 469: 13-5.
· 10-1 How would each of the following scenarios affect a firm’s cost of debt, rd(1 − T); its cost of equity, rs; and its WACC? Indicate with a plus (+), a minus (−), or a zero (0) whether the factor would raise, lower, or have an indeterminate effect on the item in question. Assume for each answer that other things are held constant, even though in some instances this would probably not be true. Be prepared to justify your answer but recognize that several of the parts have no single correct answer. These questions are designed to stimulate thought and discussion.
Effect on
rd(1 − T)
rs
WACC
a. The corporate tax rate is lowered.
__
__
__
b. The Federal Reserve tightens credit.
__
__
__
c. The firm uses more debt; that is, it increases its debt ratio.
__
__
__
d. The dividend payout ratio is increased.
__
__
__
e. The firm doubles the amount of capital it raises during the year.
__
__
__
f. The firm expands into a risky new area.
__
__
__
g. The firm merges with another firm whose earnings are countercyclical both to those of the first firm and to the stock market.
__
__
__
h. The stock market falls drastically, and the firm’s stock price falls along with the rest.
__
__
__
i. Investors become more risk-averse.
__
__
__
j. The firm is an electric utility with a large investment in nuclear plants. Several states are considering a ban on nuclear power generation.
__
__
__
· 10-2 Assume that the risk-free rate increases, but the market risk premium
· 10-16COST OF COMMON EQUITY The Bouchard Company’s EPS was $6.50 in 2018, up from $4.42 in 2013. The company pays out 40% of its earnings as dividends, and its common stock sells for $36.00.
· a. Calculate the past growth rate in earnings. (Hint: This is a 5-year growth period.)
· b. The last dividend was D0 = 0.4($6.50) = $2.60. Calculate the next expected dividend, D1, assuming that the past growth rate continues.
· c. What is Bouchard’s cost of retained earnings, rs?
· 10-20WACC The following table gives Foust Company’s earnings per share for the last 10 years. The common stock, 7.8 million shares outstanding, is now (1/1/19) selling for $65.00 per share. The expected dividend at the end of the current year (12/31/19) is 55% of the 2018 EPS. Because investors expect past trends to continue, g may be based on the historical earnings growth rate. (Note that 9 years of growth are reflected in the 10 years of data.)
The current interest rate on new debt is 9%; Foust’s marginal tax rate is 40%, and its target capital structure is 40% debt and 60% equity.
· a. Calculate Foust’s after-tax cost of debt and common equity. Calculate the cost of equity as rs = D1/P0 + g.
· b. Find Foust’s WACC
· 12-7SCENARIO ANALYSIS Huang Industries is considering a proposed project whose estimated NPV is $12 million. This estimate assumes that economic conditions wi.
· Consider how different countries approach aging. As you consid.docxgerardkortney
· Consider how different countries approach aging. As you consider different countries, think about the following:
o Do older adults live with their children, or are they more likely to live in a nursing home?
o Are older adults seen as wise individuals to be respected and revered, or are they a burden to their family and to society?
· Next, select two different countries and compare and contrast their approaches to aging.
· Post and identify each of the countries you selected. Then, explain two similarities and two differences in how the countries approach aging. Be specific and provide examples. Use proper APA format and citation. LSW10
.
· Clarifying some things on the Revolution I am going to say som.docxgerardkortney
· Clarifying some things on the Revolution
I am going to say something, and I want you to hear me.
I am a scholar of the Revolution. That's the topic of my dissertation. Please believe me when I say that I know a lot about it.
I also happen to know--and this is well-supported by historians--that the Revolution was a civil war in which, for the first several years, Revolutionaries and Loyalists were evenly matched.
I will repeat that. Evenly matched. Loyalists were not merely too cowardly to fight, and they were not old fogies who hated the idea of freedom. Most had been in the Colonies for generations. Many of them took up arms for their King and their country. And when they lost, you confiscated their homes and they fled with the clothes on their back to Canada, England, and other places of the Empire. Both sides--both sides--committed unspeakable atrocities against civilians whom they disagreed with.
Now, a lot of you love to repeat some very fervent patriotic diatribe about how great the Revolution was. That's not history. That's propaganda. Know the difference.
History has shades of gray. History is complex and ambiguous. Washington, for instance, wore dentures made from the teeth of his slaves. Benjamin Franklin's son was the last royal governor of New Jersey. Did you know that the net tax rate for Americans--they always conveniently leave this out of the textbooks--was between 1.9 and 2.1%, depending on colony.? And that was if they had paid the extra taxes on tea and paper.
And, wait for it, people who support California independence use the same logic and arguments as they did in 1775. Did you know that the Los Angeles and Washington are only a few hundred miles closer than Boston and London? That many of the same issues, point by point, are repeating here in California? So put yourself in those shoes. How many of you would have sided with the Empire (whether American or British) based on the fact that you don't know how this will shake out? Would you call someone who supports Calexit a Patriot? Revolutionary? Nutcase? Who gets to own that word, anyway?
You can choose that you would have supported the revolutionaries--but think. Think about the other side. They matter, and their experiences got to be cleansed out of history to make you feel better about the way the revolutionaries behaved during the War. Acknowledge that they are there, and that their point of view has merit, even if you not agree with it.
· Clarifying Unit III's assignment
I have noticed a few consistent problems with the letter in the Unit III issue. Here are some pointers to make it better.
1. Read the clarifying note I wrote above. Note that the taxes aren't actually as high as you have been led to believe, but the point is that they should not be assigned at all without your consent.
2. Acknowledge that this is a debate, that a certain percentage are radicalized for independence, but there are is also a law-and-order group who find this horrific, and want .
· Chapter 9 – Review the section on Establishing a Security Cultur.docxgerardkortney
· Chapter 9 – Review the section on Establishing a Security Culture. Review the methods to reduce the chances of a cyber threat noted in the textbook. Research other peer-reviewed source and note additional methods to reduce cyber-attacks within an organization.
· Chapter 10 – Review the section on the IT leader in the digital transformation era. Note how IT professionals and especially leaders must transform their thinking to adapt to the constantly changing organizational climate. What are some methods or resources leaders can utilize to enhance their change attitude?
.
· Chapter 10 The Early Elementary Grades 1-3The primary grades.docxgerardkortney
· Chapter 10: The Early Elementary Grades: 1-3
The primary grades are grades 1-3.
Although educational reform has had an effect on all children, it is most apparent in the early elementary years. Reform and change comes from a number of sources and the chapter begins by reminding you of this. Let’s examine a few of these sources...
Diversity. There has been a rise in the number of racial and ethnic minority students enrolled in the nation's public schools; this number will (most likely) continue to rise. Teaching children from different cultures and backgrounds is an important piece to account for when planning curriculum.
Standards. Standards is a reason for reform. We've already looked at standards; these are something you must keep in mind when planning lessons.
Data-Driven Instruction may sound new, but it is not a new concept to you. We’ve done a great deal of discussing the outcomes of test-taking and assessments. You've probably all heard "teaching to the test."
Technology. Today’s students have had much experience with technology, therefore, it’s important to provide them with opportunities to learn with technology. It may take a while for you to be creative and think of ways to use it in your teaching (if you haven’ t been).
Health and Wellness. Obesity is a major concern in this country. Therefore, it is important to make sure that children have the opportunity to be active. Unfortunately, due to the pressure of academics, many schools have been taking physical education/activity time out of the curriculum.
Violence: One issue that I notice this new edition of the text has excluded is violence. However, I think that this topic is important; we need to keep children safe when they are at school. As a result of 9/11 (and, not to mention that many violent events have happened on school campuses in recent years), many school districts now have an emergency system in place that they can easily use if there is any type of incident in which the children’s safety is at risk.
WHAT ARE CHILDREN IN GRADES ONE TO THREE LIKE?
Your text explains that the best way to think of a child’s development during this time is: slow and steady. During this stage, there is not much difference between boys and girls when it comes to physical capabilities. Although it is always important to not stereotype based on one’s gender, it is especially important during these years. These children are also entering into their "tween" years, thus; being sensitive to the children's and parents' needs in regards to such changes is important.
It is important to remember that children in the primary grades are in the Concrete Operations Stage. This stage is children ages 7 to 12. The term operation refers to an action that can be carried out in thought as well as executed materially and that is mentally and physically reversible.
These children are at an age in which they can compare their abilities to their peers. And, therefore, children may develop learned helplessnes.
· Chap 2 and 3· what barriers are there in terms of the inter.docxgerardkortney
· Chap 2 and 3
· what barriers are there in terms of the interpersonal communication model?
