The document describes several analyses performed on a protein sequence, including:
1. Alignment of the nucleotide and protein sequences to reference sequences using BLAST.
2. Design of primer pairs flanking exon-exon junctions.
3. Analysis of the protein sequence using various tools to predict properties like molecular weight, isoelectric point, stability, domains, localization signals, and post-translational modifications.
4. Searches using the protein sequence against pattern/profile databases to identify domains and motifs, which found immunoglobulin and transmembrane domains.
Each organism's characteristics are encoded in DNA molecules. DNA stores and transmits genetic information through long chains of nucleotides composed of deoxyribose sugar, phosphate groups, and nitrogenous bases. RNA also plays important roles in protein synthesis. Messenger RNA carries DNA's message to make proteins during transcription in the nucleus. Ribosomal and transfer RNA aid in translation in the cytoplasm, where transfer RNA transfers amino acids to form polypeptides according to mRNA codons.
A new effector pathway links ATM kinase with the DNA damage responseCostas Demonacos
The related kinases ATM (ataxia-telangiectasia mutated) and ATR (ataxia-telangiectasia and Rad3-related) phosphorylate a limited number of downstream protein targets in response to DNA damage. Here we report a new pathway in which ATM kinase signals the DNA damage response by targeting the transcriptional cofactor Strap. ATM phosphorylates Strap at a serine residue, stabilizing nuclear Strap and facilitating formation of a stress-responsive co-activator complex. Strap activity enhances p53 acetylation, and augments the response to DNA damage. Strap remains localized in the cytoplasm in cells derived from ataxia telangiectasia individuals with defective ATM, as well as in cells expressing a Strap mutant that cannot be phosphorylated by ATM. Targeting Strap to the nucleus reinstates protein stabilization and activates the DNA damage response. These results indicate that the nuclear accumulation of Strap is a critical regulator in the damage response, and argue that this function can be assigned to ATM through the DNA damage-dependent phosphorylation of Strap.
2018-05-24 Research update on Armadillo Repeat Proteins: Evolution and Design...Spencer Bliven
This document discusses armadillo repeat proteins and their potential use in protein-protein binding applications. It provides background on armadillo repeats and their biological roles. The document then discusses using armadillo repeats as an alternative to antibodies for applications like therapeutics and assays by rationally designing armadillo repeat proteins to bind specific peptide targets. It outlines the author's approach to modeling armadillo repeat evolution and using machine learning to predict binding abilities from sequence.
The document discusses several topics related to DNA replication, genetic engineering, and gene regulation:
1) It describes the basic process of DNA replication, including the roles of helicase, primase, topoisomerase, and other proteins.
2) It explains some techniques used in genetic engineering, such as restriction enzymes cutting DNA at specific sites, ligation to join DNA fragments, and gel electrophoresis to separate DNA fragments by size.
3) It discusses mechanisms of gene regulation, including repression and activation of operons in response to metabolites and how this controls enzyme production for metabolic pathways like tryptophan and lactose synthesis.
Regulation of pten activity by its carboxyl terminal autoinhibitoryChau Chan Lao
Regulation of PTEN Activity by Its Carboxyl-terminal Autoinhibitory Domain.
