This document analyzes the distribution, phylogeny, and structural characteristics of group I introns found inserted at positions 516 and 1506 in the nuclear SSU rRNA gene of the red algae genera Bangia and Porphyra. The lengths of the introns varied considerably between species. Larger introns contained open reading frames encoding putative homing endonuclease proteins. Phylogenies of the intron sequences and 18S rRNA gene sequences were congruent, supporting vertical inheritance of the introns. Structural analysis revealed a unique signature in the P5b domain of intron 516 that is specific to Bangiales.
This document describes a study that developed a new method called amplified functional DNA restriction analysis (AFDRA) to analyze the diversity of catechol 2,3-dioxygenase (C23O) genes in soil bacteria. C23O genes code for enzymes important for degrading aromatic pollutants. The researchers used AFDRA to analyze C23O genes from reference strains and soil isolates. They found that AFDRA generated distinct restriction patterns that clustered the isolates into four groups, consistent with sequence analysis. AFDRA also allowed them to determine the predominant C23O gene variants present in environmental DNA extracts from soil samples. The study demonstrates that AFDRA provides a rapid way to assess functional gene diversity in cultures and
PCR and DNA sequence analysis were used to identify potato cyst nematodes (PCN) from Victoria, Australia. Only Globodera rostochiensis was detected among 87 soil samples. Sequence analysis revealed genetically diverse G. rostochiensis populations but no variation in diagnostic primer binding sites. Real-time PCR detected DNA at lower levels than conventional PCR and distinguished species via melting peaks of 83.3°C for G. pallida and 88.7°C for G. rostochiensis. The study identified PCN species in Victoria and implications for monitoring and control strategies.
This document describes the development of 160 novel simple sequence repeat (SSR) markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries. Genomic DNA from bitter gourd was used to construct libraries enriched for 10 different repeat motifs. Of the 3,072 clones screened, 93.7% contained microsatellite repeats. Unique primer pairs were designed and validated for 151 loci. Genetic diversity analysis of 51 loci among 54 accessions found 20% were polymorphic. The markers distinguished 15 Indian varieties and 78.4% were transferable across six Momordica species. The new SSR markers will be useful for genetic studies in bitter gourd.
Molecular marker to identify gynoecious lines in bitter gourdSwati Saxena
This document discusses the identification of molecular markers associated with the gynoecious trait in bitter gourd. Twenty-four gynoecious plants were screened using 200 RAPD and 28 ISSR markers. One ISSR primer amplified a 1000 base pair fragment present in all gynoecious plants but absent in two monoecious varieties. This fragment was repeatably amplified and could serve as a diagnostic marker for gynoecy, allowing identification of the trait at an early stage for hybrid seed production.
Characterization of Arsenic contaminated Rice (Oryza Sativa L.) through RAPD ...IOSR Journals
Rice being cultivated under anaerobic condition is vulnerable to arsenite, a mobile arsenic speciation Both arsenate and arsenite are highly toxic to human body. Experiments were conducted in Nonaghata (Nadia) and De-ganga (North 24 parganas) with 40 genotypes of rice in Boro season. A few varieties have been identified with low arsenic. Simultaneously some of them were characterized at molecular level by RAPD technique. It is worth to be seen how the low grain and high grain arsenic varieties behave in RAPD fingerprinting. Fourteen out of the 18 decamer random primers showed amplification of genomic DNA in all individuals. A total of 59 fragments were scored, of these fragments, 10 (16.94%) were common to all accessions, 49 (83.06%) were polymorphic and shared by at least eight accessions. It is interesting to mention that the genotypes Azucena and Lemont have already been identified as low grain arsenic genotypes and occupied a distinct different cluster for all primers at the molecular level also. More research is needed in arsenic research in crop plants in different agro climatic situation to have a meaningful and stable conclusion so that the farmers and also the people of West Bengal do not suffer from arsenic hazards at least from the consumption of rice.
The IFNy receptor consists of two subunits, IFNGR1 and IFNGR2, that are expressed on nearly all cell surfaces. IFNGR1 mediates high-affinity ligand binding and signal transduction, while IFNGR2 plays a minor role in binding but is required for signaling. The receptor utilizes the JAK/STAT pathway, specifically JAK1, JAK2, and STAT1, to mediate many effects of IFNy by regulating immediate-early genes containing GAS promoter elements. Disrupting the JAK/STAT pathway impairs the immune response to various pathogens and tumors. Recently, mutations in IFNGR1 or IFNGR2 were found in patients with rare mycobacterial infections, showing the physiological
This document analyzed the genetic diversity of 50 Asian bitter gourd genotypes using morphological traits and molecular markers. Key findings:
1. Significant variation was found for yield and other traits based on morphological analysis, indicating genetic diversity. The highest yielding genotype was Sel-2.
2. Molecular analysis using RAPD and ISSR markers found high levels of polymorphism, with ISSR showing more polymorphic bands.
3. Cluster analyses based on morphological, RAPD, ISSR, and combined data grouped genotypes into clusters largely correlating with geographical origin and domestication status. The analyses demonstrate large genetic variability in the collection.
Introduction to Genetic Material, Physical and Chemical properties of the same and various types of coiling mechanisms as well as information about chromosomal and extra-chromosomal DNA.
This document describes a study that developed a new method called amplified functional DNA restriction analysis (AFDRA) to analyze the diversity of catechol 2,3-dioxygenase (C23O) genes in soil bacteria. C23O genes code for enzymes important for degrading aromatic pollutants. The researchers used AFDRA to analyze C23O genes from reference strains and soil isolates. They found that AFDRA generated distinct restriction patterns that clustered the isolates into four groups, consistent with sequence analysis. AFDRA also allowed them to determine the predominant C23O gene variants present in environmental DNA extracts from soil samples. The study demonstrates that AFDRA provides a rapid way to assess functional gene diversity in cultures and
PCR and DNA sequence analysis were used to identify potato cyst nematodes (PCN) from Victoria, Australia. Only Globodera rostochiensis was detected among 87 soil samples. Sequence analysis revealed genetically diverse G. rostochiensis populations but no variation in diagnostic primer binding sites. Real-time PCR detected DNA at lower levels than conventional PCR and distinguished species via melting peaks of 83.3°C for G. pallida and 88.7°C for G. rostochiensis. The study identified PCN species in Victoria and implications for monitoring and control strategies.
This document describes the development of 160 novel simple sequence repeat (SSR) markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries. Genomic DNA from bitter gourd was used to construct libraries enriched for 10 different repeat motifs. Of the 3,072 clones screened, 93.7% contained microsatellite repeats. Unique primer pairs were designed and validated for 151 loci. Genetic diversity analysis of 51 loci among 54 accessions found 20% were polymorphic. The markers distinguished 15 Indian varieties and 78.4% were transferable across six Momordica species. The new SSR markers will be useful for genetic studies in bitter gourd.
Molecular marker to identify gynoecious lines in bitter gourdSwati Saxena
This document discusses the identification of molecular markers associated with the gynoecious trait in bitter gourd. Twenty-four gynoecious plants were screened using 200 RAPD and 28 ISSR markers. One ISSR primer amplified a 1000 base pair fragment present in all gynoecious plants but absent in two monoecious varieties. This fragment was repeatably amplified and could serve as a diagnostic marker for gynoecy, allowing identification of the trait at an early stage for hybrid seed production.
Characterization of Arsenic contaminated Rice (Oryza Sativa L.) through RAPD ...IOSR Journals
Rice being cultivated under anaerobic condition is vulnerable to arsenite, a mobile arsenic speciation Both arsenate and arsenite are highly toxic to human body. Experiments were conducted in Nonaghata (Nadia) and De-ganga (North 24 parganas) with 40 genotypes of rice in Boro season. A few varieties have been identified with low arsenic. Simultaneously some of them were characterized at molecular level by RAPD technique. It is worth to be seen how the low grain and high grain arsenic varieties behave in RAPD fingerprinting. Fourteen out of the 18 decamer random primers showed amplification of genomic DNA in all individuals. A total of 59 fragments were scored, of these fragments, 10 (16.94%) were common to all accessions, 49 (83.06%) were polymorphic and shared by at least eight accessions. It is interesting to mention that the genotypes Azucena and Lemont have already been identified as low grain arsenic genotypes and occupied a distinct different cluster for all primers at the molecular level also. More research is needed in arsenic research in crop plants in different agro climatic situation to have a meaningful and stable conclusion so that the farmers and also the people of West Bengal do not suffer from arsenic hazards at least from the consumption of rice.
The IFNy receptor consists of two subunits, IFNGR1 and IFNGR2, that are expressed on nearly all cell surfaces. IFNGR1 mediates high-affinity ligand binding and signal transduction, while IFNGR2 plays a minor role in binding but is required for signaling. The receptor utilizes the JAK/STAT pathway, specifically JAK1, JAK2, and STAT1, to mediate many effects of IFNy by regulating immediate-early genes containing GAS promoter elements. Disrupting the JAK/STAT pathway impairs the immune response to various pathogens and tumors. Recently, mutations in IFNGR1 or IFNGR2 were found in patients with rare mycobacterial infections, showing the physiological
This document analyzed the genetic diversity of 50 Asian bitter gourd genotypes using morphological traits and molecular markers. Key findings:
1. Significant variation was found for yield and other traits based on morphological analysis, indicating genetic diversity. The highest yielding genotype was Sel-2.
2. Molecular analysis using RAPD and ISSR markers found high levels of polymorphism, with ISSR showing more polymorphic bands.
3. Cluster analyses based on morphological, RAPD, ISSR, and combined data grouped genotypes into clusters largely correlating with geographical origin and domestication status. The analyses demonstrate large genetic variability in the collection.
Introduction to Genetic Material, Physical and Chemical properties of the same and various types of coiling mechanisms as well as information about chromosomal and extra-chromosomal DNA.
This document discusses evidence of lateral transfer of a group IE intron between fungal and red algal small subunit rRNA genes. It finds that a group IE intron inserted at position 989 in the nuclear SSU rRNA gene of the red alga Hildenbrandia rubra is closely related to similar fungal IE introns, providing evidence the intron was laterally transferred rather than vertically inherited. Phylogenetic analysis of intron sequences and comparisons of intron secondary structures support a relationship between the red algal intron and fungal introns, making lateral transfer the most likely explanation for the intron's presence in H. rubra.
To handle complex Traits like Yield, different stress we must do modification in DNA molecular breeding techniques help us to do such changes in DNA to archive the Goals.
Reverse Breeding: a tool to create homozygous plants from the heterozygous po...Sanjay Kumar
This document provides an overview of reverse breeding, a novel plant breeding technique to directly produce homozygous parental lines from any heterozygous plant. It discusses how reverse breeding uses RNA interference to suppress meiotic recombination and produce doubled haploids from gametes, generating homozygous parental lines. The document summarizes a case study applying this to Arabidopsis thaliana and discusses applications like reconstructing hybrids, breeding at the chromosome level, and implications for food safety. Limitations and future research directions are also outlined.