Typically, communication breakdowns result from lack of understanding without clarification; often, there wasn't even an attempt at clarification. If barriers to interpersonal communication are not acknowledged and addressed, workplace productivity can suffer.
Language Differences
Interpersonal communication can go awry when the sender and receiver of the message speak a different language -- literally and figuratively. Not everyone in the workplace will understand slang, jargon, acronyms and industry terminology. Instead of seeking clarification, employees might guess at the meaning of the message and then act on mistaken assumptions. Also, misunderstandings may occur among workers who do not speak the same primary language. As a result, feelings may be hurt, based on misinterpretation of words or of body language.
Cultural Differences
Interpersonal communication may be adversely affected by lack of cultural understanding, mis-perception, bias and stereotypical beliefs. Workers may have limited skill or experience communicating with people from a different background. Many companies offer diversity training to help employees understand how to communicate more effectively across cultures and relate to those who may have different background experiences. Similarly, gender barriers can obstruct interpersonal communication if men and women are treated differently, and held to different standards, causing interpersonal conflicts in the workplace.
Personality Differences
Like any skill, some people are better at interpersonal communication than others. Personality traits also influence how well an individual interacts with subordinates, peers and supervisors. Extraversion can be an advantage when it comes to speaking out, sharing opinions and disseminating information. However, introverts may have the edge when it comes to listening, reflecting and remembering. Barriers to interpersonal communication may occur when employees lack self-awareness, sensitivity and flexibility. Such behavior undermines teamwork, which requires mutual respect, compromise and negotiation. Bullying, backstabbing and cut throat competition create a toxic workplace climate that will strain interpersonal relationships.
Generational Differences
Interpersonal communication can be complicated by generational differences in speech, dress, values, priorities and preferences. For instance, there may be a generational divide as to how team members prefer to communicate with one another. If younger workers sit in cubicles, using social networking as their primary channel of communication, it can alienate them from older workers who may prefer face-to-face communication. Broad generalizations and stereotypes can also cause interpersonal rifts when a worker from one generation feels superior to those who are younger or older. Biases against workers based on age can constitute a form of disc.
· Case Study 2 Improving E-Mail Marketing ResponseDue Week 8 an.docxgerardkortney
The document provides a case study and instructions for an assignment on improving the response rate of email marketing. Students are asked to: 1) conduct a design of experiment using the provided data to test cause-and-effect relationships, 2) determine an appropriate graphical display for the results and provide rationale, 3) recommend actions to increase email response rates with rationale, and 4) propose an overall strategy to develop a process model to increase response rates and obtain effective business processes with rationale. The assignment requires a 2-3 page paper following APA formatting guidelines.
· Briefly describe the technologies that are leading businesses in.docxgerardkortney
· Briefly describe the technologies that are leading businesses into the third wave of electronic commerce.
· In about 100 words, describe the function of the Internet Corporation for Assigned Names and Numbers. Include a discussion of the differences between gTLDs and sTLDs in your answer.
· In one or two paragraphs, describe how the Internet changed from a government research project into a technology for business users.
· In about 100 words, explain the difference between an extranet and an intranet. In your answer, describe when you might use a VPN in either.
· Define “channel conflict” and describe in one or two paragraphs how a company might deal with this issue.
· In two paragraphs, explain why a customer-centric Web site design is so important, yet is so difficult to accomplish.
· In about two paragraphs, distinguish between outsourcing and offshoring as they relate to business processes.
· In about 200 words, explain how the achieved trust level of a company’s communications using blogs and social media compare with similar communication efforts conducted using mass media and personal contact.
· Write a paragraph in which you distinguish between a virtual community and a social networking Web site
· Write two or three paragraphs in which you describe the role that culture plays in the development of a country’s laws and ethical standards.
QUESTION 1
Lakota peoples of the Great Plains are notably:
nomadic and followed the buffalo herds
Sedentary farmers, raising corn, northern beans, and potatoes
peaceful people who tried to live in harmony with neighboring tribes and the environment
religious and employed a variety of psychoactive plants during religious ceremonies
QUESTION 2
Tribal peoples of the Great Plains experienced greater ease at hunting and warfare after the introduction of:
Hotchkiss guns
smokeless gunpowder
horses
Intertribal powwows
all of the above
QUESTION 3
The Apaches and Navajos (Dine’) of the southwestern region of North America speak a language similar to their relatives of northern California and western Canada called:
Yuman
Uto-Aztecan
Tanoan
Athabaskan
Algonkian
QUESTION 4
The Navajo lived in six or eight-sided domed earth dwellings called:
wickiups
kivas
hogans
roadhouses
sweat lodge
QUESTION 5
Pueblo Indians, such as the Zuni and Hopi tribes, are descendants of the ancient people known as the:
Anasazi
Ashkenazi
Athabaskan
Aztecanotewa
Atlantean
2 points
QUESTION 6
1. Kachinas, or spirits of nature, were believed to:
Assist in the growth of crops and send rain
Help defend the Navajo against all foreign invaders
Provide medical assistance to the Hopi when doctors were not available
Combat evil spirits such as Skin-walkers or Diablitos
All of the above
2 points
QUESTION 7
1. The preferred dwellings among the Lakota Sioux were:
wickiups
adobe pueblos
pit houses
teepees
buffalo huts
2 points
QUESTION 8
1. Native Americansbenef.
· Assignment List· My Personality Theory Paper (Week Four)My.docxgerardkortney
· Assignment List
· My Personality Theory Paper (Week Four)
My Personality Theory Paper (Week Four)
DUE: May 31, 2020 11:55 PM
Grade Details
Grade
N/A
Gradebook Comments
None
Assignment Details
Open Date
May 4, 2020 12:05 AM
Graded?
Yes
Points Possible
100.0
Resubmissions Allowed?
No
Attachments checked for originality?
Yes
Top of Form
Assignment Instructions
My Personality Theory Paper
Instructions:
For this assignment, you will write a paper no less than 7 pages in length, not including required cover and Reference pages, describing a single personality theory from the course readings that best explains your own personality and life choices. You are free to select from among the several theories covered in the course to date but only one theory may be used.
Your task is to demonstrate your knowledge of the theory you choose via descriptions of its key concepts and use of them to explain how you developed your own personality. It is recommended that you revisit the material covered to date to refresh your knowledge of theory details. This is a "midterm" assignment and you should show in your work that you have studied and comprehended the first four weeks of course material. Your submission should be double-spaced with 1 inch margins on all sides of each page and should be free of spelling and grammar errors. It must include source crediting of any materials used in APA format, including source citations in the body of your paper and in a Reference list attached to the end. Easy to follow guides to APA formatting can be found on the tutorial section of the APUS Online Library.
Your paper will include three parts:
I. A brief description of the premise and key components of the theory you selected. You should be thorough and concise in this section and not spend the bulk of the paper detailing the theory, but rather just give enough of a summary of the key points so that an intelligent but uniformed reader would be able to understand its basics. If you pick a more complicated theory, you should expect explaining its premise and key components to take longer than explaining the same for one of the simpler theories but, in either case, focus on the basics and keep in mind that a paper that is almost all theory description and little use of the theory described to explain your own personality will receive a significant point deduction as will the reverse case of the paper being largely personal experience sharing with little linkage to clearly described key theory components.
II. A description of how your chosen theory explains your personality and life choices with supporting examples.
III. A description of the limitations of the theory in explaining your personality or anyone else’s.
NOTE: Although only your instructor will be reading your paper, you should still think about how much personal information you want to disclose. The purpose of this paper is not to get you to share private information, but rather to bring one .
· Assignment List
· Week 7 - Philosophical Essay
Week 7 - Philosophical Essay
DUE: Mar 22, 2020 11:55 PM
Grade Details
Grade
N/A
Gradebook Comments
None
Assignment Details
Open Date
Feb 3, 2020 12:05 AM
Graded?
Yes
Points Possible
100.0
Resubmissions Allowed?
No
Attachments checked for originality?
Yes
Top of Form
Assignment Instructions
Objective: Students will write a Philosophical Essay for week 7 based on the course concepts.
Course Objectives: 2, 3, & 4
Task:
This 4 - 5 full page (not to exceed 6 pages) Philosophical Essay you will be writing due Week 7 is designed to be a thoughtful, reflective work. The 4 - 5 full pages does not include a cover page or a works cited page. It will be your premier writing assignment focused on the integration and assessment relating to the course concepts. Your paper should be written based on the outline you submitted during week 4 combined with your additional thoughts and instructor feedback. You will use at least three scholarly/reliable resources with matching in-text citations and a Works Cited page. All essays are double spaced, 12 New Times Roman font, paper title, along with all paragraphs indented five spaces.
