The document discusses viruses with large and small DNA genomes as well as positive-strand and negative-strand RNA viruses. Herpesviruses have very large DNA genomes up to 235 kbp that encode many enzymes. Adenoviruses and phages like lambda have smaller genomes between 30-54 kbp. Animal viruses like parvoviruses and polyomaviruses have even smaller genomes around 5 kbp that tightly pack genes. Picornaviruses, togaviruses, and flaviviruses have single-stranded RNA genomes between 7-11 kbp. Coronaviruses have the largest RNA genomes around 30 kbp. Segmentation allows larger coding capacity for viruses like influenza and gemin
The hereditary material of organisms is DNA, which contains genetic information in the form of a specific nucleotide sequence. This DNA is organized into chromosomes that make up an organism's genome. Gene expression involves transcription of DNA into RNA, which may undergo processing before being translated into proteins. The proteins then fold and are transported within the cell. Regulation of gene expression controls when and how much of gene products are made to allow cells to adapt. Gene expression can be measured to provide insight into cellular processes.
1st ChIP-SAGE uses ChIP to purify chromatin, then crosslinks are reversed and linkers are ligated to DNA ends before digestion with NlaIII and MmeI to produce 21-22 bp sequence tags for cloning and sequencing.
2nd Deposition of histone variants like H2A.Z and H3.3 mark boundaries of regulatory regions in genomes and create hierarchical nucleosome stability.
3rd Interpreting ChIP experiments requires considering antibody specificity, chromatin preparation methods, and that results reflect average modification states across cells.
Chromosomes contain DNA and proteins. In eukaryotes, chromosomes are located in the nucleus and must be highly compacted to fit by binding proteins to form chromatin. Chromatin is compacted in a hierarchical manner through interactions with histone proteins to form nucleosomes, which further compact to form the 30nm fiber and loop domains that attach to the nuclear matrix, compacting the DNA over 1000-fold to fit in the cell.
This document discusses eukaryotic genomes. It begins by defining a genome and noting that eukaryotic DNA is associated with histone proteins to form chromatin fibers. These fibers condense into chromosomes during cell division. Histone modification through acetylation and methylation can relax or tighten chromatin structure to increase or decrease gene transcription. The document then discusses transcription, post-transcriptional modification, translation, and post-translational modification of proteins in eukaryotic cells.
AP Biology Ch. 15, part 2 regulation of the eukaryotic genomeStephanie Beck
1. Eukaryotic DNA is organized into chromatin through successive levels of packing around histone proteins. This organization, along with modifications like DNA methylation and histone acetylation, regulates whether DNA is condensed and genes are silenced (heterochromatin) or loose and accessible for transcription (euchromatin).
2. Gene expression is regulated at the level of transcription through control elements in DNA that bind regulatory proteins which influence the binding of RNA polymerase and initiation of transcription.
3. Additional regulation occurs after transcription through RNA processing, microRNA interference with mRNA, control of mRNA degradation, and regulation of translation through proteins that block ribosome binding. Protein levels are also controlled by post-translational modifications and
Epigenetics- Transcription regulation of gene expressionakash mahadev
This document provides information about epigenetics and histone modifications. It defines epigenetics as heritable changes in gene function that do not involve changes to the underlying DNA sequence. It discusses how histone modifications such as acetylation and methylation regulate gene expression by altering chromatin structure and recruiting other proteins. DNA methylation is also described as an important epigenetic modification that typically represses transcription. Several families of enzymes that establish these modifications, such as DNA methyltransferases and histone methyltransferases/acetyltransferases, are outlined.
1) Researchers engineered haploid plants by altering the centromeric histone CENH3. When crossed to wild-type plants, this led to missegregation of chromosomes during mitosis and the production of haploid offspring containing only the wild-type parent's genome.
2) The dyad1 mutant in Arabidopsis produces unreduced female gametes through apomeiosis, leading to triploid progeny when fertilized. This demonstrates that altering a single gene can influence meiosis and may enable engineering of apomixis.
3) Chromosome engineering techniques like modifying centromeres and recombination proteins can enable new applications in plant breeding like producing haploids, engineering apomixis,
The hereditary material of organisms is DNA, which contains genetic information in the form of a specific nucleotide sequence. This DNA is organized into chromosomes that make up an organism's genome. Gene expression involves transcription of DNA into RNA, which may undergo processing before being translated into proteins. The proteins then fold and are transported within the cell. Regulation of gene expression controls when and how much of gene products are made to allow cells to adapt. Gene expression can be measured to provide insight into cellular processes.
1st ChIP-SAGE uses ChIP to purify chromatin, then crosslinks are reversed and linkers are ligated to DNA ends before digestion with NlaIII and MmeI to produce 21-22 bp sequence tags for cloning and sequencing.
2nd Deposition of histone variants like H2A.Z and H3.3 mark boundaries of regulatory regions in genomes and create hierarchical nucleosome stability.
3rd Interpreting ChIP experiments requires considering antibody specificity, chromatin preparation methods, and that results reflect average modification states across cells.
Chromosomes contain DNA and proteins. In eukaryotes, chromosomes are located in the nucleus and must be highly compacted to fit by binding proteins to form chromatin. Chromatin is compacted in a hierarchical manner through interactions with histone proteins to form nucleosomes, which further compact to form the 30nm fiber and loop domains that attach to the nuclear matrix, compacting the DNA over 1000-fold to fit in the cell.
This document discusses eukaryotic genomes. It begins by defining a genome and noting that eukaryotic DNA is associated with histone proteins to form chromatin fibers. These fibers condense into chromosomes during cell division. Histone modification through acetylation and methylation can relax or tighten chromatin structure to increase or decrease gene transcription. The document then discusses transcription, post-transcriptional modification, translation, and post-translational modification of proteins in eukaryotic cells.
AP Biology Ch. 15, part 2 regulation of the eukaryotic genomeStephanie Beck
1. Eukaryotic DNA is organized into chromatin through successive levels of packing around histone proteins. This organization, along with modifications like DNA methylation and histone acetylation, regulates whether DNA is condensed and genes are silenced (heterochromatin) or loose and accessible for transcription (euchromatin).
2. Gene expression is regulated at the level of transcription through control elements in DNA that bind regulatory proteins which influence the binding of RNA polymerase and initiation of transcription.
3. Additional regulation occurs after transcription through RNA processing, microRNA interference with mRNA, control of mRNA degradation, and regulation of translation through proteins that block ribosome binding. Protein levels are also controlled by post-translational modifications and
Epigenetics- Transcription regulation of gene expressionakash mahadev
This document provides information about epigenetics and histone modifications. It defines epigenetics as heritable changes in gene function that do not involve changes to the underlying DNA sequence. It discusses how histone modifications such as acetylation and methylation regulate gene expression by altering chromatin structure and recruiting other proteins. DNA methylation is also described as an important epigenetic modification that typically represses transcription. Several families of enzymes that establish these modifications, such as DNA methyltransferases and histone methyltransferases/acetyltransferases, are outlined.
1) Researchers engineered haploid plants by altering the centromeric histone CENH3. When crossed to wild-type plants, this led to missegregation of chromosomes during mitosis and the production of haploid offspring containing only the wild-type parent's genome.
2) The dyad1 mutant in Arabidopsis produces unreduced female gametes through apomeiosis, leading to triploid progeny when fertilized. This demonstrates that altering a single gene can influence meiosis and may enable engineering of apomixis.
3) Chromosome engineering techniques like modifying centromeres and recombination proteins can enable new applications in plant breeding like producing haploids, engineering apomixis,
This document contains a presentation by Niwedita Kumari on the molecular basis of inheritance. The main topics covered include DNA, RNA, replication of DNA, transcription, and translation. DNA and RNA are described as well as their roles. Replication of DNA is explained as the semiconservative replication of the two strands to produce two DNA molecules. Transcription and translation are then summarized as the processes by which the genetic information in DNA is used to synthesize RNA and proteins, respectively.
The document discusses different expression vectors and systems used for recombinant protein expression. It describes key elements required for an expression vector including an origin of replication, selective marker, promoter, multiple cloning site, and terminator. It provides details on commonly used expression systems in E. coli such as the lac, tac, lambda PL, and T7 promoters. It also summarizes protein expression in yeast using the galactose-inducible GAL promoter system.
1. Chromatin remodeling is the process by which chromatin structure is dynamically modified to allow access of DNA for processes like transcription.