Cloning and Characterization of Master Regulator of Systemic Acquired Resista...Akhilesh Rawat
The document describes research that cloned the npr1 gene, which encodes the non-expresser of PR proteins 1 protein and is a master regulator of systemic acquired resistance in plants. The researchers cloned the npr1 gene from mustard using PCR and sequenced it, finding 98% identity to reported npr1 genes. They transferred the cloned gene to tobacco through Agrobacterium-mediated transformation. The putative transgenic tobacco plants were confirmed using gene-specific PCR. Overexpression of npr1 has potential to provide broad-spectrum disease resistance in crops.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
ROLE OF INHERITANCE IN CROP IMPROVEMENTVinod Pawar
1. Two studies examined the inheritance of flower color in chickpea. Crosses between plants with pink and white flowers in the parental generation resulted in pink flowers in the F1 progeny.
2. Analysis of the F2 generations found ratios of pink to white flowers that mostly fit the expected 3:1 Mendelian ratio, suggesting flower color is governed by a single gene.
3. However, one cross showed a significant deviation from the expected ratio, indicating multiple genetic factors may influence flower color in some cases.
The document summarizes research on pleiotropic adult plant resistance (PAPR) loci in wheat. Key points:
1. CIMMYT has conducted PAPR research since the 1970s, identifying loci such as Lr34, Lr46, and Lr67 that confer resistance to multiple diseases.
2. Studies mapped additional PAPR QTL in various wheat populations and identified markers for genes like Lr46, Sr2, and Yr54 useful for marker-assisted selection.
3. Research involves fine mapping genes, identifying deletion mutants, and understanding resistance mechanisms to improve durability and pyramide genes in wheat breeding.
4. An international shuttle breeding program
This document describes a DNA marker-based technology developed to identify citrus rootstocks at the seedling stage. Traditionally, Rough lemon and Rangpur lime are preferred rootstocks but are difficult to distinguish from Galgal at an early stage. Galgal is an undesirable rootstock due to susceptibility to diseases. The new technology uses microsatellite markers and PCR to differentiate Rough lemon, Rangpur lime, and Galgal based on presence or absence of DNA fragments. It provides a non-destructive method to ensure nurseries are supplying quality rootstock varieties. The technique has been transferred to agricultural organizations to benefit citrus farmers.
The Lr34 gene in wheat has provided effective resistance against rust for over 100 years. It confers partial and durable resistance by prolonging the latency period and reducing spore production. Lr34 is not race-specific and also confers resistance to other pathogens. It encodes an ATP-binding cassette (ABC) transporter protein and differs by only two amino acids from susceptible alleles. Transgenic wheat with Lr34 shows complementation of resistance, though the genetic background can influence effects. Lr34's durable resistance is likely due to its ability to transport antimicrobial compounds or prime defense responses through its function as an ABC transporter.
TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
This document describes the identification of FLOWERING LOCUS T (FT) through an activation tagging screen in Arabidopsis thaliana. The 1733 mutant tagged line flowered early and had terminal flowers. Sequencing of the tagged gene revealed it to be FT. Overexpression of FT using the 35S promoter recapitulated the 1733 phenotype, flowering very early with few leaves. FT was found to act partially downstream of CONSTANS (CO) to promote flowering in response to day length. Unlike many floral regulators, the FT protein sequence does not suggest it directly controls transcription.
B-box proteins in plants bbx family of plant transcription factorsOm Prakash Patidar
This document summarizes research on B-box proteins. It begins by describing the structure of zinc finger domains and their ability to bind DNA, RNA, or proteins. It then discusses B-box (BBX) proteins, which contain zinc finger domains and are involved in plant protein-protein interactions and transcription factor activity. The document reviews studies of BBX proteins in animals and plants, describing their roles in processes like photomorphogenesis, flowering time regulation, and shade avoidance responses. Case studies are presented on specific BBX proteins in Arabidopsis and crops like rice and soybean.
This document discusses a study that found constitutive membrane association greatly enhances the ability of Bruton's tyrosine kinase (Btk) to transform cells. The study targeted Btk to the plasma membrane using fusion proteins, which led to high tyrosine phosphorylation of Btk. Cell transformation required membrane localization of Btk, its kinase activity, phosphorylation by Src kinases, and an intact SH2 domain. The results suggest membrane localization is a critical early step in Btk activation.
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
21. Mutation Breeding in crop improvement Naveen Kumar
Mutation breeding in crop improvement can utilize both spontaneous and induced mutations. Induced mutations are caused by physical mutagens like radiation (x-rays, gamma rays, UV light) or chemical mutagens. Mutation rates can vary between genes and induced mutations occur more frequently than spontaneous mutations. Mutation breeding is useful for crop improvement by generating genetic variation for selection of desirable traits.
Glutamine methylation in Histone H2A is an RNA Polymerase I dedicated modification. The study identified and localized methylated glutamine 105 in Histone H2A. Nop1/Fibrillarian was identified as the methyltransferase that modifies Q105. The genomic landscape of Q105me was analyzed and unmodified Q105 was found to be part of a recognition motif for FACT.
Targeting Induced Local Lesions IN Genomes (TILLING) is a combined tool of plant mutagenesis and DNA Biology to investigate useful mutations at Genomic level. First time used for cotton improvement.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
tansgenic mice:methodology and applicationtinasingh30
This document discusses the generation and applications of transgenic mice. It describes four main methods for generating transgenic mice: retroviral vector method, microinjection method, engineered embryonic stem cell method, and yeast artificial chromosome transgenesis. Transgenic mice can be used as disease models and to study the biological basis of human diseases. They have been made for conditions like Alzheimer's disease and cystic fibrosis. Transgenic mice are also used as test systems to evaluate potential therapies.
Maxim is a 12-year-old boy who enjoys fishing, computer games, and his cat. He has been fishing for the last four years and caught a 1kg pike, which is pictured. He likes playing games like Need for Speed, Grand Theft Auto, and Counter Strike on the computer. He has a 4-year-old black and white cat named Boy who likes to play and gets fed milk, fish, and sausages.
This document discusses evidence of lateral transfer of a group IE intron between fungal and red algal small subunit rRNA genes. It finds that a group IE intron inserted at position 989 in the nuclear SSU rRNA gene of the red alga Hildenbrandia rubra is closely related to similar fungal IE introns, providing evidence the intron was laterally transferred rather than vertically inherited. Phylogenetic analysis of intron sequences and comparisons of intron secondary structures support a relationship between the red algal intron and fungal introns, making lateral transfer the most likely explanation for the intron's presence in H. rubra.
To handle complex Traits like Yield, different stress we must do modification in DNA molecular breeding techniques help us to do such changes in DNA to archive the Goals.
Reverse Breeding: a tool to create homozygous plants from the heterozygous po...Sanjay Kumar
This document provides an overview of reverse breeding, a novel plant breeding technique to directly produce homozygous parental lines from any heterozygous plant. It discusses how reverse breeding uses RNA interference to suppress meiotic recombination and produce doubled haploids from gametes, generating homozygous parental lines. The document summarizes a case study applying this to Arabidopsis thaliana and discusses applications like reconstructing hybrids, breeding at the chromosome level, and implications for food safety. Limitations and future research directions are also outlined.
Cloning and Characterization of Master Regulator of Systemic Acquired Resista...Akhilesh Rawat
The document describes research that cloned the npr1 gene, which encodes the non-expresser of PR proteins 1 protein and is a master regulator of systemic acquired resistance in plants. The researchers cloned the npr1 gene from mustard using PCR and sequenced it, finding 98% identity to reported npr1 genes. They transferred the cloned gene to tobacco through Agrobacterium-mediated transformation. The putative transgenic tobacco plants were confirmed using gene-specific PCR. Overexpression of npr1 has potential to provide broad-spectrum disease resistance in crops.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
ROLE OF INHERITANCE IN CROP IMPROVEMENTVinod Pawar
1. Two studies examined the inheritance of flower color in chickpea. Crosses between plants with pink and white flowers in the parental generation resulted in pink flowers in the F1 progeny.
2. Analysis of the F2 generations found ratios of pink to white flowers that mostly fit the expected 3:1 Mendelian ratio, suggesting flower color is governed by a single gene.
3. However, one cross showed a significant deviation from the expected ratio, indicating multiple genetic factors may influence flower color in some cases.
The document summarizes research on pleiotropic adult plant resistance (PAPR) loci in wheat. Key points:
1. CIMMYT has conducted PAPR research since the 1970s, identifying loci such as Lr34, Lr46, and Lr67 that confer resistance to multiple diseases.
2. Studies mapped additional PAPR QTL in various wheat populations and identified markers for genes like Lr46, Sr2, and Yr54 useful for marker-assisted selection.
3. Research involves fine mapping genes, identifying deletion mutants, and understanding resistance mechanisms to improve durability and pyramide genes in wheat breeding.
4. An international shuttle breeding program
This document describes a DNA marker-based technology developed to identify citrus rootstocks at the seedling stage. Traditionally, Rough lemon and Rangpur lime are preferred rootstocks but are difficult to distinguish from Galgal at an early stage. Galgal is an undesirable rootstock due to susceptibility to diseases. The new technology uses microsatellite markers and PCR to differentiate Rough lemon, Rangpur lime, and Galgal based on presence or absence of DNA fragments. It provides a non-destructive method to ensure nurseries are supplying quality rootstock varieties. The technique has been transferred to agricultural organizations to benefit citrus farmers.
The Lr34 gene in wheat has provided effective resistance against rust for over 100 years. It confers partial and durable resistance by prolonging the latency period and reducing spore production. Lr34 is not race-specific and also confers resistance to other pathogens. It encodes an ATP-binding cassette (ABC) transporter protein and differs by only two amino acids from susceptible alleles. Transgenic wheat with Lr34 shows complementation of resistance, though the genetic background can influence effects. Lr34's durable resistance is likely due to its ability to transport antimicrobial compounds or prime defense responses through its function as an ABC transporter.
TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
This document describes the identification of FLOWERING LOCUS T (FT) through an activation tagging screen in Arabidopsis thaliana. The 1733 mutant tagged line flowered early and had terminal flowers. Sequencing of the tagged gene revealed it to be FT. Overexpression of FT using the 35S promoter recapitulated the 1733 phenotype, flowering very early with few leaves. FT was found to act partially downstream of CONSTANS (CO) to promote flowering in response to day length. Unlike many floral regulators, the FT protein sequence does not suggest it directly controls transcription.
B-box proteins in plants bbx family of plant transcription factorsOm Prakash Patidar
This document summarizes research on B-box proteins. It begins by describing the structure of zinc finger domains and their ability to bind DNA, RNA, or proteins. It then discusses B-box (BBX) proteins, which contain zinc finger domains and are involved in plant protein-protein interactions and transcription factor activity. The document reviews studies of BBX proteins in animals and plants, describing their roles in processes like photomorphogenesis, flowering time regulation, and shade avoidance responses. Case studies are presented on specific BBX proteins in Arabidopsis and crops like rice and soybean.
This document discusses a study that found constitutive membrane association greatly enhances the ability of Bruton's tyrosine kinase (Btk) to transform cells. The study targeted Btk to the plasma membrane using fusion proteins, which led to high tyrosine phosphorylation of Btk. Cell transformation required membrane localization of Btk, its kinase activity, phosphorylation by Src kinases, and an intact SH2 domain. The results suggest membrane localization is a critical early step in Btk activation.