Details:
You will pick one of the following topics only to do your paper on:
· According to Socrates, must one heed popular opinion about moral matters? Does Socrates accept the fairness of the laws under which he was tried and convicted? Would Socrates have been wrong to escape?
· Consider the following philosophical puzzle: “If a tree falls in the forest and there's no one around to hear it, does it make a sound?” (1) How is this philosophical puzzle an epistemological problem? And (2) how would John Locke answer it?
· Evaluate the movie, The Matrix, in terms of the philosophical issues raised with (1) skepticism and (2) the mind-body problem. Explain how the movie raises questions similar to those found in Plato’s and Descartes’ philosophy. Do not give a plot summary of the movie – focus on the philosophical issues raised in the movie as they relate to Plato and Descartes.
· Socrates asks Euthyphro, “Are morally good acts willed by God because they are morally good, or are they morally good because they are willed by God?” (1) How does this question relate to the Divine Command Theory of morality? (2) What are the philosophical implications associated with each option here?
· Explain (1) the process by which Descartes uses skepticism to refute skepticism, and (2) what first principle does this lead him to? (3) Explain why this project was important for Descartes to accomplish.
Your paper will be written at a college level with an introduction, body paragraphs, a conclusion, along with in-text citations/Works Cited page in MLA formatting. Students will follow MLA format as the sole citation and formatting style used in written assignments submitted as part of coursework to the Humanities Department. Remember - any resource that is listed on the Works Cited page must .
· Assignment 3 Creating a Compelling VisionLeaders today must be .docxgerardkortney
· Assignment 3: Creating a Compelling Vision
Leaders today must be able to create a compelling vision for the organization. They also must be able to create an aligned strategy and then execute it. Visions have two parts, the envisioned future and the core values that support that vision of the future. The ability to create a compelling vision is the primary distinction between leadership and management. Leaders need to create a vision that will frame the decisions and behavior of the organization and keep it focused on the future while also delivering on the short-term goals.
To learn more about organizational vision statements, do an Internet search and review various vision statements.
In this assignment, you will consider yourself as a leader of an organization and write a vision statement and supporting values statement.
Select an organization of choice. This could be an organization that you are familiar with, or a fictitious organization. Then, respond to the following:
· Provide the name and description of the organization. In the description, be sure to include the purpose of the organization, the products or services it provides, and the description of its customer base.
· Describe the core values of the organization. Why are these specific values important to the organization?
· Describe the benefits and purpose for an organizational vision statement.
· Develop a vision statement for this organization. When developing a vision statement, be mindful of the module readings and lecture materials.
· In the vision statement, be sure to communicate the future goals and aspirations of the organization.
· Once you have developed the vision statement, describe how you would communicate the statement to the organizational stakeholders, that is, the owners, employees, vendors, and customers.
· How would you incorporate the communication of the vision into the new employee on-boarding and ongoing training?
Write your response in approximately 3–5 pages in Microsoft Word. Apply APA standards to citation of sources.
Use the following file naming convention: LastnameFirstInitial_M1_A3.doc. For example, if your name is John Smith, your document will be named SmithJ_M1_A3.doc.
By the due date assigned, deliver your assignment to the Submissions Area.
Assignment 3 Grading Criteria
Maximum Points
Chose and described the organization. The description included the purpose of the organization, the products or services the organization provides, and the description of its customer base.
16
Developed a vision statement for the organization. Ensured to accurately communicate the goals and aspirations of the organization in the vision statement.
24
Ensured that the incorporation and communication strategy for the vision statement is clear, detailed, well thought out and realistic.
28
Evaluated and explained which values are most important to the organization.
24
Wrote in a clear, concise, and organized manner; demonstrated ethical scholarship in accurate r.
· Assignment 4
· Week 4 – Assignment: Explain Theoretical Perspectives for Real-life Scenarios
Assignment
Updated
Top of Form
Bottom of Form
For each of the following three scenarios, use a chart format to assess how each traditional theoretical perspective would best explain the situation that a social worker would need to address. You may create your charts in Word or another software program of your choice. An example chart follows the three scenarios.
Scenario 1
You are a hospital social worker who is working with a family whose older adult relative is in end-stage renal failure. There are no advanced directives and the family is conflicted over what the next steps should be.
Scenario 2
You are a caseworker in a drug court. Your client has had three consecutive dirty urine analyses. She is unemployed and has violated her probation order.
Scenario 3
You are a school social worker. A teacher sends her 9-year-old student to you because he reports that he has not eaten in 2 days and there are no adults at home to take care of him.
Chart Example:
Your client, an 11-year-old girl, was removed from home because of parental substance abuse. She is acting out in her foster home, disobeying her foster parents and not following their rules.
Theory
Explanation for Scenario – please respond to the questions below in your explanation
Systems Theory
What systems need to be developed or put in place to support the child? Would Child Protective Services need to become involved? What other systems would support her and a successful outcome for being in foster care?
Generalist Theory
What is the best intervention or therapy to use based on this child’s situation? Given her circumstances, how could you best improve her functioning?
Behavioral Theory
What behaviors are being reinforced? What behaviors are being ignored or punished? What would you suggest to maintain this placement? Would this involve working with the foster parents?
Cognitive Theory
How would you help your client to examine her thinking, emotions, and behavior? What would this entail from a cognitive developmental framework?
Support your assignment with a minimum of three resources.
Length: 3 charts, not including title and reference pages
Your assignment should demonstrate thoughtful consideration of the ideas and concepts presented in the course by providing new thoughts and insights relating directly to this topic. Your response should reflect scholarly writing and current APA standards where appropriate. Be sure to adhere to Northcentral University's Academic Integrity Policy.
Assignement 3
State the function of each of the following musculoskeletal system structures: Describe the structures of the musculoskeletal system.
Skeletal muscle
Tendons
Ligaments
Bone
Cartilage
Describe each of the following types of joints:
Ball-and-socket
Hinge
Pivot
Gliding
Saddle
Condyloid
Newspaper Rubric
CATEGORY
4
3
2
1
Headline & Byline & images
16 points
Article has a .
· Assignment 2 Leader ProfileMany argue that the single largest v.docxgerardkortney
· Assignment 2: Leader Profile
Many argue that the single largest variable in organizational success is leadership. Effective leadership can transform an organization and create a positive environment for all stakeholders. In this assignment, you will have the chance to evaluate a leader and identify what makes him/her effective.
Consider all the leaders who have affected your life in some way. Think of people with whom you work—community leaders, a family member, or anyone who has had a direct impact on you.
· Choose one leader you consider to be effective. This can be a leader you are personally aware of, or someone you don’t know, but have observed to be an effective leader. Write a paper addressing the following:
· Explain how this leader has influenced you and why you think he or she is effective.
· Analyze what characteristics or qualities this person possesses that affected you most.
· Rate this leader by using a leadership scorecard. This can be a developed scorecard, or one you develop yourself. If you use a developed scorecard, please be sure to cite the sources of the scorecard. Once you have identified your scorecard, rate your leader. You decide what scores to include (for example, scale of 1–5, 5 being the highest) but be sure to assess the leader holistically across the critical leadership competencies you feel are most important (for example, visioning, empowering, strategy development and communication).
· Critique this individual’s skills against what you have learned about leadership so far in this course. Consider the following:
· How well does he/she meet the practices covered in your required readings?
· How well has he/she adapted to the challenges facing leaders today?
· If you could recommend changes to his/her leadership approach, philosophy, and style, what would you suggest? Why?
· Using the assigned readings, the Argosy University online library resources, and the Internet including general organizational sources like the Wall Street Journal, BusinessWeek, or Harvard Business Review, build a leadership profile of the leader you selected. Include information from personal experiences as well as general postings on the selected leader from Internet sources such as blogs. Be sure to include 2–3 additional resources not already included in the required readings in support of your leadership profile.
Write a 3–5-page paper in Word format. Apply APA standards to citation of sources. Use the following file naming convention: LastnameFirstInitial_M2_A2.doc.
By the due date assigned, deliver your assignment to the Submissions Area.
Assignment 2 Grading Criteria
Maximum Points
Explained how this leader has been influential and why you think the leader is effective showing analysis of the leader’s characteristics or qualities.
16
Analyzed the characteristics or qualities the leader possesses that have affected you most..
16
Rated your leader using a leadership scorecard and supported your rationale for your rating.