Leticia Odriozola, Gobind Singh, Thuong Hoang, and Andrew M. Chan
From the Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York, 10029
THE JOURNAL OF BIOLOGICAL CHEMISTRY, VOL. 282, NO. 32, pp. 23306–23315, August 10, 2007
目前已知PTEN(Phosphatase and tensin homolog)是腫瘤抑制蛋白,其由403個氨基酸組成,主要分PTPase及C2 domain,C2 domain使PTEN可與細胞膜作用連結。
PTEN之C-tail(aa 350~403)被發現具有調控PTEN自身活性之功能。前人研究指出C-tail有6個可磷酸化之位置(Thr-366、Ser-370、Ser-380、Thr-382、Thr-383及Ser-385),這些位置可調控PTEN之腫瘤抑制能力、胞內之分佈及穩定性。前人產生以上位置突變之PTEN變異株,發現這些變異株具有更強的腫瘤抑制能力,但穩定性將降低,這可能是因這些變異株具有更開放結構所致。
本報告針對研究PTEN C-tail在連結細胞膜和在其本身催化活性中扮演的功能。作者先產生一系列之PTEN磷酸化位置變異株,發現S385A會促使PTEN之membrane localization in vivo及加強phosphatase活性in vitro,而且此突變會使Ser-380/Thr-382/Thr-383 cluster的磷酸化程度降低,因此知Ser-385可透過被去磷酸化以調控PTEN。而以phosphomimic residues取代Ser-380/Thr-382/Thr-383會使上述S385A所產生之PTEN催化活性反轉。之後利用免疫沉澱方法,發現C-tail之71-amino acid region會與C2 domain上之CBR3 motif作用,暗示C-tail參與連結細胞膜之調控。最後利用合成之PTEN C-tail peptide,發現其可抑制PTEN之催化活性in vitro,而在細胞表現此peptide則會抑制PTEN之membrane localization,磷酸化之Akt量亦上升。以上實驗顯示C-tail在PTEN之membrane recruitment及PTPase活性調控中扮演Autoinhibitory domain角色。
An aminopeptidase P (PepP)-encoding gene has been cloned from Streptomyces lividans 66. The gene, pepP, was localized by deletion mapping and its nucleotide sequence was determined. The deduced amino acid sequence was found to display significant similarity to Escherichia coli PepP. The partially purified S. lividans enzyme had a 50-kDa subunit and was present as a homodimer, confirming that pepP encodes the observed intracellular PepP.
This document summarizes research on rust effectors and rust resistance genes in flax. It discusses how 20 flax rust resistance genes have been cloned and encode receptor components of the plant immune system. Four flax rust avirulence genes have been identified that encode small secreted proteins expressed in haustoria. Recognition of these avirulence proteins occurs through direct interaction with the corresponding resistance proteins. The document also discusses how stem rust effectors are delivered into plant cells and the potential application of knowledge from flax to cereal rust diseases.
Each organism's characteristics are encoded in DNA molecules. DNA stores and transmits genetic information through long chains of nucleotides composed of deoxyribose sugar, phosphate groups, and nitrogenous bases. RNA also plays important roles in protein synthesis. Messenger RNA carries DNA's message to make proteins during transcription in the nucleus. Ribosomal and transfer RNA aid in translation in the cytoplasm, where transfer RNA transfers amino acids to form polypeptides according to mRNA codons.
A new effector pathway links ATM kinase with the DNA damage responseCostas Demonacos
The related kinases ATM (ataxia-telangiectasia mutated) and ATR (ataxia-telangiectasia and Rad3-related) phosphorylate a limited number of downstream protein targets in response to DNA damage. Here we report a new pathway in which ATM kinase signals the DNA damage response by targeting the transcriptional cofactor Strap. ATM phosphorylates Strap at a serine residue, stabilizing nuclear Strap and facilitating formation of a stress-responsive co-activator complex. Strap activity enhances p53 acetylation, and augments the response to DNA damage. Strap remains localized in the cytoplasm in cells derived from ataxia telangiectasia individuals with defective ATM, as well as in cells expressing a Strap mutant that cannot be phosphorylated by ATM. Targeting Strap to the nucleus reinstates protein stabilization and activates the DNA damage response. These results indicate that the nuclear accumulation of Strap is a critical regulator in the damage response, and argue that this function can be assigned to ATM through the DNA damage-dependent phosphorylation of Strap.
2018-05-24 Research update on Armadillo Repeat Proteins: Evolution and Design...Spencer Bliven
This document discusses armadillo repeat proteins and their potential use in protein-protein binding applications. It provides background on armadillo repeats and their biological roles. The document then discusses using armadillo repeats as an alternative to antibodies for applications like therapeutics and assays by rationally designing armadillo repeat proteins to bind specific peptide targets. It outlines the author's approach to modeling armadillo repeat evolution and using machine learning to predict binding abilities from sequence.