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
21. Mutation Breeding in crop improvement Naveen Kumar
Mutation breeding in crop improvement can utilize both spontaneous and induced mutations. Induced mutations are caused by physical mutagens like radiation (x-rays, gamma rays, UV light) or chemical mutagens. Mutation rates can vary between genes and induced mutations occur more frequently than spontaneous mutations. Mutation breeding is useful for crop improvement by generating genetic variation for selection of desirable traits.
Glutamine methylation in Histone H2A is an RNA Polymerase I dedicated modification. The study identified and localized methylated glutamine 105 in Histone H2A. Nop1/Fibrillarian was identified as the methyltransferase that modifies Q105. The genomic landscape of Q105me was analyzed and unmodified Q105 was found to be part of a recognition motif for FACT.
Targeting Induced Local Lesions IN Genomes (TILLING) is a combined tool of plant mutagenesis and DNA Biology to investigate useful mutations at Genomic level. First time used for cotton improvement.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
tansgenic mice:methodology and applicationtinasingh30
This document discusses the generation and applications of transgenic mice. It describes four main methods for generating transgenic mice: retroviral vector method, microinjection method, engineered embryonic stem cell method, and yeast artificial chromosome transgenesis. Transgenic mice can be used as disease models and to study the biological basis of human diseases. They have been made for conditions like Alzheimer's disease and cystic fibrosis. Transgenic mice are also used as test systems to evaluate potential therapies.
Maxim is a 12-year-old boy who enjoys fishing, computer games, and his cat. He has been fishing for the last four years and caught a 1kg pike, which is pictured. He likes playing games like Need for Speed, Grand Theft Auto, and Counter Strike on the computer. He has a 4-year-old black and white cat named Boy who likes to play and gets fed milk, fish, and sausages.
Este documento resume la literatura del siglo XVIII en España. Explica que la Ilustración fue el movimiento intelectual dominante, promoviendo el uso de la razón y el escepticismo hacia los dogmas religiosos. El Neoclasicismo fue la manifestación literaria de la Ilustración, cultivando géneros tradicionales como la lírica, la narrativa y el teatro con un propósito didáctico. La prosa se enfocó en la educación a través de ensayos, cartas, libros de viajes y prensa. La poes
This document provides information on an armored ambulance vehicle and its features. It includes specifications for the vehicle such as dimensions, engine, and armor components. It also lists the medical equipment included for patient transport such as stretchers, first aid kits, oxygen tanks, and more. Contact information is provided for the manufacturer's head office in the US and regional office in the UAE.
The document summarizes key findings from qualitative research on how brand and trust operate in fragmented news environments. It found that while platforms fit into different consumption routines, brands remain an important vehicle for trust. Brand visibility varies across distributed platforms. The importance of social media sharers depends on the situation. Views on algorithms versus editors are mixed, and some are unaware of algorithms. Overall, people want established news brands to continue providing trusted news into the future.
This mood board document contains 4 categories of inspiration for a new indie magazine: Fashion/Style (Female), Fashion/Style (Male), Existing Indie Magazines, and Indie Artists/Bands. The mood board will pull ideas from these categories to help guide the visual style and content focus of the new magazine.
The document discusses export processing zones (EPZs), which are areas where goods may be imported and manufactured for export. EPZs provide special incentives and facilities to attract foreign investment. They aim to promote exports, generate employment, and transfer technology. Companies setting up in EPZs receive tax holidays, duty-free imports, infrastructure support, and expedited permits. The document outlines the types of industries typically found in EPZs and incentives provided, such as tax exemptions and banking facilities. It also discusses rules around importing and exporting goods to and from EPZs.
smart street light detector based on sensors. This is basically designed to reduce the power consumption of the street light. And help out to conserve more and more energy.
This document describes a vehicle accident detection system that uses GPS and GSM technology. When a vehicle accident is detected by a vibration sensor, the sensor sends a signal to an ARM controller. The controller then sends an alert message through a GSM modem to emergency services, including the location from the GPS modem. This allows emergency services to quickly locate the accident site based on the GPS coordinates received after an accident is detected.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
Ultrasonic based non contact type water level indicator using 8051Ajay Kumar
This document describes a project to build a non-contact ultrasonic water level indicator using an 8051 microcontroller. It uses an ultrasonic sensor to detect the water level by measuring the time it takes for sound waves to reflect off the water surface. The sensor is interfaced with an 8051 microcontroller which then displays the water level reading on a LCD screen. Key components include an 8051 microcontroller, ultrasonic sensor module, LCD display, and other basic electronic components. Applications include measuring liquid levels in tanks, dams, and other containers in an automated non-contact method.
Project Report on automated toll tax collection system using rfidjeet patalia
This document is a project report submitted for the degree of Bachelor of Technology in Computer Engineering. It outlines an automated toll collection system using RFID technology. The system aims to reduce traffic and manual work at toll booths by allowing vehicles to pass through without stopping. It consists of RFID tags attached to vehicles, RFID receivers at the toll booth, a PC for processing payments, and a gate control to open and close the toll booth barrier. The report describes the objectives, components, software, hardware, workflow, and advantages of the automated toll collection system using RFID technology.
This document discusses a study that found molecular and morphological evidence suggesting that the flagellate Ancyromonas is closely related to the common ancestor of metazoans, fungi, and choanoflagellates. Analyses of 18S rRNA gene sequences from major eukaryotic lineages using maximum likelihood, minimum evolution, and maximum parsimony supported Ancyromonas forming its own lineage, called Ancyromonadida, that is more closely related to opisthokonts than its nearest protist relatives. However, low bootstrap support for deep nodes limits the ability of 18S rDNA to fully resolve this aspect of eukaryotic phylogeny.
This document proposes establishing a new order, Thoreales, for the freshwater red algal family Thoreaceae based on phylogenetic and ultrastructural evidence. The study examines specimens of Nemalionopsis and Thorea using gene sequencing and electron microscopy of pit plugs. Phylogenetic trees produced from rbcL and 18S rRNA gene sequences strongly support Thoreaceae as a distinct clade separate from other families in the order Batrachospermales. Pit plug ultrastructure also differs from descriptions in Batrachospermales by having two cap layers, with the outer layer usually plate-like. The evidence indicates Thoreaceae has been misclassified in Batrachospermales and warrants being placed in its own order,
This document describes a study that analyzed the chloroplast DNA (cpDNA) in the bamboo species Gigantochloa scortechinii found in Peninsular Malaysia. The researchers developed a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) marker to detect two distinct cpDNA lineages, called the Gombak- and Langat-types. They analyzed cpDNA from G. scortechinii samples collected from four locations. Most samples (60.7%) had the Gombak-type cpDNA, suggesting it is the dominant type in Peninsular Malaysia. The existence of the two cpDNA types indicates chloroplast capture likely due to past hybridization and introgression among
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.
This study aimed to determine the phylogenetic relationships between 17 species of sea cucumbers found in Malaysia using sequences of the 16S mitochondrial rRNA gene. Phylogenetic trees were constructed using neighbor joining, maximum parsimony, and maximum likelihood methods. The trees showed five main genera of sea cucumbers were present: Molpadia, Holothuria, Stichopus, Bohadschia, and Actinopyga. However, one species of Holothuria was found to be outside of the Holothuria group, making it paraphyletic. Further studies with more samples and different mitochondrial DNA genes are needed to better understand the molecular phylogeny of sea cucumbers.
Five novel psychrophilic bacterial strains were isolated from soil samples collected above the treeline in alpine environments in Mexico and Colorado. Based on phylogenetic and chemotaxonomic analysis, the five strains represent four novel species in the genus Deinococcus. Strain PO-04-20-132 represents Deinococcus radiomollis sp. nov., strain PO-04-19-125 represents D. claudionis sp. nov., strain ME-04-01-32 represents D. altitudinis sp. nov., and strain ME-04-04-52 represents D. alpinitundrae sp. nov. The new species have optimal growth at 10°C and are more sensitive
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
Rapid Impact Assessment of Climatic and Physio-graphic Changes on Flagship G...Arvinder Singh
‘NATIONAL CONFERENCE ON MAN AND ENVIRONMENT’October 15 – 16, 2012
Organized by
Department of Zoology and Environmental Sciences, Punjabi University, Patiala (Pb.) – 147 002, India
Characterization of Arsenic contaminated Rice (Oryza Sativa L.) through RAPD ...IOSR Journals
This study characterized rice genotypes for arsenic contamination using RAPD markers. Forty rice genotypes from India and other countries were tested for arsenic levels in fields with known arsenic contamination. DNA was extracted from plants and amplified using RAPD primers. Fourteen primers produced polymorphic bands that were scored. Cluster analysis grouped genotypes into four main clusters, separating japonica types from indica. Varieties previously found to have low or high arsenic levels clustered separately, indicating RAPD may help discriminate arsenic uptake ability. Further research with more markers is needed to better predict arsenic accumulation through genetics. This study provides a preliminary analysis of using molecular markers to study genetic control of arsenic uptake in rice.
This document describes a study that used molecular methods including PCR and sequencing of the internal transcribed spacer 1 (ITS1) region to analyze the genetic diversity of anaerobic fungi in the gastrointestinal tracts of buffalo. Total DNA was extracted from rumen samples and the ITS1 region was amplified and sequenced. Sequence analysis of 12 clones showed diversity among the anaerobic fungal isolates. The results indicate that analysis of the ITS1 spacer through molecular techniques is a promising approach for comparing rumen fungal populations and diversity.
The study cloned and analyzed the GJB6 gene, which encodes the connexin 30 protein, from 16 bat species and 4 other mammals. Analysis showed purifying selection on GJB6 in mammals generally, maintaining its important role in hearing. One amino acid substitution was unique to bats, and 10 were shared among artiodactyls. The cytoplasmic loop and carboxy terminus were more variable than other domains in all mammals. The results demonstrate evolutionary conservation of GJB6 in mammals but also lineage-specific rapid evolution in some domains.
This document summarizes the history and applications of RNA interference (RNAi) and microRNAs (miRNAs) in plants. It discusses how small RNAs guide regulatory processes, how dicer and argonauts are involved, and some of the early discoveries in RNAi from the 1990s onward. It then lists several applications of RNAi/miRNAs in plants, such as improving traits like biomass, yield, stress resistance, and nutrition. Specific examples are given of overexpressing miRNAs like miR156 to increase biomass and yield in maize and rice. In conclusion, RNAi/miRNAs can be powerful tools for improving important agricultural traits in plants.
Paper to Upload, MOLECULAR PHYLOGENY OF CATFISHES.pdfOanhTrng13
This document presents a study on the molecular phylogeny of catfishes (order Siluriformes) in the Lower Mekong River Basin, based on analysis of mitochondrial DNA sequences. Thirty catfish species from nine families collected in the Lower Mekong Basin were analyzed using the 16S rRNA and COI gene regions. Phylogenetic trees were constructed using neighbor joining, Bayesian inference and maximum likelihood methods. The results showed strong support for monophyly of Siluriformes and seven of the nine studied families. However, the families Pangasiidae and Bagridae were found to be paraphyletic. Interfamilial relationships varied between analysis methods and datasets, showing inconsistencies with previous catfish phylogen
1. The structure of GUN4 from Chlamydomonas reinhardtii was determined to 3.5 Angstrom resolution. GUN4 is involved in chlorophyll biosynthesis and plastid-to-nucleus signaling.