32
Criti.
· Assignment 1 Diversity Issues in Treating AddictionThe comple.docxgerardkortney
· Assignment 1: Diversity Issues in Treating Addiction
The complexities of working with diverse populations in treating disorders, such as addictions, require special considerations. Some approaches work better with some populations than with others. For example, Alcoholics Anonymous (AA) programs are spiritually based and focus on a higher power. Some populations have difficulty with these concepts and are averse to participating in such groups.
Select a population—for example, African Americans; Native Americans; or lesbians, gays, or bisexual individuals. Research your topic by using articles from the supplemental readings for this course or from other resources such as the Web, texts, experience, or other journal articles related to diversity issues and addictions.
Write a three- to five-page paper discussing the following:
· Some specific considerations for working with your chosen population in the area of addiction treatment
· Whether your research indicates that 12-step groups work with this population
· Any special problems associated with this population that make acknowledging the addiction and seeking treatment more difficult
· Any language or other barriers that this population faces when seeking treatment
Prepare your paper in Microsoft Word document format. Name your file M4_A1_LastName_Research.doc, and submit it to the Submissions Area by the due date assigned Follow APA guidelines for writing and citing text.
Assignment 1 Grading Criteria
Maximum Points
Discussed some specific considerations for working with your chosen population in the area of addiction.
8
Discussed whether your research indicates that 12-step groups work with your chosen population.
8
Discussed any special problems associated with this population that make acknowledging the addiction and seeking treatment more difficult .
8
Discussed any language or other barriers that this population faces when seeking treatment.
8
Wrote in a clear, concise, and organized manner; demonstrated ethical scholarship in accurate representation and attribution of sources, displayed accurate spelling, grammar, and punctuation.
4
Total:
36
· M4 Assignment 2 Discussion
Discussion Topic
Top of Form
Due February 9 at 11:59 PM
Bottom of Form
Assignment 2: Discussion Questions
Your facilitator will guide you in the selection of two of the three discussion questions. Submit your responses to these questions to the appropriate Discussion Area by the due date assigned. Through the end of the module, comment on the responses of others.
All written assignments and responses should follow APA rules for attributing sources.
You will be attempting two discussion questions in this module; each worth 28 points. The total number of points that can be earned for this assignment is 56.
Minority Groups
Many minority groups experience stress secondary to their social surroundings. For example, a family living in poverty may face frequent violence. Limited income makes meeting the day-to-day need.
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UPRAHUL
This Dissertation explores the particular circumstances of Mirzapur, a region located in the
core of India. Mirzapur, with its varied terrains and abundant biodiversity, offers an optimal
environment for investigating the changes in vegetation cover dynamics. Our study utilizes
advanced technologies such as GIS (Geographic Information Systems) and Remote sensing to
analyze the transformations that have taken place over the course of a decade.
The complex relationship between human activities and the environment has been the focus
of extensive research and worry. As the global community grapples with swift urbanization,
population expansion, and economic progress, the effects on natural ecosystems are becoming
more evident. A crucial element of this impact is the alteration of vegetation cover, which plays a
significant role in maintaining the ecological equilibrium of our planet.Land serves as the foundation for all human activities and provides the necessary materials for
these activities. As the most crucial natural resource, its utilization by humans results in different
'Land uses,' which are determined by both human activities and the physical characteristics of the
land.
The utilization of land is impacted by human needs and environmental factors. In countries
like India, rapid population growth and the emphasis on extensive resource exploitation can lead
to significant land degradation, adversely affecting the region's land cover.
Therefore, human intervention has significantly influenced land use patterns over many
centuries, evolving its structure over time and space. In the present era, these changes have
accelerated due to factors such as agriculture and urbanization. Information regarding land use and
cover is essential for various planning and management tasks related to the Earth's surface,
providing crucial environmental data for scientific, resource management, policy purposes, and
diverse human activities.
Accurate understanding of land use and cover is imperative for the development planning
of any area. Consequently, a wide range of professionals, including earth system scientists, land
and water managers, and urban planners, are interested in obtaining data on land use and cover
changes, conversion trends, and other related patterns. The spatial dimensions of land use and
cover support policymakers and scientists in making well-informed decisions, as alterations in
these patterns indicate shifts in economic and social conditions. Monitoring such changes with the
help of Advanced technologies like Remote Sensing and Geographic Information Systems is
crucial for coordinated efforts across different administrative levels. Advanced technologies like
Remote Sensing and Geographic Information Systems
9
Changes in vegetation cover refer to variations in the distribution, composition, and overall
structure of plant communities across different temporal and spatial scales. These changes can
occur natural.
Exploiting Artificial Intelligence for Empowering Researchers and Faculty, In...Dr. Vinod Kumar Kanvaria
Exploiting Artificial Intelligence for Empowering Researchers and Faculty,
International FDP on Fundamentals of Research in Social Sciences
at Integral University, Lucknow, 06.06.2024
By Dr. Vinod Kumar Kanvaria
ISO/IEC 27001, ISO/IEC 42001, and GDPR: Best Practices for Implementation and...PECB
Denis is a dynamic and results-driven Chief Information Officer (CIO) with a distinguished career spanning information systems analysis and technical project management. With a proven track record of spearheading the design and delivery of cutting-edge Information Management solutions, he has consistently elevated business operations, streamlined reporting functions, and maximized process efficiency.
Certified as an ISO/IEC 27001: Information Security Management Systems (ISMS) Lead Implementer, Data Protection Officer, and Cyber Risks Analyst, Denis brings a heightened focus on data security, privacy, and cyber resilience to every endeavor.
His expertise extends across a diverse spectrum of reporting, database, and web development applications, underpinned by an exceptional grasp of data storage and virtualization technologies. His proficiency in application testing, database administration, and data cleansing ensures seamless execution of complex projects.
What sets Denis apart is his comprehensive understanding of Business and Systems Analysis technologies, honed through involvement in all phases of the Software Development Lifecycle (SDLC). From meticulous requirements gathering to precise analysis, innovative design, rigorous development, thorough testing, and successful implementation, he has consistently delivered exceptional results.
Throughout his career, he has taken on multifaceted roles, from leading technical project management teams to owning solutions that drive operational excellence. His conscientious and proactive approach is unwavering, whether he is working independently or collaboratively within a team. His ability to connect with colleagues on a personal level underscores his commitment to fostering a harmonious and productive workplace environment.
Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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This presentation includes basic of PCOS their pathology and treatment and also Ayurveda correlation of PCOS and Ayurvedic line of treatment mentioned in classics.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
আমাদের সবার জন্য খুব খুব গুরুত্বপূর্ণ একটি বই ..বিসিএস, ব্যাংক, ইউনিভার্সিটি ভর্তি ও যে কোন প্রতিযোগিতা মূলক পরীক্ষার জন্য এর খুব ইম্পরট্যান্ট একটি বিষয় ...তাছাড়া বাংলাদেশের সাম্প্রতিক যে কোন ডাটা বা তথ্য এই বইতে পাবেন ...
তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
বিসিএস ও ব্যাংক এর লিখিত পরীক্ষা ...+এছাড়া মাধ্যমিক ও উচ্চমাধ্যমিকের স্টুডেন্টদের জন্য অনেক কাজে আসবে ...
How to Fix the Import Error in the Odoo 17Celine George
An import error occurs when a program fails to import a module or library, disrupting its execution. In languages like Python, this issue arises when the specified module cannot be found or accessed, hindering the program's functionality. Resolving import errors is crucial for maintaining smooth software operation and uninterrupted development processes.
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
This presentation was provided by Steph Pollock of The American Psychological Association’s Journals Program, and Damita Snow, of The American Society of Civil Engineers (ASCE), for the initial session of NISO's 2024 Training Series "DEIA in the Scholarly Landscape." Session One: 'Setting Expectations: a DEIA Primer,' was held June 6, 2024.
The simplified electron and muon model, Oscillating Spacetime: The Foundation...RitikBhardwaj56
Discover the Simplified Electron and Muon Model: A New Wave-Based Approach to Understanding Particles delves into a groundbreaking theory that presents electrons and muons as rotating soliton waves within oscillating spacetime. Geared towards students, researchers, and science buffs, this book breaks down complex ideas into simple explanations. It covers topics such as electron waves, temporal dynamics, and the implications of this model on particle physics. With clear illustrations and easy-to-follow explanations, readers will gain a new outlook on the universe's fundamental nature.