The document discusses several topics related to DNA replication, genetic engineering, and gene regulation:
1) It describes the basic process of DNA replication, including the roles of helicase, primase, topoisomerase, and other proteins.
2) It explains some techniques used in genetic engineering, such as restriction enzymes cutting DNA at specific sites, ligation to join DNA fragments, and gel electrophoresis to separate DNA fragments by size.
3) It discusses mechanisms of gene regulation, including repression and activation of operons in response to metabolites and how this controls enzyme production for metabolic pathways like tryptophan and lactose synthesis.
Regulation of pten activity by its carboxyl terminal autoinhibitoryChau Chan Lao
Regulation of PTEN Activity by Its Carboxyl-terminal Autoinhibitory Domain.
Leticia Odriozola, Gobind Singh, Thuong Hoang, and Andrew M. Chan
From the Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York, 10029
THE JOURNAL OF BIOLOGICAL CHEMISTRY, VOL. 282, NO. 32, pp. 23306–23315, August 10, 2007
目前已知PTEN(Phosphatase and tensin homolog)是腫瘤抑制蛋白,其由403個氨基酸組成,主要分PTPase及C2 domain,C2 domain使PTEN可與細胞膜作用連結。
PTEN之C-tail(aa 350~403)被發現具有調控PTEN自身活性之功能。前人研究指出C-tail有6個可磷酸化之位置(Thr-366、Ser-370、Ser-380、Thr-382、Thr-383及Ser-385),這些位置可調控PTEN之腫瘤抑制能力、胞內之分佈及穩定性。前人產生以上位置突變之PTEN變異株,發現這些變異株具有更強的腫瘤抑制能力,但穩定性將降低,這可能是因這些變異株具有更開放結構所致。
本報告針對研究PTEN C-tail在連結細胞膜和在其本身催化活性中扮演的功能。作者先產生一系列之PTEN磷酸化位置變異株,發現S385A會促使PTEN之membrane localization in vivo及加強phosphatase活性in vitro,而且此突變會使Ser-380/Thr-382/Thr-383 cluster的磷酸化程度降低,因此知Ser-385可透過被去磷酸化以調控PTEN。而以phosphomimic residues取代Ser-380/Thr-382/Thr-383會使上述S385A所產生之PTEN催化活性反轉。之後利用免疫沉澱方法,發現C-tail之71-amino acid region會與C2 domain上之CBR3 motif作用,暗示C-tail參與連結細胞膜之調控。最後利用合成之PTEN C-tail peptide,發現其可抑制PTEN之催化活性in vitro,而在細胞表現此peptide則會抑制PTEN之membrane localization,磷酸化之Akt量亦上升。以上實驗顯示C-tail在PTEN之membrane recruitment及PTPase活性調控中扮演Autoinhibitory domain角色。
An aminopeptidase P (PepP)-encoding gene has been cloned from Streptomyces lividans 66. The gene, pepP, was localized by deletion mapping and its nucleotide sequence was determined. The deduced amino acid sequence was found to display significant similarity to Escherichia coli PepP. The partially purified S. lividans enzyme had a 50-kDa subunit and was present as a homodimer, confirming that pepP encodes the observed intracellular PepP.
This document summarizes research on rust effectors and rust resistance genes in flax. It discusses how 20 flax rust resistance genes have been cloned and encode receptor components of the plant immune system. Four flax rust avirulence genes have been identified that encode small secreted proteins expressed in haustoria. Recognition of these avirulence proteins occurs through direct interaction with the corresponding resistance proteins. The document also discusses how stem rust effectors are delivered into plant cells and the potential application of knowledge from flax to cereal rust diseases.
The document summarizes research investigating the function of the RGG box domain in the fragile X mental retardation protein (FMRP). Key findings include:
1) Methylation of specific arginine residues in the RGG box inhibits FMRP's ability to bind certain RNAs in vitro.
2) These arginine residues are required for FMRP to properly associate with polysomes.
3) The RGG box and specific arginine residues differentially affect FMRP's ability to bind different RNAs.
4) Protein arginine methyltransferases PRMT1 and PRMT3 methylate the RGG box arginines in FMRP in cells.