2. There are two main types of chromatin remodeling - covalent histone modification and ATP-dependent chromatin remodeling complexes.
3. ATP-dependent complexes use energy from ATP hydrolysis to move, eject, or restructure nucleosomes, allowing access to DNA.
4. Examples of chromatin remodeling complexes include SWI/SNF, ISWI, CHD, and INO80 families, which have different activities like nucleosome sliding or histone variant exchange.
Chloroplast DNA is usually circular with a long single copy section (LSC) and short single copy section (SSC) separated by inverted repeats. It contains around 100-200 genes encoding proteins, tRNAs, and rRNAs. These genes are involved in chloroplast gene expression and photosynthesis. Most proteins are nuclear gene products imported into chloroplasts, but the large subunit of RuBisCO is encoded by a chloroplast gene. Chloroplast genes are arranged in operon-like units and co-transcribed using different promoters. There are two RNA polymerases - PEP and NEP - that transcribe chloroplast genes. PEP resembles the bacterial polymerase while NEP resembles phage polymerases.
Chromatin modulation and role in gene regulationZain Khadim
This document discusses chromatin modulation and its role in gene regulation. It describes how DNA is packaged into chromatin through winding around histone proteins to form nucleosomes. Chromatin exists in two forms - loosely packed euchromatin and tightly packed heterochromatin. Gene expression is regulated through chromatin remodeling by mechanisms like nucleosome disruption, sliding, and transfer mediated by protein complexes like SWI/SNF. Histone modifications through processes like acetylation and methylation also influence gene regulation by altering chromatin structure. Precise control of gene expression through such chromatin modulation is important for cellular adaptation and efficient use of cellular resources.
This document discusses extrachromosomal DNA replication in prokaryotes and eukaryotes. In prokaryotes, extrachromosomal DNA is primarily found in plasmids. Plasmids replicate via rolling circle, iteron-regulated, or RNA-regulated mechanisms. In eukaryotes, extrachromosomal DNA is found in mitochondria and chloroplasts. Mitochondrial DNA replicates via a strand displacement model using DNA polymerase gamma and other specialized replication factors. Chloroplast DNA replication shares similarities but uses its own distinct replication proteins.
"Introns: Structure and Functions" during November, 2011 (Friday Seminar activity, Department of Biotechnology, University of Agricultural Sciences, Dharwad, Karnataka) by Yogesh S Bhagat (Ph D Scholar)
The document provides information about eukaryotic genome organization. It discusses that eukaryotic DNA is organized into chromosomes that are linear molecules located within the nucleus. The genome contains both coding and non-coding DNA sequences. It also describes various repetitive elements like transposons that make up a significant portion of the genome. Mobile elements can move within genomes and have contributed to genetic variation.
definition of Mitochondrial gene expression
structure of mitochondrial dna
requirment for transcriptional activity
transcription elongation and termination
post transcriptional modification
translation of mitochondrial transcripts
The document discusses genome organization in eukaryotes. It begins by defining the genome as an organism's entire hereditary information, encoded in DNA or RNA. In eukaryotes, DNA is associated with histone proteins to form chromatin fibers, which condense into chromosomes. The document then discusses various levels of chromatin organization, from DNA wrapping around nucleosomes to form beads on a string, to higher-order folding forming metaphase chromosomes. Chromatin exists in two types - loosely packed euchromatin and tightly packed heterochromatin. Overall, the document provides an overview of eukaryotic genome and chromatin organization from nucleosomes to chromosomes.
The document discusses the organization and structure of the human genome. It notes that the genome contains DNA arranged into genes on chromosomes within the cell nucleus, as well as mitochondrial DNA containing 37 genes. The human genome consists of 24 chromosomes in the nucleus plus the mitochondrial genome. DNA is organized into nucleosomes and packaged into chromatin and chromosomes. Genes encode instructions to make proteins and are regulated differently between cell types.
Transcription is the process of creating messenger RNA (mRNA) from a DNA template. It occurs in the nucleus and proceeds in the 5' to 3' direction. The antisense strand of DNA is transcribed into mRNA by RNA polymerase. Eukaryotic mRNA requires introns to be removed through post-transcriptional modification to form mature mRNA.
The document discusses gene expression and various methods used to measure it. It describes how measuring mRNA levels can indicate which genes are actively being expressed in a cell. It provides details on transcription, regulatory elements that control it, and various techniques used to study gene expression, including microarray analysis, serial analysis of gene expression (SAGE), and northern blotting.
GRAS proteins expression and purification Mesele Tilahun
The document summarizes the production and analysis of the GRAS protein Os-SCL7. It describes how the gene encoding the GRAS domain of Os-SCL7 was cloned and expressed in E. coli. The protein was then purified using nickel affinity chromatography and size exclusion chromatography. Sequence analysis revealed the protein is 378 amino acids with a predicted molecular weight of 41.5 kDa. Potential cleavage sites for specific proteases were also identified from the amino acid sequence.
The document discusses the molecular structure of genes and chromosomes. It describes how DNA is organized into chromosomes, which contain both protein-coding genes and non-coding sequences. Genes contain exons and introns, and in eukaryotes genes are further organized into transcription units. Chromatin compacts the DNA into nucleosomes and higher-order structures like the 30nm fiber. Overall the document provides an overview of the molecular organization and components that make up eukaryotic genes and chromosomes.
DNA replication occurs semi-conservatively, with each parental strand serving as a template for synthesis of a new complementary strand. This results in two identical DNA molecules, each with one original parental strand and one newly synthesized strand. Replication is initiated at the origin of replication and proceeds bidirectionally around the circular bacterial chromosome. Enzymes such as helicase unwind the parental DNA, topoisomerases relieve supercoiling, and DNA polymerase adds complementary nucleotides using the parental strands as templates.
Dna content,c value paradox, euchromatin heterochromatin, banding patternArchanaSoni3
DNA content refers to the amount of DNA in an organism's haploid chromosomes. It varies greatly between organisms, with eukaryotes generally having more DNA than prokaryotes. The amount of DNA does not always correlate with an organism's complexity, known as the C-value paradox. This is because eukaryotic DNA contains large amounts of non-coding repetitive sequences. Chromatin exists in two forms - euchromatin, which is less condensed and permits gene expression, and heterochromatin, which is highly condensed and usually silences genes. Heterochromatin forms in specific regions like centromeres and telomeres and is important for chromosome function and stability.
The document discusses several key topics related to DNA structure and function:
DNA replication ensures each cell has an exact copy of the DNA before cell division. Errors are constantly checked and repaired to maintain high fidelity. DNA is also rearranged through processes like recombination. The tightly regulated enzymes that perform these metabolic processes were demonstrated by the Meselson-Stahl experiment to replicate DNA using a semiconservative mechanism. DNA is organized through various levels of compaction into condensed chromosomes. This dynamic structure, along with features like centromeres and telomeres, helps regulate DNA accessibility and proper segregation during cell division.
This document provides an overview of the process by which DNA directs protein synthesis through transcription and translation. It discusses the flow of genetic information from DNA to mRNA to protein. Key points include: transcription produces messenger RNA from DNA templates in the nucleus; eukaryotic pre-mRNA is processed before translation; translation occurs in the cytoplasm using tRNA to add amino acids to growing polypeptide chains on ribosomes according to mRNA codons. The genetic code is nearly universal and specifies 20 amino acids using triplets of nucleotides.
Epigenetics in fisheries and aquacultureKiran Modi
Epigenetics refers to heritable phenotypic changes that do not involve alterations to the DNA sequence. Key epigenetic mechanisms in fisheries and aquaculture include DNA methylation, genome imprinting, histone modification, and chromatin remodeling. DNA methylation and histone modifications can suppress gene expression through various mechanisms like blocking transcription factor binding sites or recruiting histone modifier complexes. Genome imprinting leads to parental origin-specific gene expression and has effects on development and metabolism. These epigenetic processes modify gene activation and expression without altering the underlying genetic code.
Parvoviruses are the smallest DNA viruses, including human parvovirus B19. B19 is pathogenic in humans, infecting erythroid progenitor cells and causing fifth disease in children characterized by a rash. It can also cause aplastic crisis, hydrops fetalis in fetuses, and chronic anemia in immunocompromised patients. Diagnosis involves detecting IgG and IgM antibodies by ELISA or PCR to detect the virus. There is no treatment, though a vaccine is in clinical trials.
