Tn5 Transposase
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Tn5 Transposase is a hyperactive form of Tn5 transposase. This enzyme can be used to randomly insert Tn5 transposon into target DNA. Robust Tn5 Transposase recognizes inside end sequences, outside end sequences and mosaic end sequences of Tn5 transposon. https://www.creative-enzymes.com/product/tn5-transposase_8479.html
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Trp operon
The trp operon contains a cluster of genes involved in tryptophan biosynthesis that are under the control of a single promoter. It was the first repressible operon discovered in E. coli in 1953. The trp operon contains structural genes that encode enzymes for tryptophan synthesis, as well as a promoter, operator, and regulatory genes. Tryptophan acts as an effector molecule that binds to the repressor protein, increasing its affinity for the operator sequence and repressing transcription when tryptophan is present. The trp operon is also regulated by transcriptional attenuation, where tryptophan levels affect the formation of termination or anti-termination hairpin loops in the mRNA.
AP_Bio_Ch_15.ppt
Gene expression in eukaryotes is regulated at multiple levels, including transcription, RNA processing, mRNA degradation, and protein degradation. Transcription is controlled through chromatin remodeling, transcription factors, enhancers, promoters, and repressors. Alternative RNA splicing allows different mRNAs and proteins to be produced from the same gene. Non-coding RNAs like miRNAs can degrade mRNAs or block translation. Proteins are degraded by proteasomes and ubiquitin pathways. Microarrays allow comparison of gene expression between cell types by detecting differences in mRNA levels.
Trp operon
The document discusses the trp operon in prokaryotes. The trp operon encodes for enzymes involved in the biosynthesis of tryptophan. It consists of 5 structural genes (trpE, trpD, trpC, trpB, trpA) that are regulated by a single promoter. The expression of the operon is controlled by the trp repressor and feedback inhibition via the mechanism of attenuation. When tryptophan levels are high, the trp repressor binds to the operator region and blocks transcription. When levels are low, transcription occurs and the enzymes are produced to synthesize tryptophan via a series of reactions.
PCR (polymerase chain reaction) and Extraction of DNA from fungal plant patho...
PCR, Polymerase chain reaction, types of PCR, Template DNA, DNA polymerase, Primers, Nucleotides (DNTPs or deoxynucleotide triphosphates ), Denaturation, Annealing, Extension, Types of PCR, Multiplex PCR.
Long-range PCR.
Single-cell PCR.
Fast-cycling PCR.
Methylation-specific PCR (MSP)
Hot start PCR
High-fidelity PCR.
RAPD: Rapid amplified polymorphic DNA analysis.
Detection of fungal plant pathogen using PCR, Extraction of DNA from plant tissues,PCR amplification and detection of diagnostic amplicon
Lectut btn-202-ppt-l37. transgene silencing
Gene silencing, also known as post-transcriptional gene silencing (PTGS), occurs when a gene is switched off by mechanisms other than mutation. It was first observed when an attempt to overexpress a pigment gene in petunia resulted in loss of pigment. This was due to co-suppression of both the endogenous gene and transgene. PTGS can occur via transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) where mRNA is degraded. PTGS involves double-stranded RNA triggering cleavage and degradation of homologous mRNA through the RNA interference (RNAi) pathway, which involves dicer, siRNAs, and RISC complex.
Molecular mechanism of antisense molecules
Antisense RNA is a single-stranded RNA that is complementary to messenger RNA (mRNA) and inhibits its translation. Historically, antisense RNA effects were confused with RNA interference, which involves small interfering RNAs targeting mRNA for degradation. Antisense RNA works by forming duplexes with mRNA, blocking the ribosome from accessing nucleotides or leading to degradation. Examples include transgenic Flavr Savr tomatoes with reduced ethylene production using antisense RNA against an ethylene-producing enzyme, and natural antisense RNA in mice and humans that blocks insulin-like growth factor 2 receptor mRNA. While promising, antisense RNA drugs still face challenges in design, activity, and delivery that have limited
ATAC-seq protocol--Creative Biogene
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3 Gene expression.pdf
The document discusses gene expression and transcription. It begins by outlining the central dogma of biology, where DNA is transcribed into RNA which is then translated into protein. It then describes the regulation of transcription in eukaryotes and prokaryotes. In eukaryotes, transcription factors bind to specific DNA sequences to activate or repress transcription. Histone acetylation also regulates transcription by altering chromatin structure. The three eukaryotic RNA polymerases are described along with initiation, elongation, termination and processing of transcripts. Transcription in prokaryotes similarly involves RNA polymerase binding to promoter sequences with sigma factors and termination via Rho-dependent and independent mechanisms.