How to Add Chatter in the odoo 17 ERP ModuleCeline George
In Odoo, the chatter is like a chat tool that helps you work together on records. You can leave notes and track things, making it easier to talk with your team and partners. Inside chatter, all communication history, activity, and changes will be displayed.
Executive Directors Chat Leveraging AI for Diversity, Equity, and InclusionTechSoup
Let’s explore the intersection of technology and equity in the final session of our DEI series. Discover how AI tools, like ChatGPT, can be used to support and enhance your nonprofit's DEI initiatives. Participants will gain insights into practical AI applications and get tips for leveraging technology to advance their DEI goals.
Main Java[All of the Base Concepts}.docxadhitya5119
This is part 1 of my Java Learning Journey. This Contains Custom methods, classes, constructors, packages, multithreading , try- catch block, finally block and more.
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Nature GeNetics VOLUME 43 | NUMBER 10 | OCTOBER
2011 1 0 3 5
l e t t e r s
Brassica nigra (B genome) and B. oleracea (C genome) having
formed
the amphidiploid species B. juncea (A and B genomes), B.
4. napus
(A and C genomes) and B. carinata (B and C genomes) by
hybridiza-
tion. Comparative physical mapping studies have confirmed
genome
triplication in a common ancestor of B. oleracea11 and B.
rapa12 since
its divergence from the A. thaliana lineage at least 13–17
MYA6,7,13.
Using 72× coverage of paired short read sequences generated by
Illumina GA II technology and stringent assembly parameters,
we
assembled the genome of the B. rapa ssp. pekinensis line
Chiifu-401-42
and analyzed the assembly (Online Methods and Supplementary
Note).
The final assembly statistics are summarized in Table 1. The
assembled
sequence of 283.8 Mb was estimated to cover >98% of the gene
space
(Supplementary Table 1) and is greater than the previous
estimated
size of the euchromatic space, 220 Mb14. The assembly showed
excellent
agreement with the previously reported chromosome A03 (ref.
15) and
with 647 bacterial artificial chromosomes (BACs)14 (Online
Methods)
sequenced by Sanger technology. Integration with 199,452
BAC-end
sequences produced 159 super scaffolds representing 90% of the
assem-
bled sequences, with an N50 scaffold (N50 scaffold is a
weighted median
statistic indicating that 50% of the entire assembly is contained
5. in scaf-
folds equal to or larger than this value) size of 1.97 Mb. Genetic
mapping
of 1,427 markers in B. rapa allowed us to produce ten pseudo
chromo-
somes that included 90% of the assembly (Supplementary Table
2).
We found the difference in the physical sizes of the A. thaliana
and B. rapa genomes to be largely because of transposable
elements
(Supplementary Table 3). Although widely dispersed throughout
the
genome, as shown in Figure 1, the transposon-related sequences
were
most abundant in the vicinity of the centromeres. We estimated
that
transposon-related sequences occupy 39.5% of the genome, with
the
proportions of retrotransposons (with long terminal repeats),
DNA
transposons and long interspersed elements being 27.1%, 3.2%
and
2.8%, respectively (Supplementary Tables 4 and 5).
We modeled and analyzed protein coding genes (described in
the
Online Methods and the Supplementary Note). We identified
41,174
protein coding genes, distributed as shown in Figure 1. The
gene models
have an average transcript length of 2,015 bp, a coding length
of 1,172
bp and a mean of 5.03 exons per gene, both similar to that
observed in
A. thaliana16. A total of 95.8% of gene models have a match in
6. at least
one of the public protein databases and 99.3% are represented
among
the public EST collections or de novo Illumina mRNA-Seq data.
Among
the total 16,917 B. rapa gene families, only 1,003 (5.9%) appear
to be
lineage specific, with 15,725 (93.0%) shared with A. thaliana16
and 9,909
(58.6%) also shared by Carica papaya17 and Vitis vinifera18
(Fig. 2).
The genome of the mesopolyploid crop species Brassica rapa
The Brassica rapa Genome Sequencing Project Consortium
We report the annotation and analysis of the draft
genome
sequence of Brassica rapa accession Chiifu-401-42, a
Chinese
cabbage. We modeled 41,174 protein coding genes in
the
B. rapa genome, which has undergone genome
triplication.
We used Arabidopsis thaliana as an outgroup for
investigating
the consequences of genome triplication, such as
structural
and functional evolution. The extent of gene loss
(fractionation)
among triplicated genome segments varies, with one
of the
three copies consistently retaining a disproportionately
large
fraction of the genes expected to have been present
in its
ancestor. Variation in the number of members of
7. gene families
present in the genome may contribute to the
remarkable
morphological plasticity of Brassica species. The B.
rapa
genome sequence provides an important resource for
studying
the evolution of polyploid genomes and underpins
the genetic
improvement of Brassica oil and vegetable crops.
Model species have provided valuable insights into angiosperm
(flowering plant) genome structure, function and evolution. For
example,
A. thaliana has experienced two genome duplications since its
divergence
from Carica, with rapid DNA sequence divergence, extensive
gene loss
and fractionation of ancestral gene order eroding the
resemblance of
A. thaliana to ancestral Brassicales1. Compared with an
ancestor at just
a few million years ago, A. thaliana has undergone a ~30%
reduction in
genome size2 and 9–10 chromosomal rearrangements3,4 that
differentiate
it from its sister species Arabidopsis lyrata. Whole-genome
duplication
has been observed in all plant genomes sequenced to date. A.
thaliana has
undergone three paleo-polyploidy events5: a paleohexaploidy
(γ) event
shared with most dicots (asterids and rosids) and two
paleotetraploidy
events (β then α) shared with other members of the order
Brassicales.
8. B. rapa shares this complex history but with the addition of a
whole-
genome triplication (WGT) thought to have occurred between
13 and
17 million years ago (MYA)6,7, making ‘mesohexaploidy’ a
characteristic
of the Brassiceae tribe of the Brassicaceae8.
Brassica crops are used for human nutrition and provide
opportuni-
ties for the study of genome evolution. These crops include
important
vegetables (B. rapa (Chinese cabbage, pak choi and turnip) and
Brassica
oleracea (broccoli, cabbage and cauliflower)) as well as oilseed
crops
(Brassica napus, B. rapa, Brassica juncea and Brassica
carinata), which
provide collectively 12% of the world’s edible vegetable oil
production9.
The six widely cultivated Brassica species are also a classical
example
of the importance of polyploidy in botanical evolution,
described by
‘U’s triangle’10, with the three diploid species B. rapa (A
genome),
A full list of members appears at the end of the paper.
Received 7 March 2011; accepted 3 August 2011; published
online 28 August 2011; doi:10.1038/ng.919
http://www.nature.com/naturegenetics/
http://www.nature.com/doifinder/10.1038/ng.919
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We analyzed the organization and evolution of the genome (as
described in the Online Methods and the Supplementary Note).
B. rapa’s close relationship to A. thaliana allows Arabidopsis to
be used
as an outgroup for investigating the adaptation of the Brassica
lineage
to the triplicated state. In total, 108.6 Mb (90.01%) of the A.
12. thaliana
genome and 259.6 Mb (91.13%) of the B. rapa genome assembly
were
contained within collinear blocks. We confirmed the almost
complete
triplication of the B. rapa genome relative to A. thaliana (Fig.
3) and (by
inference) to the postulated Brassicaceae ancestral genome (n =
8). The
gene paralogues anchored in the triplicated segments
(Supplementary
Fig. 1) and their orthologs (Supplementary Table 6) dated the
meso-
hexaploidy event to between 5 and 9 MYA (Supplementary Fig.
2),
which is more recent than has been reported previously13.
The Brassica mesohexaploidy offers an opportunity to study
gene
retention in triplicated genomes. Assuming an initial count of
protein
coding genes similar to that of A. thaliana (around 30,000), the
newly
formed hexaploid would have about 90,000 genes, of which we
can now
identify only 41,174. This is typical of the substantial gene loss
that occurs
following polyploid formation in eukaryotes19–21. We
identified each of
the orthologous blocks in the B. rapa genome corresponding to
ancestral
blocks using collinearity between orthologs on the genomes of
B. rapa
and A. thaliana and found significant disparity in gene loss
across the
13. triplicated blocks (Supplementary Fig. 3). Of the 21 regions of
conserved
synteny, 20 showed significant deviations from equivalent gene
frequen-
cies (P < 0.05) (Supplementary Fig. 4). To illustrate this
variation, we
concatenated the least fractionated blocks (LF), the medium
fractionated
blocks (MF1) and the most fractionated blocks (MF2) and
calculated
the proportions of genes retained in each of these sub-genomes
relative
to A. thaliana. The LF sub-genome retains 70% of the genes
found in
A. thaliana, whereas the MF1 and MF2 sub-genomes retain
substantially
lower proportions of retained genes (46% and 36%,
respectively; Fig. 4).