The document discusses prion diseases and the protein-only hypothesis of pathogenesis. It summarizes the structures of cellular and scrapie prion protein and describes techniques used to study prion protein aggregates, including EPR spectroscopy. The document outlines research showing recombinant prion protein forms amyloid fibrils with a parallel in-register beta-sheet structure between residues 160-220. Both denaturing and native conditions produce similar amyloid fibrils, but buffer conditions can lead to structurally distinct fibrils. Substitution of single residues is also shown to produce different amyloid structures.
This thesis studied the regulation of alternative splicing of the apoptotic gene bcl-x. The author identified two proteins, hnRNP F and H, that bind to an exon element and promote the production of the pro-apoptotic Bcl-xs isoform. Subsequent work found that hnRNP K binds antagonistic elements near the Bcl-xs splice site, repressing Bcl-xs production. Finally, a large intronic region was shown to inhibit Bcl-xs under basal conditions, but this inhibition is lost when protein kinase C activity is blocked, leading to increased Bcl-xs. This suggests protein kinase C signaling controls bcl-x splicing. Defects in this pathway
Presentation made by Dr. Simon Alberti on October 30, 2015 at the Alzforum-hosted live webinar titled "Fluid Business: Could “Liquid” Protein Herald Neurodegeneration?"
More information and the recording of the session available at http://www.alzforum.org/webinars/fluid-business-could-liquid-protein-herald-neurodegeneration
Pten and eph b4 regulate the establishment of perisomatic inhibition in mouse...Taruna Ikrar
Perisomatic inhibition of pyramidal neurons is established by fast-spiking, parvalbuminexpressing interneurons (PV cells). Failure to assemble adequate perisomatic inhibition is thought to underlie the aetiology of neurological dysfunction in seizures, autism spectrum disorders and schizophrenia. Here we show that in mouse visual cortex, strong perisomatic inhibition does not develop if PV cells lack a single copy of Pten. PTEN signalling appears to drive the assembly of perisomatic inhibition in an experience-dependent manner by suppressing the expression of EphB4; PVcells hemizygous for Pten show an B2-fold increase in expression of EphB4, and over-expression of EphB4 in adult PV cells causes a dismantling of perisomatic inhibition. These findings implicate a molecular disinhibitory mechanism driving the establishment of perisomatic inhibition whereby visual experience enhances Pten signalling, resulting in the suppression of EphB4 expression; this relieves a native synaptic repulsion between PV cells and pyramidal neurons, thereby promoting the assembly of perisomatic inhibition.
Johannes Friedrich Miescher (1844-1895) was a Swiss physician and biologist who was the first researcher to isolate and identify nucleic acid. He discovered that nucleic acid is a phosphate-nitrogenous base molecule that produces protons in water, making it an acid. The document discusses DNA and RNA nucleotides and bases, transcription, translation, genes, and proteins.
This document discusses Polycomb group (PcG) proteins, which are important repressor proteins that regulate gene expression during development. It describes two main PcG complexes, PRC1 and PRC2, and their mechanisms of action, including histone modifications and chromatin compaction. The document also examines a case study on the interaction between the PcG protein LHP1 and deubiquitinating enzymes UBP12 and UBP13 in Arabidopsis thaliana. The study found that UBP12 and UBP13 interact with and help recruit LHP1 to target genes, and are involved in histone deubiquitination, which impacts gene silencing by PcG proteins.
This document summarizes several research publications on neuroscience topics:
1. One study found that acetaminophen affects central monoaminergic neurotransmission in rats, increasing serotonin levels in various brain regions and decreasing dopamine metabolites, suggesting monoamines may be involved in its analgesic action.
2. Another study showed that the benzodiazepine triazolam suppresses the induction of long-term potentiation in hippocampal neurons, consistent with its positive modulation of GABA-A receptor function.
3. A third study found that chronic treatment with either a substance P receptor antagonist or conventional antidepressant increases burst firing of neurons in the locus coeruleus, similarly to how imipramine works.