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Trp operon
The trp operon contains a cluster of genes involved in tryptophan biosynthesis that are under the control of a single promoter. It was the first repressible operon discovered in E. coli in 1953. The trp operon contains structural genes that encode enzymes for tryptophan synthesis, as well as a promoter, operator, and regulatory genes. Tryptophan acts as an effector molecule that binds to the repressor protein, increasing its affinity for the operator sequence and repressing transcription when tryptophan is present. The trp operon is also regulated by transcriptional attenuation, where tryptophan levels affect the formation of termination or anti-termination hairpin loops in the mRNA.
AP_Bio_Ch_15.ppt
Gene expression in eukaryotes is regulated at multiple levels, including transcription, RNA processing, mRNA degradation, and protein degradation. Transcription is controlled through chromatin remodeling, transcription factors, enhancers, promoters, and repressors. Alternative RNA splicing allows different mRNAs and proteins to be produced from the same gene. Non-coding RNAs like miRNAs can degrade mRNAs or block translation. Proteins are degraded by proteasomes and ubiquitin pathways. Microarrays allow comparison of gene expression between cell types by detecting differences in mRNA levels.
Trp operon
The document discusses the trp operon in prokaryotes. The trp operon encodes for enzymes involved in the biosynthesis of tryptophan. It consists of 5 structural genes (trpE, trpD, trpC, trpB, trpA) that are regulated by a single promoter. The expression of the operon is controlled by the trp repressor and feedback inhibition via the mechanism of attenuation. When tryptophan levels are high, the trp repressor binds to the operator region and blocks transcription. When levels are low, transcription occurs and the enzymes are produced to synthesize tryptophan via a series of reactions.
PCR (polymerase chain reaction) and Extraction of DNA from fungal plant patho...
PCR, Polymerase chain reaction, types of PCR, Template DNA, DNA polymerase, Primers, Nucleotides (DNTPs or deoxynucleotide triphosphates ), Denaturation, Annealing, Extension, Types of PCR, Multiplex PCR.
Long-range PCR.
Single-cell PCR.
Fast-cycling PCR.
Methylation-specific PCR (MSP)
Hot start PCR
High-fidelity PCR.
RAPD: Rapid amplified polymorphic DNA analysis.
Detection of fungal plant pathogen using PCR, Extraction of DNA from plant tissues,PCR amplification and detection of diagnostic amplicon
Lectut btn-202-ppt-l37. transgene silencing
Gene silencing, also known as post-transcriptional gene silencing (PTGS), occurs when a gene is switched off by mechanisms other than mutation. It was first observed when an attempt to overexpress a pigment gene in petunia resulted in loss of pigment. This was due to co-suppression of both the endogenous gene and transgene. PTGS can occur via transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) where mRNA is degraded. PTGS involves double-stranded RNA triggering cleavage and degradation of homologous mRNA through the RNA interference (RNAi) pathway, which involves dicer, siRNAs, and RISC complex.
Molecular mechanism of antisense molecules
Antisense RNA is a single-stranded RNA that is complementary to messenger RNA (mRNA) and inhibits its translation. Historically, antisense RNA effects were confused with RNA interference, which involves small interfering RNAs targeting mRNA for degradation. Antisense RNA works by forming duplexes with mRNA, blocking the ribosome from accessing nucleotides or leading to degradation. Examples include transgenic Flavr Savr tomatoes with reduced ethylene production using antisense RNA against an ethylene-producing enzyme, and natural antisense RNA in mice and humans that blocks insulin-like growth factor 2 receptor mRNA. While promising, antisense RNA drugs still face challenges in design, activity, and delivery that have limited
ATAC-seq protocol--Creative Biogene
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to study chromatin accessibility. The key part of the ATAC-seq procedure is the action of the transposase Tn5 on the genomic DNA of the sample.
3 Gene expression.pdf
The document discusses gene expression and transcription. It begins by outlining the central dogma of biology, where DNA is transcribed into RNA which is then translated into protein. It then describes the regulation of transcription in eukaryotes and prokaryotes. In eukaryotes, transcription factors bind to specific DNA sequences to activate or repress transcription. Histone acetylation also regulates transcription by altering chromatin structure. The three eukaryotic RNA polymerases are described along with initiation, elongation, termination and processing of transcripts. Transcription in prokaryotes similarly involves RNA polymerase binding to promoter sequences with sigma factors and termination via Rho-dependent and independent mechanisms.
Basic principle of transcription
Transcription is the process of synthesizing RNA using a DNA template. It involves three main steps - initiation, elongation, and termination. In initiation, RNA polymerase binds to promoter sequences on DNA and unwinds the double helix. In elongation, RNA polymerase moves along the DNA strand and adds complementary RNA nucleotides. Termination occurs when the polymerase reaches a terminator sequence and stops adding nucleotides. Prokaryotes and eukaryotes have similar transcription mechanisms but eukaryotes have three RNA polymerases and require additional transcription factors.