2. The structure consists of six molecules in the asymmetric unit and is predominantly alpha-helical. The structure is similar to previously solved cyanobacterial GUN4 structures, with the main differences being in several variable loops.
3. The conformational dynamics of these loops seen across GUN4 structures provides insight into how GUN4 binds protoporphyrin and magnesium protoporphyrin during chlorophyll biosynthesis.
1) The study analyzed genetic diversity in 66 finger millet accessions from Ethiopia and Eritrea using RAPD markers.
2) A total of 123 RAPD fragments were amplified using 15 primers, of which 89 (72%) were found to be polymorphic.
3) Genetic similarity between accessions ranged from 0.585 to 0.984. Cluster analysis grouped the 66 accessions into nine clusters at a similarity index of 0.83, showing high genetic variability among the accessions.
Abstract— An experiment stand of clonal orchard of masson pine, which included the 123 plus trees of 8 provenances collected from 8 provinces of Southern China, was founded at Jingshan County of Hubei province. Randomly amplified polymorphic DNA (RAPD) technique was applied to assess genetic diversity and structure for this clonal seed orchard. Total genomic DNA was extracted from fresh needle tissue with Plant Genomic DNA Extraction Miniprep System made by Viotechnology Corporation The results indicated that the clonal seed orchard of masson pine had higher genetic diversity. The average genetic diversity of the clonal seed orchard was 0.3169, the Shannon’s information index was 0.4813 respectively, and the percentage of polymorphic loci was 71.0%. Observed number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity (H), Shannon’s information index (I) and percentage of polymorphic loci (P) within population of Jiangxi, Hunan and Zhejiang were bigger than those of Guangdong, Guangxi, Anhui and Sichuan. Genetic distances among 8 populations were range from 0.0225 to 0.2175, whereas genetic identities were range from 0.8045 to 0.9777. 8 populations were clustered into 7 clusters, which showed that populations with similar latitude were clustered together and the clustering had nothing to do with geographic distributing. There was not significant correlation between genetic distance and geographic distance, while the correlation between genetic distance and latitude was more significant.
This document describes a study comparing the phylogenetic relationships of green algal taxa from the order Chlamydomonadales based on analysis of sequences from the small subunit ribosomal RNA gene in the nucleus and the large subunit ribosomal RNA gene in the chloroplast. The results from both data sets show considerable congruence and support six distinct lineages within Chlamydomonadales that include taxa from the biflagellate genus Chlamydomonas as well as a basal lineage containing quadriflagellate Carteria taxa. Both data sets support the conclusion that Chlamydomonas is not monophyletic. The chloroplast data were ambiguous regarding Carteria monophyly while the nuclear data did not support it.
This research note describes the development of 17 microsatellite loci for two species of flat periwinkles, Littorina fabalis and L. obtusata. The microsatellites were isolated from L. fabalis using next-generation sequencing and tested on individuals of both species. Seventeen loci were found to reliably amplify in both species. These new nuclear markers can be used to study species discrimination between L. fabalis and L. obtusata, investigate hybridization, and characterize divergence between L. fabalis ecotypes. The microsatellites provide a genetic tool to overcome limitations of morphological identification.
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 Carl Woese's contributions to science, particularly his discovery of the third domain of life (Archaea) through analysis of rRNA sequences. It describes how his work established the use of comparative analysis to determine rRNA secondary structure and identify structural motifs. It highlights that he envisioned comparative analysis providing details about RNA structure and energetics. The summary discusses Woese's seminal concepts regarding the need for a universal phylogenetic framework and how analysis of rRNA satisfied criteria to reconstruct evolutionary relationships across all life.
Gutell 123.app environ micro_2013_79_1803Robin Gutell
This document summarizes a study examining the host specificity of Lactobacillus bacteria associated with different hymenopteran (bee and ant) hosts. The researchers compiled nearly full-length 16S rRNA gene sequences of Lactobacillus from public databases and used these to construct phylogenetic trees. They also included shorter 16S sequences from surveys of bacteria associated with sweat bees, fungus-growing ants, and fire ants. The results showed that lactobacilli associated with honey bees and bumble bees are highly host specific, while sweat bees and ants associate with lactobacilli more closely related to those found in diverse environments or vertebrate hosts. The high host specificity seen in corbiculate bees (honey bees
Gutell R.R. (2013).
Comparative Analysis of the Higher-Order Structure of RNA.
in: Biophysics of RNA Folding. Volume editor: Rick Russell. Series title: Biophysics for the Life Sciences. Series editors: Norma Allewell, Ivan Rayment, Bertrand Garcia-Moreno, Jonathan Dinman, and Michael McCarthy. pp. 11-22. Publisher: Springer, New York, NY.
Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
An Accurate Scalable Template-based Alignment Algorithm.
Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
Lee J.C. and Gutell R.R. (2012).
A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions.
PLoS ONE, 7(5):e38203.
Gardner D.P., Ren P., Ozer S., and Gutell R.R. (2011).
Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure.
Journal of Molecular Biology, 413(2):473-483.2011. pp 15-22.
Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp 15-22.
Jiang Y., Xu W., Thompson L.P., Gutell R., and Miranker D. (2011).
R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 618-622.
Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011).
RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617.
Muralidhara C., Gross A.M., Gutell R.R., and Alter O. (2011).
Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA.
PLoS ONE, 6(4):e18768.
Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures.
The Journal of Physical Chemistry B, 114(42):13497-13506.
The document describes research on fragmentation of the large subunit ribosomal RNA (LSU rRNA) gene in oyster mitochondrial genomes. Key findings include:
1) The LSU rRNA gene is split into two fragments separated by thousands of nucleotides in three species of oysters.
2) RT-PCR and EST analysis showed the two fragments are transcribed separately in Crassostrea virginica and are not spliced together.
3) Secondary structure models of the fragmented LSU rRNA genes were predicted for C. virginica, C. gigas, and C. hongkongensis based on comparative sequence analysis. This fragmentation represents a novel phenomenon in bilateral metazoan mitochondrial genomes.
Mueller U.G., Ishak H., Lee J.C., Sen R., and Gutell R.R. (2010).
Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models.
Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 98(2):195-212.
Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. (2009).
The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.
European Journal of Phycology, 44(3):277-290.
Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P. (2009).
Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding.
Journal of Molecular Biology, 391(4):769-783.
Xu W., Ozer S., and Gutell R.R. (2009).
Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.
21st International Conference on Scientific and Statistical Database Management. June 2-4, 2009. Springer-Verlag. pp. 200-216.
Chen Y.P., Evans J.D., Murphy C., Gutell R., Zuker M., Gundersen-Rindal D., and Pettis J.S. (2009).
Morphological, Molecular, and Phylogenetic Characterization of Nosema cerenae, a Microsporidian Parasite Isolated from the European Honey Bee, Apis mellifera.
The Journal of Eukaryotic Microbiology, 56(2):142-147.
Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. (2009).
Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).
Zoologica Scripta, 38(1):43-62.
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
Join Maher Hanafi, VP of Engineering at Betterworks, in this new session where he'll share a practical framework to transform Gen AI prototypes into impactful products! He'll delve into the complexities of data collection and management, model selection and optimization, and ensuring security, scalability, and responsible use.
A tale of scale & speed: How the US Navy is enabling software delivery from l...sonjaschweigert1
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
Communications Mining Series - Zero to Hero - Session 1DianaGray10
This session provides introduction to UiPath Communication Mining, importance and platform overview. You will acquire a good understand of the phases in Communication Mining as we go over the platform with you. Topics covered:
• Communication Mining Overview
• Why is it important?
• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
Pushing the limits of ePRTC: 100ns holdover for 100 daysAdtran
At WSTS 2024, Alon Stern explored the topic of parametric holdover and explained how recent research findings can be implemented in real-world PNT networks to achieve 100 nanoseconds of accuracy for up to 100 days.
Dr. Sean Tan, Head of Data Science, Changi Airport Group
Discover how Changi Airport Group (CAG) leverages graph technologies and generative AI to revolutionize their search capabilities. This session delves into the unique search needs of CAG’s diverse passengers and customers, showcasing how graph data structures enhance the accuracy and relevance of AI-generated search results, mitigating the risk of “hallucinations” and improving the overall customer journey.
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
1. 1654
Mol. Biol. Evol. 18(9):1654–1667. 2001
᭧ 2001 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
A Structural and Phylogenetic Analysis of the Group IC1 Introns in the
Order Bangiales (Rhodophyta)
Kirsten M. Mu¨ller,*1 Jamie J. Cannone,† Robin R. Gutell,† and Robert G. Sheath*
*Department of Botany and Dean’s Office, University of Guelph, Guelph, Ontario, Canada; and †Institute of Cellular and
Molecular Biology, University of Texas at Austin
Our previous study of the North American biogeography of Bangia revealed the presence of two introns inserted
at positions 516 and 1506 in the nuclear-encoded SSU rRNA gene. We subsequently sequenced nuclear SSU rRNA
in additional representatives of this genus and the sister genus Porphyra in order to examine the distribution,
phylogeny, and structural characteristics of these group I introns. The lengths of these introns varied considerably,
ranging from 467 to 997 nt for intron 516 and from 509 to 1,082 nt for intron 1506. The larger introns contained
large insertions in the P2 domain of intron 516 and the P1 domain of intron 1506 that correspond to open reading
frames (ORFs) with His-Cys box homing endonuclease motifs. These ORFs were found on the complementary
strand of the 1506 intron in Porphyra fucicola and P. umbilicalis (HG), unlike the 516 intron in P. abbottae, P.
kanakaensis, P. tenera (SK), Bangia fuscopurpurea (Helgoland), and B. fuscopurpurea (MA). Frameshifts were
noted in the ORFs of the 516 introns in P. kanakaensis and B. fuscopurpurea (HL), and all ORFs terminated
prematurely relative to the amino acid sequence for the homing endonuclease I-Ppo I. This raises the possibility
that these sequences are pseudogenes. Phylogenies generated using sequences of both introns and the 18S rRNA
gene were congruent, which indicated long-term immobility and vertical inheritance of the introns followed by
subsequent loss in more derived lineages. The introns within the florideophyte species Hildenbrandia rubra (position
1506) were included to determine relationships with those in the Bangiales. The two sequences of intron 1506
analyzed in Hildenbrandia were positioned on a well-supported branch associated with members of the Bangiales,
indicating possible common ancestry. Structural analysis of the intron sequences revealed a signature structural
feature in the P5b domain of intron 516 that is unique to all Bangialean introns in this position and not seen in
intron 1506 or other group IC1 introns.
Introduction
Many eukaryotic genes have their coding regions
interrupted by intervening sequences or introns. Group
I introns represent a family of RNA molecules with a
specific higher-order structure and the ability to catalyze
their own excision by a common splicing mechanism
(Cech 1990). Group I introns are divided into 11 sub-
groups based on conserved primary- and secondary-
structure elements (Michel and Westhof 1990) and have
been reported in the 18S rRNA genes of numerous or-
ganisms (Johansen, Muscarella, and Vogt 1996), such as
fungi (Takashima and Nakase 1997), amoebae (De Jonck-
heere 1994; Schroeder-Diedrich, Fuerst, and Byers 1998),
and green algae (Wilcox et al. 1992; VanOppen, Olsen,
and Stam 1993; Bhattacharya et al. 1994, 1996; Bhatta-
charya 1998). Group I introns have also been reported in
several red algae, including Hildenbrandia rubra (Ragan
et al. 1993) and particularly members of the order Ban-
giales (Porphyra spiralis var. amplifolia and Bangia fus-
copurpurea [as Bangia atropurpurea] [Oliveira and Ra-
gan 1994]; Porphyra miniata, P. purpurea, P. linearis
[Oliveira et al. 1995]; Bangia spp. [Mu¨ller et al. 1998]).