Based on the analysis of synonymous base substitution rates (Ks
values),
the pairwise divergences between the three sub-genomes are
indistin-
guishable from each other (Supplementary Table 7). Our
observation of
differentially fractionated sub-genomes is consistent with the
hypothesis
that the sub-genomes MF1 and MF2 underwent substantial
fractiona-
tion in a tetraploid nucleus before fractionation commenced in
the LF
genome in a more recently formed hexaploid. However, biased
fractiona-
tion following tetraploidy (albeit less extreme than we
observed) has
been reported in A. thaliana22 and maize23, where it was
hypothesized
14. to be the result of differential epigenetic marking of the parent
genomes
(resulting in differential gene silencing and consequential
fraction), rep-
resenting an alternative hypothesis.
The retention of extensive collinear genome blocks provides a
potential opportunity for ectopic DNA recombination. By
finding and
comparing homologous gene quartets, including two α or β
duplicates
in Brassica and their respective orthologs in Arabidopsis, we
noted that,
respectively, 25% and 30% of Brassica and Arabidopsis
duplicates are
more similar to their intragenomic paralog than to their
intergenomic
ortholog, suggesting appreciable gene conversion since the
divergence of
these lineages (Supplementary Note). The sizes of the affected
regions
vary from 10 bp to >2 kb, with a majority of these apparent
conversion
events occurring in parallel in both species. Genes proximal to
telo-
meres tend to have lower nucleotide substitution rates than
distal genes
(P = 0.0004), which is likely to be a result of higher conversion
rates in
the former and is consistent with prior findings in grasses24,25.
The gene dosage hypothesis26 predicts that gene functional
categor-
ies encoding products that interact with one another or in
networks
15. table 1 summary of the final assembly statistics
Contig size Contig number Scaffold size Scaffold number
N90 5,593 10,564 357,979 159
N80 10,984 7,292 773,703 104
N70 15,947 5,308 1,257,653 77
N60 21,229 3,874 1,452,355 56
N50 27,294 2,778 1,971,137 39
Total size 264,110,991 283,823,632
Total number
(>100 bp)
60,521 40,549
Total number
(>2 kb)
14,207 794
A01
A02
A03
A04
A05
16. A06
A07
A08
A09
A10
0M 10M 20M 30M
Retrotransposons
DNA transposons
Genes (introns)
Genes (exons)
Figure 1 Chromosomal distribution of the main B. rapa genome
features.
Area charts quantify retrotransposons, genes (exons and introns)
and DNA
transposons. The x axis denotes the physical position along the
B. rapa
chromosomes in units of million (M) bases.
C. papaya
19,093
13,533
A. thaliana
29,139
16,985
B. rapa
32,543
16,917
21. interact
with other gene products should be under retained. In
accordance
with this hypothesis, we found B. rapa transcription factors with
a
detectable ortholog in A. thaliana to be significantly over
retained
(Supplementary Table 8 and Supplementary Note). We obtained
similarly consistent results for genes encoding known protein
subunits
of cytoplasmic ribosomes and for genes known to be involved
with the
proteosome. We found under retention of genes encoding
products
with few interactions, specifically those associated with DNA
repair,
nuclease activity, binding and the chloroplast (Supplementary
Table 9).
The Gene Ontology annotation classes of over retained genes
sug-
gests that genome triplication may have expanded gene families
that
underlie environmental adaptability, as observed in other
polyploid
species27. Genes with Gene Ontology terms associated with
response
to important environmental factors, including salt, cold, osmotic
stress, light, wounding, pathogen (broad spectrum) defense and
both
cadmium and zinc ions, were over retained (Fig. 5). Genes
respond-
ing to plant hormones (jasmonic acid, auxin, salicylic acid,
ethylene,
brassinosteroid, cytokinin and abscisic acid) were also over
retained.
22. Under selection, Brassica species have a remarkable propensity
for the
development of morphological variants28; we analyzed factors
poten-
tially involved in this development (Supplementary Note). One
factor
may be a general acceleration of nucleotide substitution rates.
For 2,275
orthologous groups of genes in B. rapa, A. thaliana, papaya and
grape
(Supplementary Table 10), the nucleotide substitution rates in
B. rapa
were greater than in the other plants, with average Ks (Ks is the
ratio
of the number of synonymous substitutions per synonymous
site) and
Ka (Ka is the ratio of the number of non-synonymous
substitutions per non-
synonymous site) values 69% and 24%, respectively, greater
than papaya
and 1% and 7%, respectively, greater than A. thaliana
(Supplementary
Table 11). The much slower evolutionary rate in papaya may be
explained
by its longer generation time as a perennial. Another factor may
be expan-
sion of auxin-related gene families, as auxin controls many
plant growth
and morphological developmental processes29–31. We
identified 347
B. rapa genes related to auxin synthesis, transportation, signal
transduc-
tion and inactivation, in contrast to 187 such genes present in
A. thaliana
(Supplementary Tables 12 and 13 and Supplementary Figs. 5–
14). The
23. TCP gene family is important in the evolution and specification
of plant
morphology32. This family has been amplified in B. rapa, which
contains
39 TCP genes, which is more than A. thaliana (24), grape (19)
or papaya (21)
(Supplementary Fig. 15). The regulation of flowering is key to
many
Brassica morphotypes. Mesohexaploidy has had contrasting
effects on
the genes involved. FLC (FLOWERING LOCUS C)33 has three
orthologs
in B. rapa as a consequence of the WGT (Supplementary Fig.
16).
Likewise, five of six B. rapa VRN1 (VERNALIZATION1)
genes34
U
C
H
R
5
C
H
R
4
C
H
R
3
26. 190 Mb 210 Mb 230 Mb 250 Mb
1
1
0
M
b
TNM DW F S R W E V KL QX R W J P F U N I J J A B F C A
B M XHQXBLKV H F B X N E C T B U B AOO TS OC I
QXHH D BVKV B N I A A W RH R
X
W
V
S
Q
R
U
T
P
O
N
M
L
F
27. J
I
H
G
K
E
D
C
B
A
Figure 3 Segmental collinearity of the genomes of B. rapa and
A. thaliana. Conserved collinear blocks of gene models are
shown between the ten
chromosomes of the B. rapa genome (horizontal axis) and the
five chromosomes of the A. thaliana genome (vertical axis).
These blocks are labeled A to
X and are color coded by inferred ancestral chromosome
following established convention.
100 LF
MF1 and MF2
80
60
P
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1 0 3 8 VOLUME 43 | NUMBER 10 | OCTOBER 2011
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produced by the WGT have been preserved (Supplementary
Fig. 17).
However, GI (GIGANTEA) genes35 have been limited to only
one copy
(Supplementary Fig. 18), as have the SVP (SHORT
VEGETATIVE
PHASE) genes36 (Supplementary Fig. 19) and each of the three
COL
(CONSTANS-LIKE) genes37 (Supplementary Fig. 20).
The comparison of the genomes of B. rapa and A. thaliana, as
for pre-
vious comparisons of the cereals sorghum and rice38, sheds new
light on
the evolution of genome evolution in plants important for
human nutri-
tion. Our growing understanding of the processes shaping the
triplicated
genome of the mesopolyploid B. rapa is of relevance not only
for closely
related crops species, such as B. oleracea and B. napus, but also
for other
important crops with triplicated genomes, such as bread wheat.
33. URLs. Brassica info, http://www.brassica.info/; GenoScope
database,
http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/;
Hawaii
Papaya Genome Project,
http://asgpb.mhpcc.hawaii.edu/papaya/;
Arabidopsis Information Resource, http://www.arabidopsis.org/.
MeThods
Methods and any associated references are available in the
online
version of the paper at http://www.nature.com/naturegenetics/.
Accession codes. This whole-genome shotgun project has been
depos-
ited at DDBJ/EMBL/GenBank under the accession
AENI00000000. The
version described in this paper is the first version,
AENI01000000. Full
annotation is available at http://brassicadb.org/.
Note: Supplementary information is available on the Nature
Genetics website.