Tryptophan
The trp operon in E. coli bacteria encodes genes for the biosynthesis of the amino acid tryptophan. It is regulated by the trp repressor protein - when tryptophan levels are low, the repressor does not bind to the operator, allowing transcription of the operon; when tryptophan levels are high, it binds to the operator and blocks transcription, turning the operon off. This allows the bacteria to efficiently control tryptophan production depending on environmental availability.
Eukaryotic transcription
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
Pcr
PCR is a technique used to amplify a specific region of DNA. It involves using primers that are complementary to the outer regions of the DNA sequence being targeted. During PCR, the DNA is denatured and new strands are synthesized using DNA polymerase. This results in exponential amplification of the target DNA sequence. Primers are short oligonucleotides that are selected to target a specific sequence and initiate DNA synthesis. DNA polymerase is the enzyme that copies the DNA sequence. Restriction fragment length polymorphism (RFLP) involves using restriction enzymes to cut DNA into fragments of different lengths that can then be separated by electrophoresis to identify different organisms based on unique DNA fingerprints.
2013 transcription
The document discusses transcription in prokaryotes and eukaryotes. It describes the key differences between their transcription mechanisms. In prokaryotes, RNA polymerase directly binds DNA and transcribes genes in three phases: initiation, elongation, and termination. In eukaryotes, RNA polymerase requires transcription factors to bind DNA and regulate gene expression, as transcription involves promoter elements, regulatory sequences, and RNA processing.
2013 transcription
The document discusses transcription in prokaryotes and eukaryotes. It describes the key components involved in transcription including DNA, RNA polymerases, promoters, and the three main phases - initiation, elongation, and termination. In prokaryotes, RNA polymerase binds directly to DNA and recognizes promoter sequences to initiate transcription. Eukaryotes require additional factors for transcription initiation.
RNA synthesis, processing and modification.pptx
The presentation discusses RNA synthesis, processing, and modification, explaining that RNA is synthesized from DNA through transcription by RNA polymerase. It describes the post-transcriptional modification of primary transcripts, including splicing of introns from mRNA, addition of a 5' cap and 3' poly-A tail, and modification of tRNA. The presentation also covers regulatory sequences that control transcription and the role of reverse transcription in retroviruses like HIV.
Trp operon
The document discusses the tryptophan (trp) operon in bacteria such as E. coli. The trp operon contains 5 structural genes that code for enzymes involved in the biosynthesis of tryptophan. It is regulated by a repressor protein called trpR that binds to the operator region and prevents transcription when tryptophan is present. When tryptophan levels are low, the repressor cannot bind and transcription of the structural genes occurs. The trp operon was an important early example of gene regulation and negative feedback that is commonly used to demonstrate these concepts.
Transcription
The document discusses the basic principles of gene expression from DNA to protein. It describes transcription, which is the synthesis of RNA from a DNA template, and translation, which is the synthesis of proteins from mRNA templates using ribosomes. In eukaryotes, transcription requires RNA polymerases and other transcription factors to initiate transcription from DNA. The primary transcript then undergoes processing including 5' capping, 3' polyadenylation, and splicing to form mature mRNA. The mRNA is then translated by ribosomes to produce proteins.
Polymerase chain reaction & electrophoresis
Kary Banks is considered the great mind behind PCR. He developed PCR in 1985 while working at Cetus Corporation and was awarded the Nobel Prize in 1993. PCR allows for targeted amplification of specific DNA sequences, enabling their analysis even from very small samples. It involves heating and cooling of the DNA sample in the presence of primers, DNA polymerase, and nucleotides to exponentially amplify the target sequence. The amplified DNA can then be analyzed by gel electrophoresis.
5.RNA Processing.pptx
RNA processing is required to generate mature RNA molecules from primary transcripts. It involves 5' capping, 3' cleavage and polyadenylation, and splicing. During 5' capping, a 5' cap structure is added to primary transcripts. 3' cleavage and polyadenylation generates the mature 3' end through endonucleolytic cleavage followed by poly(A) tail addition. Splicing removes introns from primary transcripts in eukaryotes, joining exons to form mature mRNAs.
trp Operon - Virtual High School (VHS) - SBI4U
trp Operon
Recall
Cells respond to their environments by modifying gene expression.
Prokaryotic cells can individually adapt to their changing environments by
regulating the expression of their genes.