This document categorizes and summarizes various viral families, their important genera, the diseases they cause, how they are transmitted, and methods for diagnosis. It covers both DNA and RNA viruses, including those that are single-stranded, double-stranded, enveloped, and non-enveloped. Many common viral diseases are discussed such as influenza, hepatitis, HIV, measles, Ebola, rabies, as well as less known illnesses. Diagnostic approaches include cell culture, serology, PCR, antigen detection, and visualization of viral structures.
This document contains a presentation by Niwedita Kumari on the molecular basis of inheritance. The main topics covered include DNA, RNA, replication of DNA, transcription, and translation. DNA and RNA are described as well as their roles. Replication of DNA is explained as the semiconservative replication of the two strands to produce two DNA molecules. Transcription and translation are then summarized as the processes by which the genetic information in DNA is used to synthesize RNA and proteins, respectively.
The document discusses different expression vectors and systems used for recombinant protein expression. It describes key elements required for an expression vector including an origin of replication, selective marker, promoter, multiple cloning site, and terminator. It provides details on commonly used expression systems in E. coli such as the lac, tac, lambda PL, and T7 promoters. It also summarizes protein expression in yeast using the galactose-inducible GAL promoter system.
1. Chromatin remodeling is the process by which chromatin structure is dynamically modified to allow access of DNA for processes like transcription.
2. There are two main types of chromatin remodeling - covalent histone modification and ATP-dependent chromatin remodeling complexes.
3. ATP-dependent complexes use energy from ATP hydrolysis to move, eject, or restructure nucleosomes, allowing access to DNA.
4. Examples of chromatin remodeling complexes include SWI/SNF, ISWI, CHD, and INO80 families, which have different activities like nucleosome sliding or histone variant exchange.
Chloroplast DNA is usually circular with a long single copy section (LSC) and short single copy section (SSC) separated by inverted repeats. It contains around 100-200 genes encoding proteins, tRNAs, and rRNAs. These genes are involved in chloroplast gene expression and photosynthesis. Most proteins are nuclear gene products imported into chloroplasts, but the large subunit of RuBisCO is encoded by a chloroplast gene. Chloroplast genes are arranged in operon-like units and co-transcribed using different promoters. There are two RNA polymerases - PEP and NEP - that transcribe chloroplast genes. PEP resembles the bacterial polymerase while NEP resembles phage polymerases.
Chromatin modulation and role in gene regulationZain Khadim
This document discusses chromatin modulation and its role in gene regulation. It describes how DNA is packaged into chromatin through winding around histone proteins to form nucleosomes. Chromatin exists in two forms - loosely packed euchromatin and tightly packed heterochromatin. Gene expression is regulated through chromatin remodeling by mechanisms like nucleosome disruption, sliding, and transfer mediated by protein complexes like SWI/SNF. Histone modifications through processes like acetylation and methylation also influence gene regulation by altering chromatin structure. Precise control of gene expression through such chromatin modulation is important for cellular adaptation and efficient use of cellular resources.
This document discusses extrachromosomal DNA replication in prokaryotes and eukaryotes. In prokaryotes, extrachromosomal DNA is primarily found in plasmids. Plasmids replicate via rolling circle, iteron-regulated, or RNA-regulated mechanisms. In eukaryotes, extrachromosomal DNA is found in mitochondria and chloroplasts. Mitochondrial DNA replicates via a strand displacement model using DNA polymerase gamma and other specialized replication factors. Chloroplast DNA replication shares similarities but uses its own distinct replication proteins.
"Introns: Structure and Functions" during November, 2011 (Friday Seminar activity, Department of Biotechnology, University of Agricultural Sciences, Dharwad, Karnataka) by Yogesh S Bhagat (Ph D Scholar)
The document provides information about eukaryotic genome organization. It discusses that eukaryotic DNA is organized into chromosomes that are linear molecules located within the nucleus. The genome contains both coding and non-coding DNA sequences. It also describes various repetitive elements like transposons that make up a significant portion of the genome. Mobile elements can move within genomes and have contributed to genetic variation.
definition of Mitochondrial gene expression
structure of mitochondrial dna
requirment for transcriptional activity
transcription elongation and termination
post transcriptional modification
translation of mitochondrial transcripts
The document discusses genome organization in eukaryotes. It begins by defining the genome as an organism's entire hereditary information, encoded in DNA or RNA. In eukaryotes, DNA is associated with histone proteins to form chromatin fibers, which condense into chromosomes. The document then discusses various levels of chromatin organization, from DNA wrapping around nucleosomes to form beads on a string, to higher-order folding forming metaphase chromosomes. Chromatin exists in two types - loosely packed euchromatin and tightly packed heterochromatin. Overall, the document provides an overview of eukaryotic genome and chromatin organization from nucleosomes to chromosomes.
The document discusses the organization and structure of the human genome. It notes that the genome contains DNA arranged into genes on chromosomes within the cell nucleus, as well as mitochondrial DNA containing 37 genes. The human genome consists of 24 chromosomes in the nucleus plus the mitochondrial genome. DNA is organized into nucleosomes and packaged into chromatin and chromosomes. Genes encode instructions to make proteins and are regulated differently between cell types.
Transcription is the process of creating messenger RNA (mRNA) from a DNA template. It occurs in the nucleus and proceeds in the 5' to 3' direction. The antisense strand of DNA is transcribed into mRNA by RNA polymerase. Eukaryotic mRNA requires introns to be removed through post-transcriptional modification to form mature mRNA.
The document discusses gene expression and various methods used to measure it. It describes how measuring mRNA levels can indicate which genes are actively being expressed in a cell. It provides details on transcription, regulatory elements that control it, and various techniques used to study gene expression, including microarray analysis, serial analysis of gene expression (SAGE), and northern blotting.
GRAS proteins expression and purification Mesele Tilahun
The document summarizes the production and analysis of the GRAS protein Os-SCL7. It describes how the gene encoding the GRAS domain of Os-SCL7 was cloned and expressed in E. coli. The protein was then purified using nickel affinity chromatography and size exclusion chromatography. Sequence analysis revealed the protein is 378 amino acids with a predicted molecular weight of 41.5 kDa. Potential cleavage sites for specific proteases were also identified from the amino acid sequence.
The document discusses the molecular structure of genes and chromosomes. It describes how DNA is organized into chromosomes, which contain both protein-coding genes and non-coding sequences. Genes contain exons and introns, and in eukaryotes genes are further organized into transcription units. Chromatin compacts the DNA into nucleosomes and higher-order structures like the 30nm fiber. Overall the document provides an overview of the molecular organization and components that make up eukaryotic genes and chromosomes.
DNA replication occurs semi-conservatively, with each parental strand serving as a template for synthesis of a new complementary strand. This results in two identical DNA molecules, each with one original parental strand and one newly synthesized strand. Replication is initiated at the origin of replication and proceeds bidirectionally around the circular bacterial chromosome. Enzymes such as helicase unwind the parental DNA, topoisomerases relieve supercoiling, and DNA polymerase adds complementary nucleotides using the parental strands as templates.
Dna content,c value paradox, euchromatin heterochromatin, banding patternArchanaSoni3
DNA content refers to the amount of DNA in an organism's haploid chromosomes. It varies greatly between organisms, with eukaryotes generally having more DNA than prokaryotes. The amount of DNA does not always correlate with an organism's complexity, known as the C-value paradox. This is because eukaryotic DNA contains large amounts of non-coding repetitive sequences. Chromatin exists in two forms - euchromatin, which is less condensed and permits gene expression, and heterochromatin, which is highly condensed and usually silences genes. Heterochromatin forms in specific regions like centromeres and telomeres and is important for chromosome function and stability.
The document discusses several key topics related to DNA structure and function:
DNA replication ensures each cell has an exact copy of the DNA before cell division. Errors are constantly checked and repaired to maintain high fidelity. DNA is also rearranged through processes like recombination. The tightly regulated enzymes that perform these metabolic processes were demonstrated by the Meselson-Stahl experiment to replicate DNA using a semiconservative mechanism. DNA is organized through various levels of compaction into condensed chromosomes. This dynamic structure, along with features like centromeres and telomeres, helps regulate DNA accessibility and proper segregation during cell division.
This document provides an overview of the process by which DNA directs protein synthesis through transcription and translation. It discusses the flow of genetic information from DNA to mRNA to protein. Key points include: transcription produces messenger RNA from DNA templates in the nucleus; eukaryotic pre-mRNA is processed before translation; translation occurs in the cytoplasm using tRNA to add amino acids to growing polypeptide chains on ribosomes according to mRNA codons. The genetic code is nearly universal and specifies 20 amino acids using triplets of nucleotides.