Stiller and Waaland (1993) reported cryptic diversity in
a number of species of Porphyra after finding large in-
sertions in the nuclear SSU rRNA genes of a number of
taxa. Oliveira et al. (1995) speculated that these introns
1 Present address: Department of Biology, University of Waterloo,
Waterloo, Ontario, Canada.
Key words: Group IC1 introns, Bangiales, phylogeny.
Address for correspondence and reprints: Robert G. Sheath,
Dean’s Office and Department of Botany, University of Guelph,
Guelph, Ontario, Canada N1G 2W1. E-mail: rsheath@uoguelph.ca.
may be a means to differentiate among geographic en-
tities within the genus Porphyra. During the course of
a study of the biogeography of Bangia in North Amer-
ica, we reported the presence of two introns in positions
516 and 1506 (Escherichia coli numbering) in the nu-
clear SSU rRNA gene (Mu¨ller et al. 1998). Subsequent
analysis of additional nuclear SSU rRNA gene sequenc-
es of Bangia and Porphyra revealed a rich source of
these introns, which are also variable in occurrence. Var-
iable occurrence of group I introns can be simply ex-
plained by two models: intron insertion or intron dele-
tion (Burke 1988). The first model, intron insertion, is
hypothesized to have begun with a gene devoid of in-
trons followed by subsequent insertion of one or more
introns (Burke 1988). The deletion model proposes a
gene initially containing one or more introns, after
which precise deletion of these introns occurs; that is,
nonmobile introns are destined to be lost over time if
they cannot reinfect homologous sites. Burke (1988)
proposed that the variable occurrence of introns in genes
may be the result of a combination of these two models.
High sequence similarity between introns is consistent
with descent from an ancestral intron that was initially
acquired and vertically inherited (Schroeder-Diedrich,
Fuerst, and Byers 1998). In addition, congruent intron
and rRNA gene phylogenies would provide support for
this theory (Bhattacharya et al. 1994, 1996; Friedl et al.
2000). The present study provides a large data set that
will allow us to test these hypotheses in context with
the phylogeny of the rhodophyte order the Bangiales.
Materials and Methods
Collections of Bangia and Porphyra collected for
molecular analyses and obtained from GenBank for the
2. Group IC1 Introns in the Bangiales 1655
present study are listed in table 1 Filaments collected
for DNA analysis were cleaned of visible epiphytes, ba-
ses were removed to prevent contamination, and the
specimens were stored atϪ20ЊC. Samples were ground
in liquid nitrogen, and the DNA was extracted according
to the protocol outlined by Saunders (1993) with mod-
ifications given in Vis and Sheath (1997). Amplification
and sequencing of the nuclear SSU rRNA gene for both
genera are as outlined in Mu¨ller et al. (1998).
Intron Amplification
The intron in position 516 was amplified in the
large fragment of the nuclear SSU rRNA gene as de-
scribed in Mu¨ller et al. (1998) using the primers G02.1
(5Ј-CGA TTC CGG AGA GGG AGC CTG-3Ј) and
G15.1 (5Ј-CTT GTT ACG ACT TCT CCT TCC-3Ј).
These fragments were then sequenced in both directions
using internal primers flanking the intron. The intron in
position 1506 was amplified using primers GO6 (5Ј-
GTT GGT GGT GCA TGG CCG TTC-3Ј) and G07 (5Ј-
TCC TTC TGC AGG TTC ACC TAC-3Ј) from Saun-
ders and Kraft (1994) as follows: initial denaturation at
95ЊC for 2 min, 35 cycles of denaturation for 1 min at
93ЊC, primer annealing at 50ЊC for 1 min, and extension
for 2 min at 72ЊC, followed by a final extension time of
3 min at 72ЊC. This intron was sequenced in both di-
rections using an internal primer at the 5Ј end of the
intron and the primer G07 (sequences for internal prim-
ers can be obtained from R.G.S.). All products were
prepared for sequencing and sequenced using the pro-
tocols outlined in Mu¨ller et al. (1998).
RNA Extraction/cDNA Production in the Bangiales
RT-PCR was used to determine if introns were pre-
sent in mature RNA or excised from all collections of
Bangia and Porphyra listed in table 1 and the Bangia
collections utilized in Mu¨ller et al. (1998). RNA was
extracted following the procedure previously outlined
for DNA extraction. Following this, 12 l of extract was
placed in a clean tube, to which 3 l of 25 mM MgCl2
and 1 l of DNAase was added. This mixture was then
left at room temperature for 2 h, after which 5 l was
loaded in a 0.5% agarose gel to determine if all DNA
had been digested within the extract. If this was the case,
the extract was then immediately placed in the freezer
at Ϫ20ЊC. RT-PCR using Titan by Boehringer Mann-
heim was used to amplify the RNA. The primers G02.1
and G09 (5Ј-ATC CAA GAA TTT CAC CTC TG-3Ј)
and G15.R (5Ј-GGA AGG AGG AGT CGT AAC AAG-
3Ј) and G07 were used to amplify the region containing
the intron in positions 516 and 1506, respectively (Saun-
ders and Kraft 1994; Mu¨ller et al. 1998). Following the
protocols for RT-PCR outlined by Boehringer Mann-
heim, the reaction consisted of master mix 1 (1 l of
RNA template; 20 M of each primer; 40 mM of dNTP;
2.5 l DTT solution; dH2O) and master mix 2 (14 l
dH2O; 5 ϫ RT-PCR buffer with MgCL2; 1 l enzyme
mix). These two master mixes were combined and
placed in a 0.5-l thin-walled PCR tube on ice. Ampli-
fication was performed as follows: initial denaturation
at 94ЊC for 2 min; 10 cycles of denaturation at 94ЊC for
30 s, primer annealing at 50ЊC for 30 s, and extension
for 2 min at 68ЊC; 25 cycles of denaturation at 94ЊC for
30 s, primer annealing at 50ЊC for 30 s, extension for 2
min at 68ЊC, plus cycle elongation for 5 s for each cycle;
and a final extension of 7 min at 68ЊC. Sequencing of
the amplified regions was carried out as previously
outlined.
Alignment of Nuclear SSU rRNA Genes and Group
IC1 Introns
The nuclear SSU rRNA gene and group IC1 intron
sequences in the present study were incorporated into
large alignments that spanned a large taxonomic range
in order to ensure optimum alignment. The new se-
quences were manually aligned with the alignment ed-
itor AE2 (developed by T. Macke; see Larsen et al.
1993) on the basis of sequence similarity and a previ-
ously established eukaryotic secondary-structure model
(Gutell 1993). The alignments were then subjected to a
process of comparative sequence analysis (Gutell et al.
1985). This process consisted of searching for compen-
sating base changes using computer programs developed
within the Gutell Laboratory (University of Texas at
Austin, http://www.rna.icmb.utexas.edu/; discussed in
Gutell et al. 1985) and using the subsequent information
to infer additional secondary-structural features. This re-
fined alignment was reanalyzed and the entire process was
repeated until the proposed structures were entirely com-
patible with the alignment. Secondary-structure diagrams
were generated with the computer program XRNA (de-
veloped by B. Weiser and H. Noller, University of Santa
Cruz). Individual secondary-structure diagrams will be
available at http://www.rna.icmb.utexas.edu/, and align-
ments can be obtained from K.M.M.
Analysis of Nuclear SSU rRNA Gene and Group I
Intron Sequences
All analyses on both the nuclear SSU rRNA gene
and the group I introns were carried out using only well-
aligned regions of the sequences. Parsimony analyses on
the two introns were carried out with PAUP 3.1.1 (Swof-
ford 1993) with a heuristic search under the constraints
of random sequence addition (100 replicates), steepest
descent, and tree bisection-reconnection (TBR) branch
swapping. The data were then subjected to bootstrap re-
sampling (1,000 replicates). Analyses of the introns
were carried out as follows: (1) the alignment gaps were
treated as missing data, and (2) the alignment gaps were
coded as independent single evolutionary events (inser-
tion or deletion) based on secondary-structure models
(Damberger and Gutell 1994). Group IC1 introns in
Chlorella ellipsoidea (GenBank accession number A:
X63520, B: D13324) were used as outgroups in the phy-
logenetic analyses. Parsimony trees could not be deter-
mined for the nuclear SSU rRNA gene due to the large
number of taxa and limited computational capacity;
however, neighbor-joining trees were calculated for this
data set. PHYLIP (Felsenstein 1993) was used to con-
struct neighbor-joining trees for both the introns and the
4. Group IC1 Introns in the Bangiales 1657
Table 1
Continued
COLLECTION COLLECTION INFORMATION/REFERENCE
GENBANK ACCESSION NOS.
18S rRNA Intron 516 Intron 1506
Porphyra rediviva . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175544 — AF172600
Porphyra spiralis var. amplifolia B . . . . . . . . Oliveira and Ragan (1994) — — L26175
P. spiralis var. amplifolia D . . . . . . . . . . . . . . Oliveira and Ragan (1994) — — L26176
P. spiralis var. amplifolia R . . . . . . . . . . . . . . Oliveira and Ragan (1994) L26177 — L26177
Porphyra suborbiculata (KY) . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013180 AB013180 —
Porphyra tenera (KK) . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013176 AB013176 AB013176
P. tenera (SK) . . . . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013175 AB013175 AB013175
P. tenera (T-1) . . . . . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) D86237 D86237 —
P. tenera (TU-3) . . . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) D86236 D86236 —
P. tenera (T8) . . . . . . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) AB000964 AB000964 —
Porphyra torta . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175552 AF172579 ?
Porphyra umbilicalis (HF) . . . . . . . . . . . . . . . Ragan et al. (1994) L26202 — —
P. umbilicalis (HG) (HG ϭ Hallig Gro¨de,
Germany) . . . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175549 — AF172602
P. umbilicalis (NJ) . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175553 AF172573 —
P. umbilicalis (NM) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013179 — —
Porphyra yezoensis . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) D79976 D79976 —
P. yezoensis (HH) . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013177 AB013177 —
P. yezoensis (OM) . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013178 AB013178 AB013178
P. yezoensis (OG-1) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017078
P. yezoensis (OG-4) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017081
P. yezoensis narawaensis . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017083
P. yezoensis (NA-2) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017075
P. yezoensis (NA-4) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017076
Porphyra sp. (Brest) . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175548 — AF172601
Porphyra sp. (Marseille) . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175546 — AF172597
Porphyra sp. (SHH) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) — ? AB017077
Porphyra sp. (SY) . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013182 AB013182 AB013182
Porphyra sp. (Wales) . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175554 AF172574 —
NOTE.—The abbreviations UTEX, CCAP, and CCMP are for culture collections. Other abbreviations for taxa not noted were obtained from the GenBank file
and represent those assigned by the original authors or the collector of the material.
a Intron not present.
b Intron not sequenced, or presence or absence unknown.
nuclear SSU rRNA genes using a matrix of distance val-
ues estimated according to the Kimura two-parameter
model (Kimura 1980) with a transition/transversion ratio
of 2.0 and a single-category substitution rate, as well as
the Jukes and Cantor (1969) model (intron data set
only). These data sets were also subjected to bootstrap
resampling. Maximum-likelihood analysis was carried
out using the puzzle function in PAUP (version 4.0 beta
2a) as described by Strimmer and von Haeseler (1996)
with 1,000 puzzling steps. The nuclear SSU rRNA gene
sequence analyses of the Bangiales were run using Er-
ythrotrichia carnea (L26189) and Erythrocladia sp.