Bacteria can adjust to their environments using a special sequence of DNA
known as an operon, which controls the synthesis of protein in response to the environment. An operon has three key areas on the DNA strand: the promoter, the operator, and the transcription unit. The bacteria Escherichia coli need the amino acid tryptophan to survive. Amazingly, if tryptophan is not readily available in its environment, E. coli will actually make its own tryptophan from another compound by activating a metabolic pathway called the trp operon (trp for tryptophan). This metabolic process “shuts off’ as soon as tryptophan is readily available again. How the trp Operon Works Tryptophan is made using a sequence of five different enzymatic reactions. The genes that code for these five enzymes are clustered together on the same chromosome. A single promoter transcribes the entire cluster at once. In this way, the cell can turn “off” or “on” the entire series of functionally associated genes simultaneously. Let’s look at the molecules that cause these switches to be “on” or “off”. 1. How does gene regulation involving the trp repressor protein differ from what you observed with the lac repressor in the previous lesson? (2 points) 2. Based on your understanding of gene regulation in the cell and the function of the trp operon, describe how this process would be affected if there was a mutation in the operator region so that the operator could not carry out its function. (4 points) 3. What would be the result in this process of a genetic mutation that altered the shape of the trp repressor protein? (4 points)
Lac Operon
The document summarizes gene regulation in prokaryotes and eukaryotes. In prokaryotes, genes are organized into operons that are regulated by repressor or inducible systems like the tryptophan and lactose operons. The tryptophan operon is turned off by a repressor when tryptophan levels are high. The lactose operon is induced when lactose is present and glucose levels are low. In eukaryotes, gene expression is controlled through chromatin structure, pre-transcriptional and post-transcriptional regulation involving transcription factors and RNA processing, and pre-translational and post-translational regulation involving translation initiation, protein processing and degradation.
Transcription in prokaryotes and eukaryotes.pdf
1. Transcription is the process of copying DNA into mRNA, which carries genetic information from DNA in the nucleus to the cytoplasm for protein production. RNA polymerase copies one DNA strand into a complementary mRNA strand.
2. In prokaryotes, RNA polymerase initiates transcription by binding to promoter sequences upstream of genes. It then elongates the mRNA as it moves along the DNA template. Termination occurs via rho-dependent or rho-independent signals.
3. In eukaryotes, transcription requires transcription factors to recruit RNA polymerase to the promoter. The initial pre-mRNA product undergoes processing before becoming a mature mRNA for translation.
Trp operon
The trp operon is a group of genes in E. coli bacteria that encodes enzymes for the biosynthesis of tryptophan. It was the first repressible operon discovered in 1953. The trp operon is expressed when tryptophan levels are low and repressed when tryptophan levels are high through a negative feedback mechanism. Specifically, tryptophan binds to the trp repressor, causing a conformational change that allows it to bind to the operator region and prevent transcription. Additionally, the trp operon uses an attenuation mechanism to control expression, where stem loop structures form to allow or prevent transcription depending on tryptophan levels.
Post transcription
This document summarizes various aspects of post-transcriptional processing of RNA in eukaryotes. It discusses:
1) Primary transcripts (hnRNA) that are processed in the nucleus before being exported to the cytoplasm. Processing includes 5' capping, splicing of introns, and 3' polyadenylation.
2) Splicing of pre-mRNA involves recognition of splice sites, branch formation using an internal A, and ligation of exons via transesterification reactions. This is catalyzed by the spliceosome, a large complex containing 5 snRNAs and associated proteins.
3) Other types of RNA processing addressed include rRNA and tRNA processing, as well as different classes of
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Translation of Proteins.ppt
1) DNA is transcribed into mRNA, which is then processed and exported from the nucleus to the cytoplasm.
2) In the cytoplasm, mRNA attaches to ribosomes to begin translation. Amino acids are activated and attached to specific tRNAs.
3) Translation occurs as tRNAs add amino acids to the growing polypeptide chain based on the mRNA codons. Ribosomes move along the mRNA during this process until a stop codon is reached and the completed protein is released.
Eukaryotic transcription
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This document summarizes eukaryotic transcription by RNA polymerases. It discusses the three types of RNA polymerases (I, II, and III) found in eukaryotic cells, what genes each polymerase transcribes, and the basic stages and mechanisms of transcription (initiation, elongation, termination). It also describes the promoters, processing, and other regulatory elements involved in eukaryotic transcription.Enzymes in Blood Lipid Metabolism.pdf
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Similar to Tn5 Transposase
Basic principle of transcription
Transcription is the process of synthesizing RNA using a DNA template. It involves three main steps - initiation, elongation, and termination. In initiation, RNA polymerase binds to promoter sequences on DNA and unwinds the double helix. In elongation, RNA polymerase moves along the DNA strand and adds complementary RNA nucleotides. Termination occurs when the polymerase reaches a terminator sequence and stops adding nucleotides. Prokaryotes and eukaryotes have similar transcription mechanisms but eukaryotes have three RNA polymerases and require additional transcription factors.
Tryptophan
The trp operon in E. coli bacteria encodes genes for the biosynthesis of the amino acid tryptophan. It is regulated by the trp repressor protein - when tryptophan levels are low, the repressor does not bind to the operator, allowing transcription of the operon; when tryptophan levels are high, it binds to the operator and blocks transcription, turning the operon off. This allows the bacteria to efficiently control tryptophan production depending on environmental availability.