Epigenetics in fisheries and aquacultureKiran Modi
Epigenetics refers to heritable phenotypic changes that do not involve alterations to the DNA sequence. Key epigenetic mechanisms in fisheries and aquaculture include DNA methylation, genome imprinting, histone modification, and chromatin remodeling. DNA methylation and histone modifications can suppress gene expression through various mechanisms like blocking transcription factor binding sites or recruiting histone modifier complexes. Genome imprinting leads to parental origin-specific gene expression and has effects on development and metabolism. These epigenetic processes modify gene activation and expression without altering the underlying genetic code.
Parvoviruses are the smallest DNA viruses, including human parvovirus B19. B19 is pathogenic in humans, infecting erythroid progenitor cells and causing fifth disease in children characterized by a rash. It can also cause aplastic crisis, hydrops fetalis in fetuses, and chronic anemia in immunocompromised patients. Diagnosis involves detecting IgG and IgM antibodies by ELISA or PCR to detect the virus. There is no treatment, though a vaccine is in clinical trials.
This document categorizes and summarizes various viral families, their important genera, the diseases they cause, how they are transmitted, and methods for diagnosis. It covers both DNA and RNA viruses, including those that are single-stranded, double-stranded, enveloped, and non-enveloped. Many common viral diseases are discussed such as influenza, hepatitis, HIV, measles, Ebola, rabies, as well as less known illnesses. Diagnostic approaches include cell culture, serology, PCR, antigen detection, and visualization of viral structures.
Parvovirus is a small, single-stranded DNA virus that causes diseases like fifth disease and aplastic anemia. It is around 22 nm in diameter with an icosahedral capsid but no envelope. Symptoms of parvovirus infection include fever, chills, and a bright red, raised "slap cheek" rash on the face and lacy rash on the extremities. Treatment focuses on supportive care with ibuprofen for fever as a vaccine remains in trials.
Hepatitis B virus is a partially double-stranded DNA virus that can be transmitted both horizontally through infected blood or body fluids and vertically from mother to child. It has a 42nm enveloped virion structure containing DNA and antigen proteins. HBV replicates through reverse transcription and has 4 overlapping reading frames that encode the surface, core and polymerase proteins. HBV infection may be acute and self-limiting or develop into chronic lifelong infection. Diagnosis involves detecting hepatitis B antigens and antibodies. Current treatments include interferon which stimulates immunity, and nucleoside analogues like lamivudine and adefovir which inhibit viral replication but resistance can develop. Prevention is through vaccination and immunoglobulin administration to exposed newbor
This document summarizes key information about Hepatitis B virus (HBV):
- HBV is the smallest known DNA virus that causes hepatitis and infects the liver. It has a circular DNA genome contained within a 42nm nucleocapsid surrounded by surface antigens.
- HBV particles exist in both infectious and non-infectious forms. Infectious virions contain the viral genome, proteins and surface antigens while non-infectious spheres and filaments contain only surface antigens.
- HBV is highly resistant and can survive outside the body for over 7 days. It is transmitted through blood and bodily fluids, sexually, and from mother to child during birth. Chronic infection may lead to liver
This document discusses rotavirus prevention and control. It provides an overview of rotavirus epidemiology, transmission, clinical presentation, diagnosis and treatment. It discusses infection control measures including handwashing and vaccination. Two oral rotavirus vaccines are described and their efficacy, safety and use in HIV-infected infants is summarized. Surveillance efforts in South Africa and Africa are outlined. WHO recommendations for rotavirus vaccination through routine immunization programs are also mentioned.
Rotavirus is a leading cause of severe diarrhea in children under 5 globally. Two rotavirus vaccines, Rotarix and RotaTeq, have proven safe and effective in reducing severe rotavirus disease and deaths. Based on evidence from trials in developing countries showing significant public health impact, WHO now strongly recommends that rotavirus vaccines be included in all national immunization programs worldwide. The first dose should be given between 6-15 weeks of age.
This document outlines a biology lecture on the diversity of microorganisms. It discusses the classification of microbes into three domains: Archaea, Bacteria, and Eukarya. Within these domains, different types of prokaryotes and eukaryotes are described, including bacteria, archaea, fungi, algae, protozoa, helminths, and viruses. Various identification techniques for microbes are also mentioned.
The common cold is a viral infectious disease that spreads easily. Symptoms include sore throat and nasal congestion. There is no cure, and one must wait for it to run its course. The average person gets 2-3 colds per year. While not life-threatening, the cold can be a nuisance by making it difficult to focus on tasks and causing people to avoid those infected. A cure for the common cold would help make dealing with life's troubles more bearable.
The document discusses the common cold, which is a viral infection of the upper respiratory tract that causes symptoms like a runny nose, sore throat, sneezing, and coughing. It affects both children and adults and spreads easily through direct or indirect contact with infected secretions. While the cold is usually mild and self-limiting, complications can sometimes occur like sinusitis, ear infections, or bronchitis. Treatment focuses on relieving symptoms with over-the-counter medications and getting plenty of rest.
Mr. Sniffle, a 35-year-old male, is experiencing symptoms of a common cold including congestion, cough, and achy feeling. The most likely diagnosis is the common cold. You advise Mr. Sniffle that antibiotics are not needed and the best treatment is rest, fluids, and potentially an intranasal decongestant. Cough suppressants and expectorants may help symptoms but there is limited evidence for their effectiveness. Kissing is unlikely to transmit the virus.
The document discusses the structure, classification, and replication of viruses. It begins by describing different viral structural components, including the capsid, envelope, and nucleic acid core. Viruses are classified based on their nucleic acid composition and structure, focusing on whether they have DNA or RNA genomes and whether they are enveloped or not. The document also examines different capsid structures like icosahedral, helical, and complex shapes. It provides examples of representative virus families and discusses how viruses are named.
El rotavirus es un patógeno viral ubicuo que causa diarrea aguda, principalmente en niños menores de 2 años. Se transmite por la vía fecal-oral y puede provocar deshidratación grave e incluso la muerte si no se trata adecuadamente. Los síntomas incluyen diarrea acuosa severa, vómitos y fiebre. El diagnóstico se realiza detectando el antígeno viral en las heces mediante pruebas de inmunocromatografía. El tratamiento se enfoca en la rehidratación oral o
genome structure and repetitive sequence.pdfNetHelix
Welcome to our channel, where science meets discovery! In today's enlightening video, we unravel the mysteries of life at its most fundamental level - the chromosomes.
Join us on an exhilarating journey deep within the human cell as we explore the intricate architecture and organization of these tiny yet immensely powerful structures.
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Biochem recombinant dna technology(29.6.10)MBBS IMS MSU
Recombinant DNA technology allows scientists to isolate and amplify specific genes from large genomes using techniques like polymerase chain reaction (PCR), molecular cloning, and hybridization. PCR uses DNA polymerase to exponentially amplify short regions of DNA flanked by primer sequences. It relies on the heat-resistant Taq polymerase enzyme from Thermus aquaticus. Molecular cloning involves inserting foreign DNA into bacterial plasmids which are then replicated within bacterial cells. This allows isolation and amplification of the gene of interest.
The document discusses various components that make up genomes, including genes, repetitive sequences, and different types of DNA. It describes the human genome in particular, noting it contains around 3 billion base pairs, with 3% coding for proteins. Around 40-50% is repetitive sequences from transposition. Genomics is defined as the study of genomes, including gene mapping and sequencing. Key components of genomes discussed include transposable elements like SINEs, LINEs, LTR retrotransposons, and other interspersed repeats. Comparative analysis of genome sequences can provide insights into gene number and function.
Plasmids are small, circular DNA molecules that are self-replicating and carried by bacteria. They range in size from 2-100kb and can contain genes for antibiotic resistance. Bacterial genomes exist as a single circular chromosome that is highly condensed and packaged. Viruses have RNA or DNA genomes that are either single or double-stranded. Their genomes must be able to be recognized and expressed by their host cell. Mitochondria and chloroplasts originated from endosymbiotic bacteria and contain their own genomes that are maternally inherited and range in size and structure between species. Plant mitochondrial DNA can be much larger than animals.