(L26188) as outgroups. These taxa were determined to
be basal to the Bangiales and have been previously used
as outgroup taxa for this order (Ragan et al. 1994; Oliv-
eira et al. 1995; Mu¨ller et al. 1998).
Results
Sequence data for all intron sequences were sub-
mitted to GenBank, and accession numbers are given in
table 1. Presence and absence of introns within the nu-
clear SSU rRNA gene Bangiales is depicted in figure 4.
Letters and numbers behind taxonomic names refer to
various collections that are listed in table 1, of which
some represent standard state, provincial, or country
codes, whereas others are arbitrary numbers or initials
of the author of the particular sequence. Due to the dif-
ficulty in delineating species in Bangia (Mu¨ller et al.
1998) and the lack of a definitive global key for Por-
phyra species, identification of species that are used in
the molecular analyses should be considered tentative.
Thus, many of the analyses in the present study will
focus more on the relationship among the intron se-
quences and nuclear SSU rRNA gene within the two
genera than on morphological species within each ge-
nus, other than for characters that would not be disputed
(e.g., monostromatic vs. distromatic). With respect to
Bangia, based on the findings in Mu¨ller et al. (1998),
all freshwater collections (AT22, BI12, GL, IR, IT, and
NL) should be classified as B. atropurpurea, while col-
lections from marine locations have provisionally been
given the name B. fuscopurpurea until they can be dif-
ferentiated morphologically.
Using RT-PCR it was determined that neither in-
tron is present in the mature rRNA, indicating that these
introns are excised (not shown). Thirty-three nuclear
SSU rRNA gene sequences from Bangia and 52 from
Porphyra were examined for the presence of either in-
tron in position 516 (intron 516) (E. coli numbering sys-
tem) and position 1506 (intron 1506). Of these 52 Por-
phyra specimens, there were 39 complete sequences of
the nuclear SSU rRNA gene; the remainder consisted of
5. 1658 Mu¨ller et al.
FIG. 1.—Phylogenetic conservation of Rhodophyta (Bangiophy-
ceae) group I (IC1) introns (18S rRNA positions 516 and 1506) su-
perimposed onto the Bangia sp. (IR) group I (IC1) intron secondary
structure (18S rRNA position 1506). Positions with a nucleotide in
Ͼ95% of sequences are shown: ACGU—95ϩ% conserved; acgu—
90%–95% conserved; ●—80%–90% conserved; o—Ͻ80% conserved.
Otherwise, the regions are represented by arcs. Positions shown in
small square boxes and arcs with dashed lines represent features that
distinguish the 516 and 1506 introns (described in table 3). The exon
sequences that flank the intron are indicated with x’s.
species for which the nuclear SSU rRNA gene could not
be obtained (difficulty in obtaining sequences, or sample
was not sequenced) but sequences of some introns were
available. Among the 33 collections of Bangia, 21 were
determined to have intron 516 (64%), and 13 were ob-
served to have intron 1506 (39%). Only 10 (30%) col-
lections contained neither intron, and 11 (33%) collec-
tions had both introns (fig. 4). Within Porphyra, 20
(40%) of 50 nuclear SSU rRNA gene sequences were
determined to have intron 516, and 26 (52%) contained
intron 1506. Only 14 (28%) Porphyra sequences had
either intron, and 10 (20%) contained both introns (fig.
4).
Structural Characteristics of Group IC1 Introns in the
Bangiales
All of the rRNA introns in Bangia and Porphyra
were determined to belong to the CI subgroup of the
group I introns based on characteristic primary- and sec-
ondary-structure features (fig. 1) (Michel and Westhof
1990; Damberger and Gutell 1994). The lengths of these
introns within the Bangiales varied considerably, rang-
ing from 467 to 998 nt for intron 516 and ranging from
509 to 1,082 nt for intron 1506 (table 1). Figure 1 is a
consensus diagram of all of the group IC1 introns in the
Bangiales. Both introns were observed to have large in-
sertions within the P1 (12–567 nt), P2 (62–553 nt), P5
(3–91 nt), P6b (10–84 nt), and P9.2 (5–53 nt) domains
(fig. 1). The large insertions in the P1 and P2 domains
were found in introns 1506 and 516, respectively (fig.
1), whereas the other insertions (P5, P6b, and P9) were
similar in size between both the 516 and the 1506 in-
trons. The majority of the base pairs in the P4 and P7
helices are highly conserved (Ͼ95%) between both sets
of introns, whereas the remaining helices are less con-
served. The single positions and base pair ‘‘signatures’’
that distinguish the 516 and 1506 introns are shown as
square boxes and dashed lines in figure 1 and detailed
in table 3. Approximately half of these nucleotides and
the 5Ј positions of the base pairs noted in table 3 (and
depicted in fig. 1) are purines (A, G) in the 516 intron
and are pyrimidines (C, U) in intron 1506 (positions 2,
25, 26, 97:277, 216:257, 217:256, 262:312, 322:326,
and 335:364 [relative to Tetrahymena thermophila]). All
of these positions are highly conserved (Ͼ95%) with the
exception of base pair 97:277 (Ͼ90%, Ͻ95%). Position
172 and the 322:326 base pair have no homologous po-
sition with respect to T. thermophila. These three posi-
tions are highly conserved in both introns (Ͼ95%). Fig-
ure 2 highlights the differences between the 516 and
1506 introns in the P5b and P8 domains. The P5b helix
(fig. 2a) is one of the most distinct features of the 516
intron. This bifurcated helix, present in all of the Ban-
giales 516 introns, replaces the typical single helix pre-
sent in all IC1 introns, including the Bangialean 1506
introns (fig. 2a). The P8 domain (fig. 2b) is also distinct,
primarily on the basis of helix length. In the 516 version
of this structure, the 3-bp helix is capped by a tetraloop,
while the 1506 structure has a longer helix capped by a
variable-length hairpin loop.
Haugen et al. (1999) determined that P. spiralis var.
amplifolia (R) appeared to contain an open reading
frame (ORF) corresponding to a 149-amino-acid His-
Cys box protein within the P1 extension of the 1506
intron, as does P. tenera (KK) within the P2 extension
of the 516 intron. Johansen, Embley, and Willassen
(1993) noted that the His-Cys box motif is a hallmark
of nuclear homing endonucleases. Examination of these
domains in the bangialean introns within the present
study revealed that this ORF is present in those taxa
containing large extensions within the P1 or P2 domain
for 1506 and 516 introns, respectively. Table 2 high-
lights the sizes of the P2 domain (516 intron) and the
P1 domain (1506 intron) for all collections examined in
the study and the presence or absence of the His-Cys
box motif. The size of the P2 domain in the 516 intron
ranged from 62 to 552 nt, with only those Ͼ414 nt con-
taining an ORF and His-Cys box motif. This motif has
not previously been reported in the 516 intron for the
following taxa: B. fuscopurpurea (Helgoland), B. fus-
copurpurea (MA), P. abbottae, P. kanakaensis, and P.
tenera (SK). The P1 domain in the 1506 intron ranged
from 53 to 521 nt, and the His-Cys box motif was found
only in those with larger insertions in this region: P.
fucicola and P. umbilicalis (previously unreported).
6. Group IC1 Introns in the Bangiales 1659
FIG. 2.—Gallery highlighting differences between introns 516 and 1506 using consensus diagrams and individual secondary-structure
diagrams. a, P5b region of intron 516, showing bangialean consensus and differences among specific taxa. b, P5b region of intron 1506, showing
a bangialean consensus and differences specific among taxa. c, Consensus of the P8 regions of introns 516 and 1506 in the Bangiales. For
consensus diagrams, positions with a nucleotide in Ͼ95% of sequences are shown: ACGU—95ϩ% conserved; acgu—90%–95% conserved;
●—80%–90% conserved; o—Ͻ80% conserved. Otherwise, the regions are represented by arcs.
Haugen et al. (1999) noted that the ORF within the
P1 extension for intron 1506 was determined to be on
the complementary strand to that encoding the SSU
rRNA, and this was also the case for the ORF in the
previously unreported taxa (P. fucicola and P. umbili-
calis). However, this was not true for the ORF in the P2
extensions for the 516 introns, which were found on the
same strand as that encoding the SSU rRNA. Figure 3
depicts an amino acid alignment of the His-Cys box
motif region in the P1 domain of the 1506 intron and
the P2 domain of the 516 intron. As noted by Haugen
et al. (1999), P. spiralis var. amplifolia (R) and the en-
donuclease I-Ppo I were identical in 16 out of the 29
amino acids. The two new additional amino acid se-
quences, P. fucicola and P. umbilicalis (HG), were iden-
tical in 13 amino acids to the I-Ppo I endonuclease.
However, the amino-acid sequence for the His-Cys box
in the 516 introns was identical in only 9 or 10 amino
acids (fig. 3). Haugen et al. (1999) also noted frame-
shifts in the ORF of P. spiralis var. amplifolia (R) and
B. fuscopurpurea (1). Frameshifts were noted in the
ORF of the 516 introns in P. kanakaensis and B. fus-
copurpurea (HL); however, the remaining sequences
were not found to have frameshifts, although they all
terminated prematurely relative to the amino acid se-
quence for the homing endonuclease I-Ppo I (fig. 3).
This raises the possibility that these sequences are pseu-
dogenes; however, endonuclease activity in the Bangi-
ales was not tested in this study and needs to be inves-
tigated in further detail.
Phylogenetic Analysis of Introns
Figure 4 depicts a neighbor-joining tree derived
from the analysis of the nuclear SSU rRNA genes (par-
simony analyses were unobtainable due to the very long
computation time required) upon which the presence
(ϩ) and absence (Ϫ) of both introns have been mapped.
From these analyses, there appear to be multiple losses
of both introns. For example, the first major clade of
Bangia and Porphyra at the bottom of the tree contains
three smaller clusters in which there have been at least
two losses of the 1506 intron along each lineage (fig.
4). This same trend is even more evident in the larger
Bangia-Porphyra clade, where taxa possessing an intron
are intermingled with those that do not. There does not
appear to be any consistent trend with respect to pres-
ence or absence of either intron; however, it does appear
that the more derived a taxon is, the more likely the
intron will be absent (e.g., P. miniata (CCAP 1379/2),
P. amplissima, P. miniata, and P. miniata (NF)) (fig. 4).
Sequences of collections of B. atropurpurea were de-
termined to have identical nuclear SSU rRNA gene se-
quences, and all collections contained only intron 516.