Eukaryotic transcription
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
Pcr
PCR is a technique used to amplify a specific region of DNA. It involves using primers that are complementary to the outer regions of the DNA sequence being targeted. During PCR, the DNA is denatured and new strands are synthesized using DNA polymerase. This results in exponential amplification of the target DNA sequence. Primers are short oligonucleotides that are selected to target a specific sequence and initiate DNA synthesis. DNA polymerase is the enzyme that copies the DNA sequence. Restriction fragment length polymorphism (RFLP) involves using restriction enzymes to cut DNA into fragments of different lengths that can then be separated by electrophoresis to identify different organisms based on unique DNA fingerprints.
2013 transcription
The document discusses transcription in prokaryotes and eukaryotes. It describes the key differences between their transcription mechanisms. In prokaryotes, RNA polymerase directly binds DNA and transcribes genes in three phases: initiation, elongation, and termination. In eukaryotes, RNA polymerase requires transcription factors to bind DNA and regulate gene expression, as transcription involves promoter elements, regulatory sequences, and RNA processing.
2013 transcription
The document discusses transcription in prokaryotes and eukaryotes. It describes the key components involved in transcription including DNA, RNA polymerases, promoters, and the three main phases - initiation, elongation, and termination. In prokaryotes, RNA polymerase binds directly to DNA and recognizes promoter sequences to initiate transcription. Eukaryotes require additional factors for transcription initiation.
RNA synthesis, processing and modification.pptx
The presentation discusses RNA synthesis, processing, and modification, explaining that RNA is synthesized from DNA through transcription by RNA polymerase. It describes the post-transcriptional modification of primary transcripts, including splicing of introns from mRNA, addition of a 5' cap and 3' poly-A tail, and modification of tRNA. The presentation also covers regulatory sequences that control transcription and the role of reverse transcription in retroviruses like HIV.
Trp operon
The document discusses the tryptophan (trp) operon in bacteria such as E. coli. The trp operon contains 5 structural genes that code for enzymes involved in the biosynthesis of tryptophan. It is regulated by a repressor protein called trpR that binds to the operator region and prevents transcription when tryptophan is present. When tryptophan levels are low, the repressor cannot bind and transcription of the structural genes occurs. The trp operon was an important early example of gene regulation and negative feedback that is commonly used to demonstrate these concepts.
Transcription
The document discusses the basic principles of gene expression from DNA to protein. It describes transcription, which is the synthesis of RNA from a DNA template, and translation, which is the synthesis of proteins from mRNA templates using ribosomes. In eukaryotes, transcription requires RNA polymerases and other transcription factors to initiate transcription from DNA. The primary transcript then undergoes processing including 5' capping, 3' polyadenylation, and splicing to form mature mRNA. The mRNA is then translated by ribosomes to produce proteins.
Polymerase chain reaction & electrophoresis
Kary Banks is considered the great mind behind PCR. He developed PCR in 1985 while working at Cetus Corporation and was awarded the Nobel Prize in 1993. PCR allows for targeted amplification of specific DNA sequences, enabling their analysis even from very small samples. It involves heating and cooling of the DNA sample in the presence of primers, DNA polymerase, and nucleotides to exponentially amplify the target sequence. The amplified DNA can then be analyzed by gel electrophoresis.
5.RNA Processing.pptx
RNA processing is required to generate mature RNA molecules from primary transcripts. It involves 5' capping, 3' cleavage and polyadenylation, and splicing. During 5' capping, a 5' cap structure is added to primary transcripts. 3' cleavage and polyadenylation generates the mature 3' end through endonucleolytic cleavage followed by poly(A) tail addition. Splicing removes introns from primary transcripts in eukaryotes, joining exons to form mature mRNAs.
trp Operon - Virtual High School (VHS) - SBI4U
trp Operon
Recall
Cells respond to their environments by modifying gene expression.
Prokaryotic cells can individually adapt to their changing environments by
regulating the expression of their genes.
Bacteria can adjust to their environments using a special sequence of DNA
known as an operon, which controls the synthesis of protein in response to the environment. An operon has three key areas on the DNA strand: the promoter, the operator, and the transcription unit. The bacteria Escherichia coli need the amino acid tryptophan to survive. Amazingly, if tryptophan is not readily available in its environment, E. coli will actually make its own tryptophan from another compound by activating a metabolic pathway called the trp operon (trp for tryptophan). This metabolic process “shuts off’ as soon as tryptophan is readily available again. How the trp Operon Works Tryptophan is made using a sequence of five different enzymatic reactions. The genes that code for these five enzymes are clustered together on the same chromosome. A single promoter transcribes the entire cluster at once. In this way, the cell can turn “off” or “on” the entire series of functionally associated genes simultaneously. Let’s look at the molecules that cause these switches to be “on” or “off”. 1. How does gene regulation involving the trp repressor protein differ from what you observed with the lac repressor in the previous lesson? (2 points) 2. Based on your understanding of gene regulation in the cell and the function of the trp operon, describe how this process would be affected if there was a mutation in the operator region so that the operator could not carry out its function. (4 points) 3. What would be the result in this process of a genetic mutation that altered the shape of the trp repressor protein? (4 points)
Lac Operon
The document summarizes gene regulation in prokaryotes and eukaryotes. In prokaryotes, genes are organized into operons that are regulated by repressor or inducible systems like the tryptophan and lactose operons. The tryptophan operon is turned off by a repressor when tryptophan levels are high. The lactose operon is induced when lactose is present and glucose levels are low. In eukaryotes, gene expression is controlled through chromatin structure, pre-transcriptional and post-transcriptional regulation involving transcription factors and RNA processing, and pre-translational and post-translational regulation involving translation initiation, protein processing and degradation.