This document summarizes key differences between prokaryotic and eukaryotic genomes. Prokaryotic genomes are typically smaller, usually contained in a single circular DNA molecule within the nucleoid. The DNA is highly compacted via supercoiling. Genes have compact organization with little non-coding DNA. Operons, where genes are expressed as a unit, are common. Repetitive DNA, transposons, and pathogenicity islands can be transferred horizontally and influence virulence. In contrast, eukaryotic genomes are larger with linear chromosomes, more non-coding DNA, introns, and complex gene regulation.
1. The document discusses microbial genetics and the flow of genetic information. It defines key terms like genetics, genes, genome, genotype, and phenotype.
2. It describes the structure of DNA and how it carries genetic information as a double-stranded molecule made up of nucleotides. DNA replication is semi-conservative and involves unwinding the strands, creating an RNA primer, and synthesizing new strands in the 5' to 3' direction.
3. The process of transcription is described, where RNA polymerase reads the genetic code from DNA and synthesizes mRNA, which is then translated to produce proteins. Both prokaryotes and eukaryotes undergo transcription but differ in initiation, processing, and coupling with
The document summarizes key aspects of eukaryotic genome complexity. It notes that while eukaryotic genomes are generally larger than prokaryotic genomes, genome size does not correlate directly with genetic complexity. Much of the increased size of eukaryotic genomes is due to noncoding sequences, including introns within genes and repetitive sequences between genes. Introns account for much more DNA than exons in higher eukaryotes. Other factors contributing to large eukaryotic genomes include repeated genes and families, as well as mobile repetitive elements like transposons. The DNA is tightly packaged into chromatin and condensed into linear chromosomes for mitosis.
Chromosomes contain an organism's genetic material and come in different structures depending on the organism. Bacteria typically have a single circular chromosome while eukaryotes have multiple linear chromosomes in the nucleus. Genetic material is highly compacted through various mechanisms to fit inside cells. In eukaryotes, DNA is wrapped around histone proteins to form nucleosomes, which further compact to form a 30nm fiber and loop domains that attach to a nuclear matrix, compacting the DNA over 1000-fold to fit in the nucleus.
This document discusses various components that make up genomes. It describes how genomes contain both coding and non-coding DNA sequences. The non-coding portions include repetitive elements like short interspersed elements (SINEs), long interspersed elements (LINEs), endogenous retroviruses, and DNA transposons. Genome complexity is measured using DNA renaturation kinetics, where more complex genomes with greater unique sequences renature more slowly. Comparative genomics and identifying repetitive elements helps characterize genome structure and functional elements.
Bioinformatics is the interdisciplinary study of biology and computer science. It involves developing tools to analyze large amounts of biological data, such as genetic sequences. There are two main building blocks studied in bioinformatics: nucleic acids like DNA and RNA, and proteins. DNA stores genetic information that is transcribed into RNA, which is then translated into proteins according to the genetic code. Technological advances have led to an explosion of biological data that requires bioinformatics approaches to analyze and interpret.
This document discusses DNA replication. It begins by explaining that DNA must be replicated accurately to maintain genetic information through cell divisions. It then discusses several key aspects of DNA replication:
1) DNA replication is semi-conservative, meaning the parental DNA strands separate and each acts as a template for a new complementary strand.
2) Replication occurs bidirectionally from replication origins. The leading strand replicates continuously while the lagging strand replicates discontinuously in fragments called Okazaki fragments.
3) Replication initiates at specific sites called replication origins that are recognized by origin-binding proteins. Eukaryotes have multiple origins per chromosome while prokaryotes have a single origin.
It concludes by
Recombinant DNA technology allows scientists to isolate and amplify specific genes from an organism's genome. There are three main approaches: polymerase chain reaction (PCR) to make copies of a gene region; cell-based molecular cloning using bacterial plasmids and restriction enzymes; and hybridization techniques using labeled probes to detect complementary DNA sequences. PCR is a powerful method that uses the enzyme DNA polymerase to exponentially amplify a targeted DNA region defined by primer sequences.
Genome organisation in eukaryotes...........!!!!!!!!!!!manish chovatiya
This document discusses the organization of eukaryotic genomes. It explains that eukaryotic genomes are much larger than prokaryotic genomes, with most of the DNA being non-coding. Eukaryotic genomes contain multiple linear chromosomes, introns, repetitive sequences, and both coding and non-coding RNA genes. The document also describes different types of repetitive elements like tandem repeats, transposons, retrotransposons, LINEs, SINEs and their roles in increasing genome size. Overall, the document provides an overview of the complex structure of eukaryotic genomes compared to simpler prokaryotic genomes.
Prokaryotic genetic material differs from eukaryotes in several key ways:
1. Prokaryotes lack a membrane-bound nucleus and have their DNA located in the nucleoid. They typically have a single circular chromosome while eukaryotes have multiple linear chromosomes.
2. Prokaryotic genes are arranged in operons and expressed together, whereas eukaryotic genes each have their own promoter and are independently expressed.
3. DNA replication in prokaryotes is rapid and ongoing, starting from a single origin of replication site, while eukaryotes tightly regulate replication during the cell cycle.
1. Eukaryotic genomes contain nuclear DNA as well as organelle DNA from mitochondria and chloroplasts. Genome size, or C-value, varies greatly between species from 106 bp in prokaryotes to over 1011 bp in some amphibians.
2. Renaturation kinetics can be used to measure genome complexity based on how quickly denatured DNA strands reanneal, with more common sequences reassociating faster. A COT curve plots the percentage of renatured DNA over time at different DNA concentrations.
3. Eukaryotic genomes contain genes, repetitive sequences like satellites and transposons, and non-coding DNA. While genes and complexity generally increase together in lower e
The document discusses the C-value paradox, which is the lack of relationship between genome size and organism complexity. It provides data on the wide range of genome sizes across different taxonomic groups. Introns and exons are described, with exons comprising the coding sequences and introns being removed from transcripts by splicing. Alternative splicing can generate multiple protein isoforms from a single gene. Repeated sequences, including satellites, minisatellites, microsatellites, transposons, SINEs and LINEs comprise a large portion of eukaryotic genomes.
1. Eukaryotic DNA contains repetitive and non-repetitive segments. Repetitive DNA makes up around 50% of the human genome and consists of sequences that are present in copies numbering over a million.
2. Repetitive DNA is divided into highly, moderately, and uniquely repetitive sequences based on copy number. Highly repetitive sequences are present in over 100,000 copies and include satellite and centromeric DNA. Moderately repetitive sequences have between 100-10,000 copies, like ribosomal RNA genes.
3. Non-repetitive or unique sequences make up around 50% of the human genome and contain protein-coding genes and other sequences required for gene expression that generally exist in only
Transcriptional and post transcriptional regulation of gene expressionDr. Kirti Mehta
Gene expression is regulated at the transcriptional and post-transcriptional levels. Transcriptional regulation involves proteins binding to promoter and enhancer sequences to control RNA polymerase recruitment and initiation of transcription. Eukaryotic gene expression requires transcription factors, coactivators, and basal transcription factors to assemble the transcription initiation complex. Post-transcriptional regulation influences RNA processing, transport, translation, and degradation.
Exploring low emissions development opportunities in food systemsCIFOR-ICRAF
Presented by Christopher Martius (CIFOR-ICRAF) at "Side event 60th sessions of the UNFCCC Subsidiary Bodies - Sustainable Bites: Innovating Low Emission Food Systems One Country at a Time" on 13 June 2024
There is a tremendous amount of news being disseminated every day online about dangerous forever chemicals called PFAS. In this interview with a global PFAS testing expert, Geraint Williams of ALS, he and York Analytical President Michael Beckerich discuss the hot-button issues for the environmental engineering and consulting industry -- the wider range of PFAS contamination sites, new PFAS that are unregulated, and the compliance challenges ahead.
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Monitor indicators of genetic diversity from space using Earth Observation dataSpatial Genetics
Genetic diversity within and among populations is essential for species persistence. While targets and indicators for genetic diversity are captured in the Kunming-Montreal Global Biodiversity Framework, assessing genetic diversity across many species at national and regional scales remains challenging. Parties to the Convention on Biological Diversity (CBD) need accessible tools for reliable and efficient monitoring at relevant scales. Here, we describe how Earth Observation satellites (EO) make essential contributions to enable, accelerate, and improve genetic diversity monitoring and preservation. Specifically, we introduce a workflow integrating EO into existing genetic diversity monitoring strategies and present a set of examples where EO data is or can be integrated to improve assessment, monitoring, and conservation. We describe how available EO data can be integrated in innovative ways to support calculation of the genetic diversity indicators of the GBF monitoring framework and to inform management and monitoring decisions, especially in areas with limited research infrastructure or access. We also describe novel, integrative approaches to improve the indicators that can be implemented with the coming generation of EO data, and new capabilities that will provide unprecedented detail to characterize the changes to Earth’s surface and their implications for biodiversity, on a global scale.