Interestingly, some collections of B. fuscopurpurea
that were identical with regard to nuclear SSU rRNA
gene sequences were variable with regard to possession
of either or both introns. For example, the collection
from Greece contained both introns 516 and 1506; how-
ever, the other collection from Australia, with which it
was identical, did not contain the 1506 intron. In addi-
8. Group IC1 Introns in the Bangiales 1661
Table 3
Differences Between the 516 and 1506 Introns at Single
Positions or Base Pairs Using Tetrahymena thermophila
Position Numbering
T. thermophila Intron 516 Intron 1506
2 . . . . . . . . . . . . . .
25 . . . . . . . . . . . . .
26 . . . . . . . . . . . . .
97:277 . . . . . . . . .
98 . . . . . . . . . . . . .
160 . . . . . . . . . . . .
172a . . . . . . . . . . .
205 . . . . . . . . . . . .
216:257 . . . . . . . .
217:256 . . . . . . . .
262:312 . . . . . . . .
272 . . . . . . . . . . . .
281 . . . . . . . . . . . .
304 . . . . . . . . . . . .
313:413 . . . . . . . .
322:326a . . . . . . .
335:364 . . . . . . . .
G
A
G
A:U
C
A
U
U
G:C
G:C
G:C
U
C
G
A:U
G:C
A:U
U
U
U
u:g
U
G
C
C
C:G
C:G
C:G
G
U
A
G:C
C:G
C:G
NOTE.—Each position number shown is the nearest T. thermophila nucleo-
tide. Uppercase letters indicate that nucleotides are conserved in at least 95% of
the sequences. Lowercase letters indicate conservation between 90% and 95%.
a No homologous position exists in the T. thermophila sequence.
FIG. 3.—Alignment of open reading frames (ORFs) coding for
endonuclease-like amino acid sequences highlighting the His-Cys box
motif from the 516 and 1506 introns in the Bangiales. A, 516 introns:
Porphyra abbottae (P. abb.), Porphyra kanakaensis (P. kana.), Por-
phyra tenera (KK) (P. ten. (KK)), P. tenera (SK) (P. ten. (SK)), Ban-
gia fuscopurpurea (Helgoland) (B. fusc. (HL)), and B. fuscopurpurea
(MA) (B. fusc. (MA)). B, 1506 introns: Porphyra spiralis var. ampli-
folia (R), Porphyra umbilicalis (HG) (P. umb. (HG)), Porphyra fuci-
cola, and B. fuscopurpurea (1) (B. fusc. (1)). Identical positions are
indicated by dots, alignment gaps are indicated by dashes, and residues
inferred from reading frameshift corrections are shown in bold low-
ercase letters. Conserved residues proposed to be directly involved in
zinc binding (C100, C105, H110, C125, C132, H134, C138) and the
active site (H98, N119) of the I-PpoI endonuclease (Flick et al. 1998)
are indicated. The His-Cys box motif and frameshifts for P. tenera
(KK), P. tenera (SK), B. fuscopurpurea (1), and P. spiralis var. am-
plifolia (R) were previously noted by Haugen et al. (1999).
tion, the collection from Ireland (IR) contained both in-
trons 516 and 1506, whereas the other collections (WA
and TX), with which it was nearly identical (differing
by 8 bp) contained neither intron. A similar pattern oc-
curred in B. fuscopurpurea from Massachussetts (MA),
which did not contain the intron 1506, yet it was present
in the other collections with nearly identical sequences
(Helgoland and Nice, differing by 5 bp). Within Por-
phyra, this was only seen in one case: Porphyra ye-
zoensis (HH) did not contain intron 1506, whereas P.
yezoensis (OM) did.
Well-supported clades are along biogeographic
lines with few exceptions, but the presence or absence
of introns does not appear to be consistent based on
geographic locations. For example, the well-supported
clade (100% bootstrap) of B. fuscopurpurea containing
primarily collections from the Atlantic and Mediterra-
nean (NC, NJ, Greece, Helgoland, Nice, MA [with the
exception of the Pacific samples from Australia and
Mexico]) all contained intron 516, except the sample
from Mexico, and the samples from Massachusetts and
Australia did not contain intron 1506. Distromatic taxa
(subgenus Diploderma) of Porphyra, P. miniata (CCAP
1379/2, NF) and P. amplissima (2), contained neither
intron, whereas other species of Porphyra belonging to
the subgenera Diplastida and Porphyra were variable in
containing either intron.
Introns occur frequently within the Chlorophyta,
but within the Rhodophyta, Bangia, Porphyra, and Hil-
denbrandia are the only genera currently known to con-
tain introns (Ragan et al. 1993). This trend raises the
question of whether the introns within Hildenbrandia
and the Bangiales might be related. Hence, figure 5 also
includes the two 1506 introns from H. rubra and one
chlorophyte algae, C. ellipsoidea (A, B). This figure pre-
sents the one most-parsimonious tree based on analysis
of 1,025 parsimony-informative characters of well-
aligned positions of the group IC1 intron in positions
516 and 1506. This tree has a length of 4,589 steps and
a consistency index (CI) (a measure of the amount of
homoplasy exhibited by the set of characters: for no
homoplasy, CI ϭ 1) of 0.4988. This data set was also
analyzed by coding the gaps as single evolutionary
events (e.g., 10 consecutive gaps are treated as one event
rather than 10 separate events), whereas in the previous
analysis, they were treated as missing data. This analysis
depicted little change in the topologies of the trees; in
fact, the resolution was much lower than when the gaps
were treated as missing characters.
9. 1662 Mu¨ller et al.
FIG. 4.—Presence (ϩ) and absence (Ϫ) of group IC1 introns in positions 516 (first symbol) and 1506 (second symbol) mapped on an 18S
rRNA gene neighbor-joining tree. Lengths of branches in tree correspond to sequence divergence calculated using the Kimura (1980) two-
parameter model.
Figure 5 clearly depicts the 516 and 1506 intron
sequences as two separate clades that are generally well
supported (516: 100% maximum-parsimony [MP] boot-
strap; 50% quartet puzzling values [QPS]; 100% neigh-
bor-joining [NJ] bootstrap; 1506: 98% MP bootstrap;
Ͻ50% QPS; 99% NJ bootstrap). The two introns in H.
rubra are well associated with each other (100% MP
bootstrap; 88% QPS; 95% NJ bootstrap) and are well
positioned within the 1506 intron sequence clade of the
Bangiales (89% MP bootstrap; 89% QPS; 99% NJ boot-
strap). The introns in P. spiralis var. amplifolia (position
1506) are positioned on a branch that is basal to the
cluster containing the 1506 intron sequences from the
Bangiales and H. rubra.
Both the nuclear SSU rRNA gene NJ tree (fig. 4)
and the phylogenetic tree using intron sequences (fig. 5)
show similar trends. For example, the well-supported
(100% bootstrap support; fig. 5) cluster containing B.
fuscopurpurea from New Jersey (NJ), Nice, Australia,
Greece, North Carolina (NC), Helgoland, and Massa-
chusetts (MA) is also present in the intron phylogenetic
tree for both the 1506 (100% MP bootstrap; 99% QPS;
92% NJ bootstrap) and 516 introns (98% MP bootstrap;
Ͻ50% QPS; 70% NJ bootstrap) (fig. 5). In addition, the
collections from Ireland, Newfoundland (NF), and B.
fuscopurpurea (2) also cluster together within the nu-
clear SSU rRNA gene analysis (93% bootstrap) and the
intron phylogeny for both intron insertion sites. This re-
lationship is fairly well supported for the 1506 intron
sequences (72% MP bootstrap; 94% QPS; 83% NJ boot-
strap) but not for the 516 intron sequences (61% MP
bootstrap; Ͻ50% QPS; Ͻ50% NJ bootstrap) (fig. 5).
Similarly, the 516 intron sequences within the
freshwater taxon B. atropurpurea from the British Isles
(BI12), Netherlands (NL), Great Lakes (GL), Italy (IT),
and Ireland (IR) are positioned in a well-supported clade
(100% MP bootstrap; 57% QPS; 85% NJ bootstrap), as
are the sequences of the nuclear SSU rRNA gene for
these collections. In addition, none of the freshwater col-
lections contained intron 1506. The relationship of the
10. Group IC1 Introns in the Bangiales 1663
FIG. 5.—The one most-parsimonious tree based on analysis of 1,025 phylogenetically informative characters of well-aligned positions of
the group IC1 intron in positions 516 and 1506 in the order Bangiales (length ϭ 4,589, consistency index ϭ 0.4988). The first number above
a branch represents bootstrap support (1,000 replicates) for maximum parsimony, the second value is the percentage of times that a particular
cluster was found among the 1,000 intermediate steps (QPS) using quartet puzzling, and the final value represents bootstrap resampling for
distance analysis (1,000 replicates). Numbers below branches represent Bremer indices or decay values.
marine collection from the Virgin Islands (VIS7) was
unresolved (Ͻ55% bootstrap support) in both the intron
analyses, and it is only weakly associated (62% boot-
strap) with one of the main clades in the NJ nuclear
SSU rRNA gene tree.
The relationship among the introns in Porphyra is
not as well resolved as that in Bangia. However, some
groupings are evident in all three analyses. For example,
Porphyra sp. (SY) and P. pseudolinearis (TT) are close-
ly associated in the nuclear SSU rRNA gene phylogeny
(75% bootstrap), and the 516 intron sequences for these
two taxa are also well associated (99% MP bootstrap;
Ͻ50% QPS; 99% NJ bootstrap) (fig. 5). In addition, the
clade consisting of P. tenera (T1, TU-3), P. umbilicalis
(NJ), P. yezoensis, and P. yezoensis (HH, OM) is present
in the nuclear SSU rRNA gene phylogeny (although not
well supported), and this cluster is also seen for the 516
introns for these taxa in figure 5 (100% MP bootstrap;
97% QPS; 76% NJ bootstrap). A close relationship
among Porphyra rediviva, Porphyra sp. (Brest), and P.
umbilicalis (HG) is reflected in both the nuclear SSU
rRNA gene tree (100% bootstrap) and the 1506 portion
of the intron phylogeny, with the relationship between
P. rediviva and Porphyra sp. (Brest) being well sup-
ported (100% MP bootstrap; 100% QPS; 75% NJ boot-
strap) and the 1506 intron sequence being only weakly
associated with the previous clade (Ͻ50% MP boot-
strap; 64% QPS; Ͻ50% NJ bootstrap). A grouping of
Porphyra 1506 intron sequences consisting primarily of
collections from Japan (P. yezoensis (OM, OG-1, OG-
4, NA-2, NA-4), P. yezoensis narawaenis, P. tenera
(KK, SK), P. pseudolinearis (TT), Porphyra sp. (SHH))
is moderately supported (82% MP bootstrap; 83% QPS;
Ͻ50% NJ bootstrap). This trend is not, however, reflect-
11. 1664 Mu¨ller et al.
ed in the nuclear SSU rRNA gene tree, where the rela-
tionship among many of the Japanese taxa is close but
unresolved (Ͻ50% support). Many of the other relation-
ships seen in the nuclear SSU rRNA gene NJ tree are
similar to those in the intron trees, but most are not well
supported by bootstrap analysis (Ͻ60%). The sequence
divergence in the intron at position 516 varied consid-
erably, ranging from 0% to as high as 31.0%. The se-
quence divergence for the intron in position 1506 was
higher than that for the 516 intron (31.0% vs. 44.3%).