Transcription in prokaryotes and eukaryotes.pdf
1. Transcription is the process of copying DNA into mRNA, which carries genetic information from DNA in the nucleus to the cytoplasm for protein production. RNA polymerase copies one DNA strand into a complementary mRNA strand.
2. In prokaryotes, RNA polymerase initiates transcription by binding to promoter sequences upstream of genes. It then elongates the mRNA as it moves along the DNA template. Termination occurs via rho-dependent or rho-independent signals.
3. In eukaryotes, transcription requires transcription factors to recruit RNA polymerase to the promoter. The initial pre-mRNA product undergoes processing before becoming a mature mRNA for translation.
Trp operon
The trp operon is a group of genes in E. coli bacteria that encodes enzymes for the biosynthesis of tryptophan. It was the first repressible operon discovered in 1953. The trp operon is expressed when tryptophan levels are low and repressed when tryptophan levels are high through a negative feedback mechanism. Specifically, tryptophan binds to the trp repressor, causing a conformational change that allows it to bind to the operator region and prevent transcription. Additionally, the trp operon uses an attenuation mechanism to control expression, where stem loop structures form to allow or prevent transcription depending on tryptophan levels.
Post transcription
This document summarizes various aspects of post-transcriptional processing of RNA in eukaryotes. It discusses:
1) Primary transcripts (hnRNA) that are processed in the nucleus before being exported to the cytoplasm. Processing includes 5' capping, splicing of introns, and 3' polyadenylation.
2) Splicing of pre-mRNA involves recognition of splice sites, branch formation using an internal A, and ligation of exons via transesterification reactions. This is catalyzed by the spliceosome, a large complex containing 5 snRNAs and associated proteins.
3) Other types of RNA processing addressed include rRNA and tRNA processing, as well as different classes of
ENZYMES IN RECOMBINANT DNA TECHNOLOGY
DNA modifying enzymes play important roles in recombinant DNA technology. DNA polymerase synthesizes DNA from deoxyribonucleotides and is essential for DNA replication. It consists of subunits that carry out polymerase and exonuclease activities. Reverse transcriptase generates cDNA from an RNA template. Alkaline phosphatase, phosphatase, kinase and methyltransferases modify DNA through addition or removal of phosphate groups or methyl groups and are used in cloning experiments and DNA sequencing. Terminal transferase adds nucleotides to DNA ends. Restriction enzymes are inhibited by DNA methylation.
Digestion in gene cloning
Restriction enzyme digestion is a common technique used in gene cloning to prepare DNA fragments for insertion into a vector. Restriction enzymes recognize specific sequences in DNA and cleave the bonds between nucleotides at that site. The amount of restriction enzyme needed in microliters to completely digest one microgram of substrate DNA in one hour at the optimal temperature is defined as one unit of restriction enzyme activity. Restriction digestion is performed as part of gene cloning to isolate the desired DNA fragment, which is then inserted into a vector for cloning.
Translation of Proteins.ppt
1) DNA is transcribed into mRNA, which is then processed and exported from the nucleus to the cytoplasm.
2) In the cytoplasm, mRNA attaches to ribosomes to begin translation. Amino acids are activated and attached to specific tRNAs.
3) Translation occurs as tRNAs add amino acids to the growing polypeptide chain based on the mRNA codons. Ribosomes move along the mRNA during this process until a stop codon is reached and the completed protein is released.
Eukaryotic transcription
Eukaryotic transcriptionMarudhar Kesari Jain College for Women Vaniyambadi - 635 751, Tamil Nadu, INDIA.