ACknowledGmenTS
This work was primarily funded by the Chinese Ministry of
Science and
Technology, Ministry of Agriculture, Ministry of Finance, the
National Natural
Science Foundation of China. Other funding sources included:
Core Research
Budget of the Non-profit Governmental Research Institution;
the European Union
7th Framework Project; funds from Shenzhen Municipal
Government of China;
34. the Danish Natural Science Research Council; National
Academy of Agricultural
Science and the Next-Generation Biogreen21 Program, Rural
Development
Administration, Korea; the Technology Development Program
for Agriculture and
Forestry, Ministry for Food, Agriculture, Forestry and Fisheries,
Korea; United
Kingdom’s Biotechnology and Biological Sciences Research
Council; Institute
National de la Recherche Agronomique, France; Japanese
Kazusa DNA Research
Institute Foundation; National Science Foundation, USA;
Bielefeld University,
Germany; the Australian Research Council; the Australian
Grains Research
and Development Corporation; Agriculture and Agri-Food
Canada; and the
National Research Council of Canada’s Plant Biotechnology
Institute. See the
Supplementary Note for a full list of support and
acknowledgments.
AUTHoR ConTRIBUTIonS
Principal investigators: Xiaowu Wang, J. Wu, S.L., Y.B., J.-
H.M. and I.B.
DNA and transcriptome sequencing: Bo Wang (group leader),
Xiaowu Wang
(group leader), B.C. (group leader), Jun Wang (BGI), K.W., J.
Wu, S.L., W.H.,
B.-S.P., I.B., D.E., I.A.P.P., J.-H.M., H.A., Bernd Weisshaar,
Shusei Sato, H.H., S.T.,
A.G.S., Y. Lim, G.B., J.B., C.L., C.G., J.P., S.-J.K., J.A.K.,
M.T., F.F., E.S., M.G.L., C.K.,
K.H., Y.N., P.J.B. and C.D. Sequence assembly: Junyi Wang
(group leader), Jun Wang
35. (BGI), D.M., Y. Li, X.X., Bo Liu, Silong Sun, Z.Z., Z.L.,
Binghang Liu, Q.C., Shu
Zhang, Y.B., Zhiwen Wang, X.Z., C.S., J.Y. and J.J. Anchoring
to linkage maps:
J. Wu (group leader), W.H. (group leader), G.J.K., Y. Lim, B.-
S.P., I.B., J.B., D.E.,
Yan Wang, Bo Liu, Silong Sun, Jun Wang (Rothamsted),
I.A.P.P., J. Meng, Hui
Wang, J.D., Y. Liao, Y.B., Haiping Wang, M.J., J.-S.K., S.-
R.C., N.R. and A.H.
Annotation: Y.B. (group leader), S.L. (group leader), R.L.,
W.F., Q.H., F.C., Bo Liu,
D.E., J. Min, Jianwen Li, C.P., H.Z., Shunmou Huang, B.C.,
J.J., H.B., G.L., N.D. and
M.T. Stabilizing the genome of a polyploidy dicotyledonous
species: F.C. (group
leader), Sanwen Huang (group leader), Y.B., Xiaowu Wang, B.
Li, S.C., Y.Y., J.X. and
C.T. Comparative genomics: Xiaowu Wang (group leader),
J.C.P. (group leader),
Xiyin Wang (group leader), I.B., F.C., H.T., G.C., H.G., T.-
H.L., Jinpeng Wang and
Zhenyi Wang. Retention of genes duplicated by polyploidy:
M.F. (group leader),
A.H.P. (group leader), F.C., H.T., Bo Liu, Silong Sun, L.F.,
Z.X., M.Z., Jingping Li,
H.J. and X.T. Characteristics of a crop genome: J. Wu (group
leader), X.L. (group
leader), R.S., Hanzhong Wang, Y.D., Xiaowu Wang, Hui Wang,
J.D., D.S., Y.Q.,
Shujiang Zhang, F.L., L.W. and Yupeng Wang.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
36. Published online at http://www.nature.com/naturegenetics/.
Reprints and permissions information is available online at
http://www.nature.com/
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Xiaowu wang1, Hanzhong wang2, Jun wang3,4, Rifei Sun1, Jian
wu1, Shengyi liu2, Yinqi Bai3, Jeong-Hwan mun5,
Ian Bancroft6, Feng Cheng1, Sanwen Huang1, Xixiang li1, wei
Hua2, Junyi wang3, Xiyin wang7–9,
michael Freeling10, J Chris Pires11, Andrew H Paterson9,
Boulos Chalhoub12, Bo wang3, Alice Hayward13,14,
Andrew G Sharpe15, Beom-Seok Park5, Bernd weisshaar16,
Binghang liu3, Bo li3, Bo liu1, Chaobo Tong2,
Chi Song3, Christopher duran13,17, Chunfang Peng3, Chunyu
Geng3, Chushin koh15, Chuyu lin3,
david edwards13,17, desheng mu3, di Shen1, eleni
Soumpourou6, Fei li1, Fiona Fraser6, Gavin Conant18,
Gilles lassalle19, Graham J king20, Guusje Bonnema21, Haibao
Tang10, Haiping wang1, Harry Belcram12,
Heling Zhou3, Hideki Hirakawa22, Hiroshi Abe23, Hui Guo9,
Hui wang1, Huizhe Jin9, Isobel A P Parkin24,
Jacqueline Batley13,14, Jeong-Sun kim5, Jérémy Just12,
Jianwen li3, Jiaohui Xu3, Jie deng1, Jin A kim5,
Jingping li9, Jingyin Yu2, Jinling meng25, Jinpeng wang7,8,
Jiumeng min3, Julie Poulain26, Jun wang20,
katsunori Hatakeyama27, kui wu3, li wang7,8, lu Fang1, martin
Trick6, matthew G links24, meixia Zhao2,
mina Jin5, nirala Ramchiary28, nizar drou6, Paul J
Berkman13,17, Qingle Cai3, Quanfei Huang3, Ruiqiang li3,
Satoshi Tabata22, Shifeng Cheng3, Shu Zhang3, Shujiang
Zhang1, Shunmou Huang2, Shusei Sato22, Silong Sun1,
Soo-Jin kwon5, Su-Ryun Choi28, Tae-Ho lee9, wei Fan3, Xiang
Zhao3, Xu Tan9, Xun Xu3, Yan wang1,
Yang Qiu1, Ye Yin3, Yingrui li3, Yongchen du1, Yongcui
liao1, Yongpyo lim28, Yoshihiro narusaka29,
54. Yupeng wang8, Zhenyi wang7,8, Zhenyu li3, Zhiwen wang3,
Zhiyong Xiong11 & Zhonghua Zhang1
1Institute of Vegetables and Flowers, Chinese Academy of
Agricultural Sciences (IVF, CAAS), Beijing, China. 2Oil Crops
Research Institute, Chinese Academy
of Agricultural Sciences, Wuhan, Hubei, China. 3BGI-
Shenzhen, Shenzhen, China. 4Department of Biology,
University of Copenhagen, Copenhagen, Denmark.
5Department of Agricultural Biotechnology, National Academy
of Agricultural Science, Rural Development Administration,
Suwon, Korea. 6John Innes Centre,
Norwich Research Park, Colney, Norwich, UK. 7Center for
Genomics and Computational Biology, School of Life Sciences,
Hebei United University, Tangshan, Hebei, China.
8School of Sciences, Hebei United University, Tangshan,
Hebei, China. 9Plant Genome Mapping Laboratory, University
of Georgia, Athens, Georgia, USA.
10Department of Plant and Microbial Biology, University of
California, Berkeley, California, USA. 11Division of Biological
Sciences, Bond Life Sciences Center,
University of Missouri, Columbia, Missouri, USA.
12Organization and Evolution of Plant Genomes, Unité de
Recherche en Génomique Végétale, Unité Mixte de
Recherché 1165, (Inland Northwest Research Alliance-Centre
National de la Recherche Scientifique, Université Evry Val
d’Essonne), Evry, France. 13University
of Queensland, School of Agriculture and Food Sciences,
Brisbane, Queensland, Australia. 14Australian Research Council
Centre of Excellence for Integrative
Legume Research, Brisbane, Queensland, Australia. 15National
Research Council-Plant Biotechnology Institute, Saskatoon,
Saskatchewan, Canada. 16Center for
Biotechnology, Bielefeld University, Bielefeld, Germany.
17Australian Centre for Plant Functional Genomics, Brisbane,
Queensland, Australia. 18Division of Animal
58. h
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41. Delcher, A.L., Phillippy, A., Carlton, J. & Salzberg, S.L.
Fast algorithms for large-scale
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2478–2483 (2002).
42. Parkin, I.A. et al. Segmental structure of the Brassica napus
genome based on
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765–781 (2005).