Interestingly, the 1506 introns in P. spiralis var. ampli-
folia (Oliveira and Ragan 1994) were quite distant from
all other Porphyra and Bangia taxa, ranging from 30.3%
to 44.3% sequence divergence.
Discussion
Introns within the nuclear SSU rRNA gene from
members of the Bangiales have been reported several
times within the past few years (Stiller and Waaland
1993; Oliveira and Ragan 1994; Oliveira et al. 1995;
Mu¨ller et al. 1998). The presence and absence of these
introns presents us with an opportunity to examine lat-
eral intron transfer events and the evolutionary history
of introns within the order Bangiales. Oliveira et al.
(1995) speculated that these introns could also be used
to discern biogeographic or specific entities within the
genus Porphyra, as they determined that variants of the
group IC1 intron were present in different geographic
populations of this alga. Due to the considerable number
and variation (as high as 40%) in the introns in Por-
phyra and Bangia, this system is well suited to address-
ing some of these issues. In addition, group I introns
that lack endonuclease coding regions appear to be non-
mobile and provide a potentially valuable tool for trac-
ing the evolutionary history of these sequences (Bhat-
tacharya 1998).
The similarity in phylogenies between the 516 and
1506 introns and their nuclear SSU rRNA genes sug-
gests that these introns have not been mobile during the
evolution of the Bangiales. Introns have been docu-
mented in the nuclear-encoded rRNA genes of different
Naegleria species. The majority of these occur at the
516 position of the nuclear SSU rRNA gene. A more
extensive analysis of the Naegleria nuclear SSU rRNA
genes revealed that this intron is absent in the majority
of the species’ nuclear SSU rRNA genes (De Jonckheere
1994). De Jonckheere (1994) hypothesized that since
there was probably no selective advantage arising from
the presence of these introns, they were eliminated in
many of the descendants. In the case of the Bangiales,
it appears that after initial acquisition of the introns in
the ancestor of these taxa, there was subsequent vertical
inheritance and evolution within the order (and species)
and in some cases loss of the introns in either insertion
site, as the intron phylogenies are very similar to that
of the host gene. An alternative and less favorable hy-
pothesis is that frequent lateral transfers within the order
may have taken place, but this would result in intron
phylogenies that would be widely discordant with the
nuclear SSU rRNA gene phylogenies (Bhattacharya et
al. 1994).
The similarity among group I intron and nuclear
SSU rRNA gene phylogenies has also been reported for
other eukaryotic taxa. Takashima and Nakase (1997)
noted that introns had been transferred horizontally to
distinct insertion sites in the yeast-like fungus Tilletiop-
sis flava and then inherited vertically. Similarly, introns
1506 and the nuclear SSU rRNA gene sequences share
similar phylogenies in members of the green algal order
Zygnematales (Bhattacharya et al. 1994). Wilcox et al.
(1992) also postulated that the distribution of introns
within other green algal taxa could be explained by in-
heritance of these sequences along with the gene. How-
ever, VanOppen, Olsen, and Stam (1993) concluded that
nuclear group I introns in green algae have arisen sev-
eral times and do not appear to be lineage-specific and
disagreed that the distribution of introns could be ex-
plained by vertical inheritance within the green algae as
postulated by Wilcox et al. (1992). In the case of the
Bangiales, the latter scenario appears to be possible. For
instance, the intron phylogenies appear to be in accor-
dance with the gene phylogenies, indicating long-term
immobility and vertical inheritance.
The evolutionary history of the Bangiales is quite
long, as bangiophyte taxa have been reported in the fos-
sil record from the Proterozoic (1,200 MYA) (Butter-
field, Knoll, and Swett 1990), and the conchocelis stage
of Porphyra has been reported in fossils up to 425 MYA
(Campbell 1980). In terms of utilizing the introns within
the Bangiales as specific or geographic markers as spec-
ulated by Oliveira and Ragan (1994), the present study
does not appear to indicate this possibility. In fact, anal-
yses of the group I introns appear to provide further
evidence for the synonymy of these two genera, as in-
tron phylogenies are congruent with those of the nuclear
SSU rRNA gene. This is not surprising, as other molec-
ular studies using nuclear and chloroplast genes have
indicated that these taxa are not monophyletic genera
(Mu¨ller et al. 1998). Thus, attempts at constructing a
phylogenetic classification within the order based on
morphology, life histories, and molecular analyses, and,
in this case, intron sequences, have been problematic.
The observation that similar group I introns are dis-
tributed across different genomes and phylogenetically
distant taxa is taken as evidence that intron transfer is
relatively common (Burke 1988). The clustering of
group I introns in phylogenetic trees from distinct in-
sertion sites suggests that these introns may be traced
back to one or more events in which the introns were
inserted into rRNA and vertically inherited or lost (Bhat-
tacharya et al. 1994; Bhattacharya 1998). Within the
Zygnematales, bootstrap analyses yielded little support
for the single origin of all group I introns at different
insertion sites within rRNA (Bhattacharya et al. 1994).
It is difficult to determine if this is the case with the
introns within the Bangiales due to the lack of a suitable
outgroup. Nonetheless, all of the 516 and 1506 introns
form two separate clades distinct from each other. High
sequence similarity between introns is consistent with
descent from an ancestral intron that was initially ac-
12. Group IC1 Introns in the Bangiales 1665
quired and vertically inherited (Schroeder-Diedrich,
Fuerst, and Byers 1998). In the protist Acanthamoeba,
low sequence identity (highly variable) among introns
in four different positions suggests that the intron ac-
quisition occurred independently at the four positions
after divergence of the taxa within the tree (Schroeder-
Diedrich, Fuerst, and Byers 1998). There is high se-
quence identity (0% sequence divergence in some cases)
among many of the introns sequenced within the Ban-
giales; however, there is also considerable variability.
For example, the 1506 introns in P. spiralis var. ampli-
folia (B, D, R) differ from all other intron sequences by
30%–44% sequence divergence. Despite this, P. spiralis
var. amplifolia is well supported as grouping with the
remaining 1506 introns.
Homing-Endonuclease Pseudogenes in the Bangiales
The mobility of nuclear group I introns may depend
on homing through the expression of intron-encoded
homing endonucleases (Belfort and Roberts 1997). The
His-Cys box is one of several types of homing endo-
nucleases that is restricted to group I introns (Johansen,
Embley, and Willassen 1993). Haugen et al. (1999) de-
scribed unusual P1 extensions within the nuclear SSU
rRNA introns of Bangia and Porphyra. Their analysis
showed that the intron sequences contained His-Cys box
reading frames within the P1 extension and that these
may represent homing-endonuclease pseudogenes. They
also demonstrated that the ORF in the 1506 intron of P.
spiralis var. amplifolia occurred on the strand comple-
mentary to that encoding the SSU rRNA gene and group
I intron. The present study also observed this phenom-
enon for the P1 domain in the introns at position 1506
for P. fucicola and P. umbilicalis (HG), both of which
also contained the His-Cys box motif noted in P. spiralis
var. amplifolia. The introns in the 516 position that con-
tained an ORF as well as a His-Cys box motif were
within the P2 domain and not on the complementary
strand, as seen in the 1506 introns. Haugen et al. (1999)
also noted frameshifts in the 3Ј end of the P. spiralis
var. amplifolia intron ORF which resulted in a truncated
C-terminal end and would explain the lack of cleavage
activity in the in vitro translated protein. Haugen et al.
(1999) suggested that the truncation and frameshifts
seen in the Bangialean intron ORFs may be the result
of selection against endonuclease expression which
would lethally cleave chromosomal DNA. Only two of
the new sequences in this study had frameshifts, P. kan-
akaensis and B. fuscopurpurea (Helgoland), and all se-
quences were found to terminate prematurely. This may
indicate that these ORFs are no longer functional; how-
ever, endonuclease activity has not been studied in these
sequences and needs to be investigated.
Secondary-Structure Signatures of the Group IC1
Introns in the Bangiales
In 1987, Woese rationalized that the examination
of higher-order structure from a phylogenetic perspec-
tive would enable us to examine the stages of evolution
of rRNA structure and aid in extrapolating the signifi-
cance of changes and variation in rRNA. Subsequently,
Winker and Woese (1991) delineated the three primary
domains using structural characteristics of 16S rRNA.
They defined two types of signature characters: (1) ho-
mologous positions whose compositions are (very near-
ly) constant (present in at least 94% of the representative
sequences) within each of the domains or kingdoms and
are characteristic of at least one, and (2) nonhomologous
structures that characterize and distinguish the various
groupings (e.g., structures that are present in one group
and absent in another and/or structural units that differ
strikingly from one group to another). Within these two
types there are different examples of phylogenetically
constrained elements ranging from single nucleotides
and base pairs to hairpin loops, noncanonical pairing,
insertions, deletions, and combinations of these ele-
ments, along with coaxial stacked helices or differences
in numbers between homologous structures (Gutell
1992).
In the present study, the Bangiales were observed
to have sequence and structural elements, or ‘‘signa-
tures,’’ that differentiate these introns from each other
as well as from other available intron sequences. As
noted previously, the P5b domain in the 516 introns of
the Bangiales contains a bifurcated helix that distin-
guishes these introns from all other group IC1 introns
(fig. 2a). This element is not present in the P5b domain
in the 1506 bangialean introns and is an example of a
nonhomologous signature. The variation in length in the
P8 domain of the 1506 introns is also unique to the
Bangiales and is not seen in the bangialean 516 introns.
In addition to these structural elements, the introns in
the Bangiales can be differentiated based on nonhomol-
ogous and homologous single-nucleotide and base pair
signatures (table 3). For example, nucleotide 172 and
base pair 322:326 have no homologous positions with
respect to T. thermophila and can be considered non-
homologous signatures defining these introns. The two
introns can be differentiated based on nucleotide and
base pair signatures. For example, position 205 is a U
in intron 516 (conserved in Ͼ95% of the sequences) and
a C in intron 1506 (conserved in Ͼ95% of the sequenc-
es). These unique structural and sequence signatures
provide further evidence that the introns in positions 516
and 1506 are probably the result of a single (although
separate from each other) lateral transfer event and sub-
sequent vertical inheritance. In addition, these structural
signatures may provide a means for determining the pos-
sible origin of the Bangialean 516 and 1506 introns if
an ancestral intron still exists. This information also
yields a basis for utilizing introns to differentiate dif-
ferent phyla/organisms or to determine the origin of in-
trons based on structural characteristics.
Acknowledgments
This research was supported by NSERC grant RGP
0183503 to R.G.S., NIH grant GM 48207 to R.R.G., and
an OGS Scholarship to K.M.M. Technical assistance in
DNA sequencing by Angela Holliss is gratefully ac-
knowledged. We thank John Stiller, Alison Sherwood,
13. 1666 Mu¨ller et al.
Ron Deckert, Blair Brace, Wilson Freshwater, Mary Ko-
ske, and John West for help in collecting or providing
samples for this study.
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DAVID IRWIN, reviewing editor
Accepted April 10, 2001