This document summarizes eukaryotic transcription by RNA polymerases. It discusses the three types of RNA polymerases (I, II, and III) found in eukaryotic cells, what genes each polymerase transcribes, and the basic stages and mechanisms of transcription (initiation, elongation, termination). It also describes the promoters, processing, and other regulatory elements involved in eukaryotic transcription.Similar to Tn5 Transposase (20)
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Blood lipids refer to a group of fatty substances present in blood, mainly including cholesterol and triglycerides. There are generally two forms of cholesterols circulating in the bloodstream: low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Abnormal lipid level in blood is always associated with a number of diseases, such as high blood pressure, coronary arteries, hypothyroidism, type 2 diabetes, obesity, pancreatitis, et al. https://diagnostic-enzymes.creative-enzymes.com/blood-lipids.html
Native Bacillus licheniformis Protease at Creative Enzymes
A protease is an enzyme that helps proteolysis: protein catabolism by hydrolysis of peptide bonds. The native Bacillus licheniformis protease belongs to the serine endopeptidase subtilisin family, which breaks the peptide bond non-specifically under alkaline conditions. The enzyme is active in aqueous solutions and in some organic solvents such as dry octane. The protease is inactivated by serine active-site inhibitors, such as phenylmethylsulfonyl fluoride (PMSF) and diisopropyl fluorophosphate. https://www.creative-enzymes.com/product/native-bacillus-licheniformis-protease_936.html
Molecular biology grade lyophilized powder of Recombinant Proteinase K
Proteinase K is a broad-spectrum serine protease originally isolated from the fungus Engyodontiumalbum (Tritirachium album). The enzyme was named "proteinase K" for its ability to digest keratin. Structural and molecular biology studies suggest that the enzyme belongs to the subtilisin family characterized by a catalytic triad (Asp39-His9-Ser2) in the active site. Proteinase K has no pronounced cleavage specificity and the preferential cleavage site is the peptide bond adjacent to hydrophobic amino acids. https://www.creative-enzymes.com/product/proteinase-k-from-tritirachium-album-limber-recombinant_3427.html
Food Grade B-Amylase
β-Amylase hydrolyzes the a-(1,4)glucan linkages in polysaccharides of three or more a-(1,4)linked D-glucose units. Natural substrates such as starch and glycogen are broken down intoglucose and maltose. β-amylase, also known as starch β-1,4-galactosidase, is an exo-amylase that cleaves the separated a-1,4 bonds from non-reducing ends when acting on starch and produces maltose. Because amylase changes the configuration of C1 in the hydrolysate maltose molecule from alpha type to beta type during the hydrolysis process, it is named β-amylase. https://www.creative-enzymes.com/product/-amylase-food-grade-_3167.html
Native Bacillus licheniformis Protease
A protease is an enzyme that helps proteolysis: protein catabolism by hydrolysis of peptide bonds. The nave Bacillus licheniformis protease belongs to the serine endopeptidase subtilisin family, which breaks the peptide bond non-specifically under alkaline conditions. The enzyme is active in aqueous solutions and in some organic solvents such as dry octane. The protease is inactivated by serine active-site inhibitors, such as phenylmethylsulfonyl fluoride (PMSF) and diisopropylfluorophosphate. https://www.creative-enzymes.com/product/native-bacillus-licheniformis-protease_936.html
Proteinase K
Proteinase K is a stable and highly reactive serine protease. Evidence from crystal and molecular structure studies indicates the enzyme belongs to the subtilisin family with an active-site catalytic triad (Asp39-His69-Ser224). It is stable in a broad range of environments:pH, buffer salts, detergents (SDS), and temperature. In the presence of 0.1-0.5% SDS, proteinase K retains activity and will digest a variety of proteins and nucleases in DNA preparations without compromising the integrity of the isolated DNA. https://www.creative-enzymes.com/product/proteinase-k-from-tritirachium-album-limber-recombinant_3427.html
What Are Probiotics?
Probiotics are living microorganisms that co-exist with humans. Different from pathogenic microorganisms, probiotics are beneficial, and sometimes essential to health. For example, intake of probiotics can increase the number of beneficial bacteria in the intense, maintain the dynamic balance of intestinal flora, and enhance
gastrointestinal health. https://www.creative-enzymes.com/cate/probiotics_99.html
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Blood lipids refer to a group of fatty substances present in the blood, mainly including cholesterol and triglycerides. There are generally two forms of cholesterols circulating in the bloodstream: low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Abnormal lipid level in blood is always associated with a number of diseases, such as high blood pressure, coronary arteries, hypothyroidism, type 2 diabetes, obesity, pancreatitis, et al. https://diagnostic-enzymes.creative-enzymes.com/blood-lipids.html
Explore creative enzymes's enzyme products for triglyceride kit
A Triglyceride Kit is used to measure triglyceride concentration in mammalian samples. The triglyceride assay is easy and sensitive. Triglycerides are converted to free fay acids and glycerol. Glycerol is then oxidized to generate a product that reacts with a probe to generate colour and fluorescence. Creative Enzymes provides enzymes that are essential to produce triglyceride kits. https://diagnostic-enzymes.creative-enzymes.com/glycerol-3-phosphate-oxidase-from-pediococcus-sp-item-10.html
Creative Enzymes's Diagnostic Enzymes for POC Biosensor
Point-of-care testing (POCT) refers to a group of immediate test approaches that are implemented near or at the site of patient care. Various portable and handheld instruments and test kits, or biosensors, have supplemented the POC. Creative Enzymes serves diagnostic enzyme products to optimize your POC biosensors. https://diagnostic-enzymes.creative-enzymes.com/poct-bio-sensor.html
Explore Enzymes Involved in Blood Lipid Metabolism at Creative Enzymes
Blood lipids include cholesterol and triglycerides, which exist in two forms: LDL and HDL. Abnormal blood lipid levels are associated with diseases like high blood pressure and diabetes. Creative Enzymes supplies enzymes involved in blood lipid metabolism like cholesterol esterase, cholesterol oxidase, and glucose-6-phosphate dehydrogenase for research and industrial use. They provide information on product sources and contact details.