The modification of an existing product or the formulation of a new product to fill a newly identified market niche or customer need are both examples of product development. This study generally developed and conducted the formulation of aramang baked products enriched with malunggay conducted by the researchers. Specifically, it answered the acceptability level in terms of taste, texture, flavor, odor, and color also the overall acceptability of enriched aramang baked products. The study used the frequency distribution for evaluators to determine the acceptability of enriched aramang baked products enriched with malunggay. As per sensory evaluation conducted by the researchers, it was proven that aramang baked products enriched with malunggay was acceptable in terms of Odor, Taste, Flavor, Color, and Texture. Based on the results of sensory evaluation of enriched aramang baked products proven that three (3) treatments were all highly acceptable in terms of variable Odor, Taste, Flavor, Color and Textures conducted by the researchers.
Download the Latest OSHA 10 Answers PDF : oyetrade.comNarendra Jayas
Latest OSHA 10 Test Question and Answers PDF for Construction and General Industry Exam.
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To Help OSHA 10 trainees to pass their pre-test and post-test we have prepared set of 390 question and answers called OSHA 10 Answers in downloadable PDF format. The OSHA 10 Answers question bank is prepared by our in-house highly experienced safety professionals and trainers. The OSHA 10 Answers document consists of 390 MCQ type question and answers updated for year 2024 exams.
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1. ‘LARGE’ DNA GENOMES
double-stranded DNA genomes
• In many respects, these viruses are genetically
very similar to the host cells that they infect.
Two examples :
• members of families;
1. Herpesviridae
2. Adenoviridae
2. • Herpesviridae-
• large family( more than 100 different members)
• 8 human herpesviruses, all share overall a common
genome structure but
• Differ in genome organization and at the level of
nucleotide sequence.
• Based on their nucleotide sequence and biological
properties ;
• The family is divided into 3 subfamilies,
(Table 3.1).
3.
4. • Herpesviruses
• very large genomes composed of up to 235 kbp
• linear,
• double-stranded DNA and
• large and complex virus particles containing
about 35 virion polypeptides.
• All encode a variety of enzymes involved in
1. nucleic acid metabolism,
2. DNA synthesis, and
3. protein processing (e.g., proteinkinases).
5. • The different members of the family are all similar in terms of structure and
genome organization (Figure 3.5a) but
• not all herpesvirus genomes consist of two covalently joined sections, a
unique long (UL) and a unique short (US) region, each bounded by inverted
repeats.
• The repeats allow structural rearrangements of the unique regions;
therefore, these genomes exist as a mixture of four isomers, all of which are
functionally equivalent (Figure 3.5b).
• Herpesvirus genomes also contain multiple repeated sequences and,
depending on the number of these, the genome size of various isolates can
vary by up to 10 kbp .
6. • Herpes Simplex Virus (HSV)
• Genome -double-stranded DNA,152 kbp.
• Virus contains about 80 genes, densely packed with
overlapping reading frames. Each gene is expressed from its
own promoter .
The prototype member of the family is herpes simplex virus (HSV).
7. Adenoviruses
• Genomes- -Linear, double-stranded DNA ( 30 to 38 kbp)
-contain 30 to 40 genes (Figure 3.6).
-The terminal sequence (100 to 140 bp) of each
DNA strand is an inverted repeat .
- denatured single strands form ‘panhandle’
structures, important in DNA replication,
as is a 55-kDa protein (terminal protein);
covalently attached to the 5’end of each strand.
-During genome replication, this protein acts as a
primer, initiating the synthesis of new DNA strands.
• The expression of the genes more complex.
• Clusters of genes are expressed from a limited number of shared
promoters.
• Multiply spliced mRNAs and alternative splicing patterns are used to
express a variety of polypeptides from each promoter .
9. ‘SMALL’ DNA GENOMES
• Enterobacteria -The filamentous phage M13 .
• The genome consists of 6.4 kb of single-stranded, (+)sense, circular DNA
and encodes 10 genes.
• M13 capsid can be expanded by the addition of further protein subunits.
Hence, the genome size can also be increased by the addition of extra
sequences in the nonessential intergenic region without becoming
incapable of being packaged into the capsid.
10. • The packaging -more rigid in phage Lambda, only DNA of between 46–54 kbp of the
normal genome size (49 kbp) can be packaged into the virus particle.
• During the later stages of replication - assembly , long concatemers of phage DNA
that are produced is packaged into the phage heads.
• when a complete genome has been incorporated the DNA is cleaved at a specific
sequence by a phage-coded endonuclease This enzyme leaves a 12-bp 5’ overhang
on the end of each of the cleaved strands, known as the cos site. (Figure 3.7).
• Hydrogen bond formation between these ‘sticky ends’ can result in the formation of
a circular molecule.
• In a newly infected cell, the gaps on either side of the cos site are closed by DNA
ligase, and it is this circular DNA that undergoes vegetative replication or integration
into the bacterial chromosome.
11.
12. • Enterobacteria phage T4
• virus genome
• double-stranded DNA, 160 kbp .
• terminal redundancy.
• Replication produces long concatemers of DNA, cleaved by a specific endonuclease.
• lengths of DNA incorporated into the particle are somewhat longer than a complete genome
length (Figure 3.8) Hence, some genes are repeated at each end of the genome.
13. Animal viruses ,small DNA genomes
• Two groups- Parvoviruses and Polyomaviruses.
1) Parvovirus
• Genomes -linear, non-segmented, single-stranded DNA of about 5 kb.
• Most of the strands packaged into virions are (-)sense, but some parvoviruses
package equal amounts of (+) and (-) strands, and all appear to package at least a
proportion of (+)sense strands.
• These are very small genomes- contain only two genes:
• Rep: encodes transcription proteins , and
• cap: encodes the coat proteins.
• However, the expression of these genes is complex.
• The ends of the genome have palindromic sequences of about 115 nt, which form
‘hairpins’ are essential for the initiation of genome replication (Figure 3.9).
14.
15. Polyomaviruses
• Genomes- ds circular DNA , 5 kbp.
• Within the particles, the virus DNA assumes a supercoiled form and is
associated with four cellular histones:H2A, H2B, H3, and H4 .
• The genomic organization of these viruses has evolved to pack the
maximum information (six genes) into minimal space (5 kbp) achieved by
the use of both strands of the genome DNA and overlapping genes
(Figure 3.10).
• VP1 is encoded by open reading frame (ORF), but the VP2 and VP3 genes
overlap so that VP3 is contained within VP2. The origin of replication is
surrounded by noncoding regions which control transcription.
16. • Polyomaviruses also encode ‘T-antigens,’ which are proteins that can be detected
by sera from animals bearing polyomavirus-induced tumours.
• These proteins bind to the origin of replication - are involved both in DNA
replication and in the transcription of virus genes.
17. POSITIVE-STRAND RNA VIRUSES
• The size of single-stranded RNA genomes is limited by
1. the fragility of RNA and the tendency of long strands
to break.
2. RNA genomes tend to have higher mutation rates
than those composed of DNA since are copied less
accurately.
3. This tendency has tend to drive RNA viruses toward
smaller genomes.
SsRNA genomes vary in size;
• Coronaviruses (approximately 30 kb long) to
• Bacteriophages -MS2 and Qbeta (about 3.5 kb).
18. Picornaviruses
• The Picornavirus genome - consists of (+) sense SsRNA molecule
• Mol. wt. between 7.2 kb in human rhinoviruses (HRVs) to 8.5 kb in foot-and-mouth
disease viruses (FMDVs), contain a number of features conserved in all picornaviruses :
• At the 5’ end - a long (600–1200 nt) untranslated region (UTR) ,important in translation,
virulence, and possibly encapsidation, as well as
• A shorter 3’ untranslated region (50–100 nt) , necessary for (-)strand synthesis
during replication.
• The 5’ UTR contains a ‘clover-leaf ’ secondary structure known as the internal
ribosomal entry site (IRES) .
• The rest of the genome encodes a single polyprotein , 2100 -2400 amino acids.
• Both ends of the genome are modified—
• The 5’end by a covalently attached small, basic protein VPg (23 amino acids), and
• The 3’ end by polyadenylation (Figure 3.11).