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Genomewise. Genome Res. 14,
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identification of ortholog groups for
eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).
47. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4:
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oNLINe MeThods
Genome sequencing and assembly. Approximately 72-fold
shotgun coverage was
generated using Illumina GA II sequencing from short (~200
bp), medium (~500 bp)
and long (~2 kb, 5 kb and 10 kb) insert libraries (Supplementary
Note and
Supplementary Table 14). The raw Illumina reads were filtered
for duplicates,
adaptor contamination and low quality before assembly into
preliminary scaffolds
using SOAPdenovo39 run with default parameters. We first
assembled the reads
from the short insert size (≤500 bp) libraries into contigs using
Kmer (de bruijn
60. graph kmer) overlap information and ensured the resulting
contigs were unique by
determining an unambiguous path in the de bruijn graph. This
resulted in contigs
with an N50 length of 1.1 kb, achieving a total length of 222
Mb; the long insert size
mate-paired libraries (≥2 kb) were not used initially because the
chimaeric reads
common to such libraries can generate incorrect sequence
overlaps. After obtaining
the unique contigs, we mapped all available paired-end reads to
these contigs to
connect adjacent contigs. In order to avoid interleaving and to
reduce the impact of
the insert-size deviation of any sequencing library, we used a
hierarchical assembly
method, constructing the scaffolds step by step by adding data
from each library
separately ranked according to insert size from smallest to
largest. This obtained
scaffolds with an N50 length of 347 kb and a total genome
length of 288 Mb. Most
of the remaining gaps between contigs probably occur in
repetitive regions, so we
identified the paired-end reads with only one end mapped to a
unique contig and
performed local assembly with the unmapped end to fill small
gaps within the scaf-
folds. The resulting assembly had a final contig N50 length of
27 kb (Supplementary
Table 15). In total, 32-Mb gaps were closed. A total of 199,452
BAC-end Sanger
sequences retrieved from http://www.brassica-
rapa.org/BRGP/bacEndList.jsp were
used to construct the super scaffolds. The gaps within the
scaffolds were filled in as
61. previously described40. The expected genome size of B. rapa
was estimated from the
distribution of 17-mer depth as assessed from the filtered
sequence data using meth-
ods previously described40. The peak depth of 17-mers was at
15-folds and a total
7,287,899,150 17-mers were obtained. We obtained an
estimated genome size of
485 Mb by dividing the total number of 17-mers by the peak
depth.
Validation of assembly. NUCmer41 was used to compare the
sequence of chromo-
some A03 assembled here by whole-genome shotgun sequencing
(WGS A03) to the
same chromosome assembled by BAC Sanger sequencing (BAC
A03) previously
reported15 (Supplementary Note and Supplementary Fig. 21).
The total sizes of
WGS A03 and BAC A03 are approximately 31.72 Mb and 32.70
Mb, respectively,
with slightly more repeat sequences assembled using the BAC
approach (9.82 Mb
in BAC A03 and 5.68 Mb in WGS A03) (Supplementary Table
16). There were
more gaps observed in BAC A03 (1,035/1,358,889 bp, number
of gaps/total size of
gaps) than in WGS A03 (858/844,319 bp) (Supplementary Table
17). We identi-
fied 44 obvious inversions (>1 kb) between the two assemblies.
Evidence provided
by studying the mapped paired ends, the depth of the mapped
reads and gaps at
the boundaries for 38 inversions supported the WGS assembly
(Supplementary
Fig. 22a,b), and 6 inversions remained ambiguous
62. (Supplementary Fig. 23c).
To evaluate the accuracy of the assembly on a local scale, the
sequence of
647 complete BAC clones (phase 2 and phase 3) that had been
deposited in NCBI
and had been genetically mapped (see URLs) were compared
with their equivalent
WGS sequence (Supplementary Table 18).
Integration of shotgun assembly with genetic maps. The
scaffolds were
anchored to the B. rapa genetic linkage map using 1,427
uniquely aligned
markers from an integrated linkage map developed from four
populations
(Supplementary Table 19). In addition, 1,054 markers mapped
to the B. napus
A genome were used to verify and aid the alignment.
Chromosomes were ori-
entated by alignment to the reference A genome linkage groups
from Parkin
et al.42 (equivalent to N1-N10). Where genetic information was
not available
from Brassica maps, scaffold order and/or orientation was
inferred based on
evidence of conserved collinearity with the A. thaliana gene
order.
Protein coding gene annotation. In addition to available
Brassica EST data
(downloaded from dbEST at NCBI 10 July 2010), we generated
a total of 27.1
million Illumina RNA-Seq paired-end reads, 19.9 million of
which were from
Chiifu-401-42 and 7.2 million of which were from a Caixin
accession, L58, to
63. verify the predicted gene models (Supplementary Fig. 24). For
Chiifu-401-42,
equally mixed total RNA isolated from eight different tissues
and growth con-
ditions was used: leaves, roots and floral stems from plants
grown in pots;
2-week-old etiolated seedlings; shoots from plants grown
hydroponically
under normal conditions; and leaves from plants treated with
0.5% NaCl at
4 °C and 37 °C for 24 h. For L58, equally mixed total RNA was
isolated from
similar tissues with the addition of germinating seeds, callus
and pods.
The genome assembly was premasked for class I and class II
transposable
elements, and Genscan and Augustus were used to carry out de
novo predic-
tions with gene model parameters trained from A. thaliana.
Genes with less
than 150 bp of coding sequence were filtered out. For
homology-based gene
prediction, we aligned A. thaliana, C. papaya, Populus
trichocarpa, V. vinifera
and Oryza sativa protein sequences to the B. rapa genome using
TBLASTN
(at an E value of 1 × 10−5) for fast alignment and Genewise43
for precise align-
ment. The Unigene sequences of B. rapa and the Brassica ESTs
downloaded
from NCBI were aligned to the B. rapa genome using BLAT and
assembled
by PASA44 based on genomic location. As the fragmental exons
in ESTs data
64. might lead to pseudo alignments, we filtered out the results with
intron(s)
more than 10,000 bp. GLEAN45 was used to combine de novo
gene sets and
homology-based gene sets and incorporated the expressed
sequence data
described above as supporting evidence (Supplementary Tables
20 and 21 and
Supplementary Figs. 24 and 25). In addition, those predicted B.
rapa proteins
that aligned to the Repbase transposable element protein
database (E value
1 × 10−5 at ≥50%) were filtered out.
The B. rapa predicted proteins were annotated based on
alignment to the Swiss-
Prot and TrEMBL databases with BLASTP at E value 1 × 10−5.
InterPro was used
to annotate motifs and domains by comparison with publicly
available databases
including Pfam, PRINTS, PROSITE, ProDom and SMART. The
Gene Ontology
information for each gene code was extracted from the InterPro
results.
To identify and estimate the number of potential orthologous
gene fami-
lies between B. rapa, V. vinifera, A. thaliana and C. papaya, we
applied the
OrthoMCL pipeline46 using standard settings (BLASTP E value
< 1 × 10−5) to
compute the all-against-all similarities.
Inter- and intra-genomic alignments. The synteny within and
between spe-
cies was constructed by McScan (MATCH_SCORE: 50,
65. MATCH_SIZE: 5,
GAP_SCORE: –3, E_VALUE: 1E–05). An all-against-all
BLASTP comparison
provided the pairwise gene information and P value for a
primary clustering.
Then, paired segments were extended by identifying clustered
genes using
dynamic programming. This method was used to build the
genome synteny
blocks of B. rapa versus B. rapa, A. thaliana, C. papaya, P.
trichocarpa,
V. vinifera and O. sativa, and A. thaliana versus A. thaliana.
Phylogenetic analyses of biologically important gene families.
Gene sequences
from grape, papaya and Arabidopsis were downloaded from the
GenoScope
database, the Hawaii Papaya Genome Project and the
Arabidopsis Information
Resource, respectively (see URLs). Previously reported
Arabidopsis and Brassica
gene sequences were downloaded from GenBank. The protein
sequences of the
genes were used to determine homologs in grape, papaya, A.
thaliana and B. rapa
by performing BLASTP searches at E value 1 × 10−10.
Alignment of each family
was performed by running MEGA with default parameters47
and subjected to
careful manual checking to remove highly divergent sequences
from further
analysis. The retrieved protein sequences were used to
reconstruct phylogenies
using the neighbor-joining approach implemented in MEGA47.
A bootstrapping
test was performed using 100 repetitive samplings for each gene
66. family.
http://www.brassica-rapa.org/BRGP/bacEndList.jsp
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