Creative Enzymes: Antiallergic Probiotic Formula
Probiotics may exhibit antiallergic effects by degradation or structural modification of enteral antigens, stabilization of aberrant microbiota, improvement of the gut-barrier function, secretion regulation of pro-inflammatory mediators, and development of the immune system. https://probiotic.creative-enzymes.com/multi-strain-probiotics/antiallergic-formula.html
Enzyme immobilization
As an enzyme expert, Creative Enzymes is engaged in providing the best products and services for worldwide researchers, especially for enzymes modification. Immobilization is one of the most popular methods that were initially developed for biotechnology processes. Creative Enzymes offers enzyme immobilization services with reliable outcomes, improved performance, and surface analysis. https://www.creative-enzymes.com/service/Enzyme-Modification-By-Immobilization_366.html
Featured enzyme products for diagnostic use
Creative Enzymes is a worldwide leading company in diagnostic enzymes manufacturing and supply. We are committed to providing our customers with diverse enzyme products and custom enzyme-related services for medical and research diagnosis. Relying on our professional team and state-of-art technologies, we have gained solid reputation for having top of the line products and services.
Probiotics Powder
Creative Enzymes is a professional and experienced supplier of probiotics. In the past decade, Creative Enzymes mainly provides enzyme-related products and services. With the continuous expansion of business areas and scale, we have set foot in other areas and established a sound probiotic production and supply chain. Based on our high-quality products and services, as well as the unique advantages of large-scale production, our probiotic products are widely favored by industrial customers and scientific research customers.
Enzymes for Research and Diagnostic Use
The document discusses enzyme products from Creative Enzymes Inc. that are used for diagnostic purposes. It begins by explaining what enzymes are and their role in metabolic processes and disease diagnosis. Specific enzymes that can indicate various diseases like liver diseases, cancer, and cardiac disorders are mentioned. The document then lists over 20 enzyme products available from Creative Enzymes that are used in clinical analysis to diagnose conditions. It provides information on what each enzyme is used for and concludes with contact information for the company.
Enzyme immobilization
As an enzyme expert, Creative Enzymes is engaged in providing the best products and services for worldwide researchers, especially for enzymes modification. Immobilization is one of the most popular methods that were initially developed for biotechnology processes. Creative Enzymes offers enzyme immobilization services with reliable outcomes, improved performance, and surface analysis.
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EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
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the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
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hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skillsCytokines and their role in immune regulation.pptx
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https://ashpc.eu/
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Nucleic Acid-its structural and functional complexity.
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Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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Phenomics assisted breeding in crop improvement
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
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genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
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Equivariant neural networks and representation theory
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
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I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
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mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
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Tn5 Transposase
- 1. Email: info@crea ve-enzymes.com Tn5 Transposase Transposase is an enzyme that binds to the end of a transposon and catalyzes its movement to another part of the genome by a “cut and paste” mechanism or a replica ve transposi on mechanism. Tn5 Transposase (Tnp) is a member of the RNase superfamily of proteins which includes retroviral integrases. Learn More Product Informa on Product Name Tn5 Transposase Concentra on 1,000 U/ml Cat No. NATE-1629 Unit Defini on One unit Tn5 transposase is defined as the amount of enzyme that cleaves 1μg DNA fragment containing recogni on sequence in 1 hour at 37°C. EC No. EC 2.7.7 Source E.coli Synonyms Transposase Storage Store at -20°C Product Applica ons Robust Tn5 Transposase recognizes inside end sequences, outside end sequences, and mosaic end sequences of Tn5 transposon. This enzyme can be used to randomly insert Tn5 transposon into target DNA. Applica ons of this product mainly include: ● In vitro transgenic experiment ● Random library construc on for second-genera on sequencing Crea ve Enzymes also provides other enzyme products for research or industry uses. Please contact us for any product needs. Learn More Contact Informa on Email: info@crea ve-enzymes.com 45-1 Ramsey Road, Shirley, NY 11967, USA Tel: 1-631-562-8517 www.crea ve-enzymes.com Fax: 1-631-938-8127