19.
20. Togaviruses
• The togavirus genome - (+)sense ,Ss ,non-segmented
• RNA of approximately 11.7 kb.
• It has the following features:
• It resembles cellular mRNAs (5’ methylated cap &
3’poly(A) sequences).
• Expression is achieved by two rounds of translation,
• first producing nonstructural proteins encoded in the 5’
part of the genome and
• later structural proteins from the 3’ part.
21. Flaviviruses
• The genome is one single-stranded, (+)sense RNA molecule
of about 10.5 kb with the following features:
• It has a 5’ methylated cap, but in most cases the RNA is not
polyadenylated at the 3’ end.
• Genetic organization differs from that of the togaviruses;
• the structural proteins are encoded in the 5’ part of the
genome and nonstructural proteins in the 3’ part.
• Expression is similar to that of the picornaviruses, involving
the production of a polyprotein.
22. Coronaviruses
• The genome consists of non-segmented, single-stranded, (+)sense RNA,
approximately 27 to 30 kb long, the longest of any RNA virus.
• It also has the following features:
• It has a 5’ methylated cap and 3’ poly(A), and the vRNA functions directly as
mRNA.
• The 5’ 20-kb segment of the genome is translated first to produce a virus
polymerase, which then produces a full-length (-)sense strand.
• This (-)sense strand is used as a template to produce mRNA as a set of transcripts,
all with an identical 5’ nontranslated leader sequence of 72 nt and coincident 3’
polyadenylated ends.
• Each mRNA is monocistronic, the genes at the 5’ end being translated from the
longest mRNA and so on. These unusual cytoplasmic structures are produced not
by splicing (posttranscriptional modification) but by the polymerase during
transcription.
23. (+)Sense RNA Plant Viruses
• The majority (but not all) of plant virus families have (+)sense RNA genomes.
• The genome of tobacco mosaic virus (TMV) is a well-studied example(Figure
3.12):
• The TMV genome is a 6.4-kb RNA molecule that encodes four genes.
• There is a 5’ methylated cap, and 3’ end of the genome contains extensive
secondary structure but no poly(A) sequences.
• Expression- distinct from that of togaviruses,
• Producing non-structural proteins by direct translation of the open reading
frame encoded in the 5’ part of the genome and
• the virus coat protein and further non-structural proteins from two
subgenomic RNAs encoded by the 3’ part.
24.
25. NEGATIVE-STRAND RNA VIRUSES
• Viruses are a little more diverse than the positive- stranded viruses ,(difficulties of
expression).
• They have larger genomes encoding more genetic information. So, segmentation is a
common but not a universal feature of such viruses .
• None of these genomes is infectious as purified RNA.
• Although a gene encoding an RNA-dependent RNA polymerase has recently been
found in some eukaryotic cells, most uninfected cells do not contain enough
RNAdependent RNA polymerase activity to support virus replication, and, because the
(-)sense genome cannot be translated as mRNA without the virus polymerase
packaged in each particle, these genomes are effectively inert.
• Some of the viruses described are not strictly negative-sense but are ambisense, as
they are part (-)sense and part (+)sense.
• Ambisense coding strategies occur in both plant viruses and animal viruses
• Plant viruses(e.g., the Tospovirus genus of the bunyaviruses, and tenuiviruses such as
rice stripe virus) and
• Animal viruses (the Phlebovirus genus of the bunyaviruses, and arenaviruses).
26. Bunyaviruses
• have single-stranded, (-)sense, segmented RNA.
• The genome has the following features:
• The genome is comprised of three molecules:
L (8.5 kb), M (5.7 kb), and S(0.9 kb).
• All three RNA species are linear, but in the virion they appear
circular because
the ends are held together by base-pairing. The three segments
are not present
• in virus preparations in equimolar amounts.
• In common with all (-)sense RNAs, the 5’ ends are not capped and
the 3’ ends are not polyadenylated.
27. Arenaviruses
• genomes consist of linear, single-stranded RNA.
• There are two genome segments: L (5.7 kb) and S (2.8 kb). Both
have an ambisense organization.
Paramyxoviruses
• Members of the Paramyxoviridae have nonsegmented (-)sense RNA
of 15 to 16 kb.
• Typically, six genes are organized in a linear arrangement (3’–NP–
P/C/V–M–F–HN–L–5’) separated by repeated sequences:
• a polyadenylation signal at the end of the gene, an intergenic
sequence (GAA), and a translation start signal at the beginning of
the next gene.
28. Rhabdoviruses
• Viruses of the Rhabdoviridae have nonsegmented,
(-)sense RNA of approximately 11 kb.
• There is a leader region of approximately 50 nt at the 3’
end of the genome and
• a 60 nt untranslated region (UTR) at the 5’ end of the vRNA.
• Overall, the genetic arrangement is similar to that of
paramyxoviruses, with a conserved polyadenylation signal
at the end of each gene and short intergenic regions
between the five genes.
29. SEGMENTED AND MULTIPARTITE VIRUS
GENOMES
• Segmented
• virus genomes - are divided into two or more physically separate
molecules of nucleic acid, all of which are then packaged into a single virus
Particle.
• In contrast, multipartite genomes are also segmented but each genome
segment is packaged into a separate virus particle.
• These discrete particles are structurally similar-contain the same
component proteins, but they often differ in size depending on the length
of the genome segment packaged.
30. Segmentation of the virus genome has a number of advantages
and disadvantages.
• Advantages
• Physical properties of nucleic acids, due to shear forces - Physical breakage of the
long molecules of genome results in its biological inactivation, as it cannot be
completely transcribed, translated, or replicated.
• Segmentation reduces the probability of breakages due to shearing, thus
increasing the total potential coding capacity of the entire genome
• The problem of strand breakage is particularly relevant for single-stranded RNA,
which is much more chemically labile than double-stranded DNA.
• The longest single-stranded RNA genomes - coronaviruses, 30 kb, but
• the longest double-stranded DNA virus genomes are considerably longer (e.g.,
Mimivirus at up to 800 kbp).
• Disadvantages.
• All the individual genome segments must be packaged into each virus particle or
the virus will be defective as a result of loss of genetic information.
31. • To understand the complexity of these genomes,
• consider the organization of a segmented virus genome (influenza A virus) and a multipartite
genome (geminivirus).
• The influenza virus
• genome is composed of eight segments (in influenza A and B strains; seven in influenza C) of
single-stranded, (-)sense RNA (Table 3.2).
• The identity of the proteins encoded by each genome segment were determined originally by
genetic analysis of the electrophoretic mobility of the individual segments from reassortant
viruses.
• The eight segments have common nucleotide sequences at the 5’ and 3’ ends which are
necessary for replication of the genome . These sequences are complementary to one
another, and, inside the particle, the ends of the genome segments are held together by
base pairing and form a panhandle structure , involved in replication.
• The RNA genome segments are not packaged as naked nucleic acid but in association with
the gene 5 product, the nucleoprotein, and are visible in electron micrographs as helical
structures.
• Biochemically and genetically, each genome segment behaves as an individual, discrete
entity; however, in electron micrographs of influenza virus particles disrupted with nonionic
detergents, the nucleocapsid has the physical appearance of a single, long helix.
32. • Geminiviruses
• the genome consists of a single stranded DNA molecule of approximately 2.7 kb.
• The DNA packaged into these virions has been designated as (+)sense, although both the
(+)sense and (-)sense strands found in infected cells contain protein-coding sequences.
• The genome of geminiviruses in the genus Begmovirus is bipartite and consists of two circular, single-
stranded DNA molecules, each of which is packaged into a discrete particle .
• Both genome strands are approximately 2.7 kb long and differ from one another completely in
nucleotide sequence, except for a shared 200-nt non-coding sequence involved in DNA replication.
• The two genomic DNAs are packaged into entirely separate capsids. Because establishment
• of a productive infection requires both parts of the genome.
• Although geminiviruses do not multiply in the tissues of their insect vectors (non-propagative
transmission), a sufficiently large amount of virus is ingested and subsequently deposited onto a new
host plant to favour such superinfections.
• Both of these examples show a high density of coding information.
• In influenza virus, genes 7 and 8 both encode two proteins in overlapping reading frames.
• In geminiviruses, both strands of the virus DNA found in infected cells contain coding information, some
of which is present in overlapping reading frames.
• It is possible that this high density of genetic information is the reason why these viruses have
• resorted to divided genomes, in order to regulate the expression of this information.
33. REVERSE TRANSCRIPTION AND
TRANSPOSITION
• universal theory, called the ‘central dogma of molecular biology’—namely, that all cells (and hence viruses)
work on a simple organizing principle: the unidirectional flow of information from DNA, through RNA, into
proteins.
• In 1963, Howard Temin showed that the replication of retroviruses, whose particles contain RNA genomes,
was inhibited by actinomycin D, an antibiotic that binds only to DNA. The replication of other RNA viruses is
not inhibited by this drug.
• when Temin and David Baltimore simultaneously published the observation that retrovirus particles contain
an RNAdependent DNA polymerase: reverse transcriptase.
• It is now known that retrotransposons with striking similarities to retrovirus genomes form a substantial part
of the genomes of all higher organisms, including humans.
• The concept of transposable genetic elements—specific sequences that are able to move from one position in
the genome to another—was put forward by Barbara McClintock in the 1940s. Such transposons fall into two
groups:
• Simple transposons, which do not undergo reverse transcription and are found in prokaryotes (e.g., the
genome of enterobacteria phage Mu).
• Retrotransposons, which closely resemble retrovirus genomes and are bounded by long direct repeats (long
terminal repeats, or LTRs); these move by means of a transcription/reverse transcription/integration
mechanism and are found in eukaryotes (the Metaviridae and Pseudoviridae).
34. • Both types show a number of similar properties:
• They are believed to be responsible for a high proportion of apparently
spontaneous mutations.
• They promote a wide range of genetic rearrangements in host cell genomes, such
as deletions, inversions, duplications, and translocations of the neighbouring
cellular DNA.
• The mechanism of insertion generates a short (3–13 bp) duplication of the DNA
sequence on either side of the inserted element.
• The ends of the transposable element consist of inverted repeats, 2 to 50 bp
long.
• Transposition is often accompanied by replication of the element often occurs
with prokaryotic transposition.
• Transposons control their own transposition functions, encoding proteins that act
on the element -
• in cis (affecting the activity of contiguous sequences on the same nucleic acid
molecule) or
• in trans (encoding diffusible products acting on regulatory sites in any stretch of
nucleic acid present in the cell).
35. • Enterobacteria phage Mu infects E. coli
• containing a linear, double-stranded DNA genome of about 37 kb, with hostcell- derived sequences
of between 0.5 and 2 kbp attached to the right-hand end of the genome (Figure 3.16).
• Mu is a temperate bacteriophage whose replication can proceed through two pathways;
1. one involves integration of the genome into that of the host cell and results in lysogeny, and
2. other is lytic replication, which results in the death of the cell.
• Integration of the phage genome into that of the host bacterium occurs at random sites.
Integrated phage genomes are known as prophage, and integration is essential for the
establishment of lysogeny.
• At intervals in bacterial cells lysogenic for Mu, the prophage undergoes transposition to a
different site in the host genome.The mechanism leading to transposition is different from that
responsible for the initial integration of the phage genome (conservative, does not involve
replication) and is a complex process requiring numerous phage-encoded and hostcell proteins.
• Transposition is tightly linked to replication of the phage genome and results in the formation of
a ‘cointegrate’—that is, a duplicate copy of the phage genome flanking a target sequence in
which insertion has occurred.
• The original Mu genome remains in the same location where it first integrated and is joined by a
second integrated genome at another site. (Not all prokaryotic transposons use this process.
36. There are two consequences of such a transposition:
1. The phage genome is replicated during this process (advantageous for the virus) and,
2. The sequences flanked by the two phage genomes (which form repeated sequences)
are at risk of secondary rearrangements, including deletions, inversions, duplications,
and translocations (possibly but not necessarily deleterious for the host cell).-
37. • Retrovirus genomes have four unique features:
• They are the only viruses that are truly diploid.
• They are the only RNA viruses whose genome is produced
by cellular transcriptional machinery (without any
participation by a virus-encoded polymerase).
• They are the only viruses whose genome requires a
specific cellular RNA (tRNA) for replication.
• They are the only (+)sense RNA viruses whose genome
does not serve directly as mRNA immediately after
infection.
38. • During the process of reverse transcription
two single stranded (+)sense RNA molecules (virus genome )
converted into
a double-stranded DNA molecule somewhat longer than the RNA
templates due to the duplication of direct repeat sequences at each
end—the long terminal repeats (LTRs) (Figure 3.19).
39. • Reverse transcription has important consequences for
retrovirus genetics.
• it is a highly error-prone process, because reverse transcriptase does not
carry out the proofreading functions performed by cellular DNA-dependent
DNA polymerases.
• This results in the introduction of many mutations into retrovirus genomes
and, consequently, rapid genetic variation .
• In addition, the process of reverse transcription promotes genetic
recombination, because two RNAs are packaged into each virion and used
as the template for
reverse transcription, recombination can and does occur between the
two strands.
• Although the mechanism responsible for this is not clear, if one of the RNA
strands differs from the other (for example, by the presence of a mutation)
and recombination occurs, then the resulting virus will be genetically
distinct from either of the parental viruses
40. • After reverse transcription is complete, the double-stranded DNA migrates into the
nucleus, still in association with virus proteins.
• The mature products of the pol gene are, in fact, a complex of polypeptides that
include three distinct enzymatic activities: reverse transcriptase and RNAse H,
which are involved in reverse transcription,and integrase, which catalyses
integration of virus DNA into the host cell chromatin, after which it is known as
the provirus (Figure 3.20).
• Three forms of double-stranded DNA are found in retrovirus-infected cells
following reverse transcription: linear DNA and two circular forms that contain
either one or two LTRs.
• From the structure at the ends of the provirus,believed that the two-LTR circle was
the form used for integration. In recent years, systems that have been developed
to study the integration of retrovirus DNA in vitro show that it is the linear form
that integrates.
• This discrepancy can be resolved by a model in which the ends of the two LTRs are
held in close proximity by the reverse transcriptase–integrase complex. The net
result of integration is that 1 to 2 bp are lost from the end of each LTR and 4 to 6
bp of cellular DNA are duplicated on either side of the provirus.
41.
42.
43. • Following integration, the DNA provirus genome becomes essentially a
collection of cellular genes and is at the mercy of the cell for expression.
• There is no mechanism for the precise excision of integrated proviruses,
although proviruses may sometimes be lost or altered by modifications of
the cell genome.
• The only way out for the virus is transcription, forming a full-length mRNA
(minus the terminally redundant sequences from the LTRs). This RNA is
the vRNA, and two copies are packaged into virions (Figure 3.19).
• There are, however, two different genome strategies used by viruses that
involve reverse transcription.
• One strategy, as used by retroviruses and , the packaging of RNA into
virions as the virus genome.
• The other, used by hepadnaviruses and caulimoviruses, switches the RNA
and DNA phases of replication results in DNA virus genomes achieved by
utilizing reverse transcription.
44. Hepadnaviruses
• Hepatitis B virus (HBV) is the prototype member of the family
Hepadnaviridae.
• HBV virions are spherical, lipid-containing particles, 42 to 47 nm
diameter,
• which contain a partially double-stranded (‘gapped’) DNA genome, plus an
RNA dependent DNA polymerase (i.e., reverse transcriptase) (Figure 3.21).
Hepadnaviruses have very small genomes consisting of a (-)sense strand
of 3.0 to 3.3 kb (varies between different hepadnaviruses) and a (+)sense
strand of 1.7 to 2.8 kb(varies between different particles).
• On infection of cells, three major genome transcripts are produced: 3.5-,
2.4-, and 2.1-kb mRNAs. All have the same polarity (i.e., are transcribed
from the same strand of the virus genome) and the same 3’ ends but have
different 5’ ends (i.e., initiation sites).
45. • These transcripts are heterogeneous in size, and encodes four known genes in the
virus:
• C encodes the core protein.
• P encodes the polymerase.
• S encodes the three polypeptides of the surface antigen:
pre-S1, pre-S2, and S (which are derived from alternative start sites).
• X encodes a transactivator of virus transcription (and possibly cellular genes).
• Closed circular DNA is found soon after infection in the nucleus of the cell and is
probably the source of the above transcripts. This DNA is produced by repair of the
gapped virus genome as follows:
• 1.Completion of the (+)sense strand
• 2. Removal of a protein primer from the (-)sense strand and an oligoribonucleotide
primer from the (+)sense strand
• 3. Elimination of terminal redundancy at the ends of the (-)sense strand
• 4. Ligation of the ends of the two strands