Bacteria regulate their gene expression through operon systems that turn genes on and off in response to environmental conditions. Operons group genes encoding enzymes in the same metabolic pathway under a single promoter. In repressible operons like the tryptophan operon, the presence of an end product like tryptophan causes it to bind a repressor protein and block transcription. In inducible operons like the lactose operon, the presence of a nutrient like lactose causes it to bind the repressor protein and induce transcription. This allows bacteria to efficiently regulate their metabolism and only produce necessary enzymes.
The document discusses several topics related to DNA and genetics including DNA replication, restriction enzymes, gel electrophoresis, PCR, DNA sequencing, cloning, and gene expression. It provides figures to illustrate key concepts and techniques such as how restriction enzymes cut DNA, how gel electrophoresis separates DNA fragments by size, how PCR amplifies a target DNA sequence, and the process of cloning a gene into a bacterial plasmid.
The document discusses DNA replication. It describes how DNA replication is semiconservative, with each parental DNA strand serving as a template to produce two new double-stranded DNA molecules. The key steps involve helicase unwinding the DNA, topoisomerase managing supercoils, single-stranded binding proteins coating the exposed strands, primase synthesizing RNA primers, and DNA polymerase extending the primers to replicate the new strands.
Presentation made by Dr. Paul Taylor on October 30, 2015 at the Alzforum-hosted live webinar titled "Fluid Business: Could “Liquid” Protein Herald Neurodegeneration?"
More information and the recording of the session available at http://www.alzforum.org/webinars/fluid-business-could-liquid-protein-herald-neurodegeneration
Traditionally the gene expression pathway was regarded as being composed of independent steps, from RNA transcription to protein translation. To-date there is increasing evidence for coupling between the different processes of the pathway, specifically between transcription and splicing. Given the extensive cross-talk between these processes, we derived a transcription-splicing integrated network. The nodes of the network included experimentally verified human proteins belonging to three groups of regulators: Transcription factors (TFs), splicing factors (SFs) and kinases. The nodes were wired by instances of predicted transcriptional and alternative splicing regulation. Analysis of the network indicated a pervasive cross-regulation among the nodes, specifically; SFs were significantly more often regulated by alternative splicing relative to the two other subgroups, while TFs were more extensively controlled by transcriptional regulation. In particular, we found a significant preference of specific pairs of TF-TF and SF-SF to regulate their target genes, SFs being the most regulated group via independent and combinatorial binding of SFs. Consistent with the extensive cross-regulation among the splicing and transcription factors, the subgroup of kinases within the network had the highest density of predicted phosphorylation sites. The prevalent regulation of the regulatory proteins was further supported by computational analysis of the protein sequences, demonstrating the propensity of these proteins to be highly disordered relative to other proteins in the human proteome. Overall, our systematic study reveals that an organizing principle in the logic of integrated networks favor the regulation of regulatory proteins by the specific regulation they conduct. Based on these results we propose a new regulatory paradigm, postulating that fine-tuned gene expression regulation of the master regulators in the cell is commonly achieved by cross-regulation.
This document describes a proposed method to map neural circuits in the Drosophila olfactory system using chemical control of flp-frt recombination. The researchers plan to fuse the flippase gene to a destabilizing domain, allowing chemical control of flippase activity and recombination through the stabilizing ligand trimethoprim. This would enable sparse labeling of individual neurons using a GFP reporter to trace their projections, avoiding issues with current heat shock methods. The proposed method involves cloning a UAS-flp-DD construct, transfecting Drosophila, and predicting the system would allow mapping neuronal projections by varying ligand levels to control the number of labeled neurons.
Sex determination in fruit flies is controlled through alternative splicing of pre-mRNAs. The sex lethal (Sxl) protein determines whether splicing produces functional proteins that develop the fly as male or female. In females, Sxl allows splicing that produces functional transformer (Tra) and doublesex (Dsx) proteins, directing female development. In males without Sxl, Tra and Dsx are spliced to nonfunctional forms, resulting in male development. This mechanism involves different promoters, exon skipping, and alternative splice site selection to ultimately generate either male or female flies through their gene expression patterns.
1. The document presents research on transcription factor regulation during mammalian hibernation using the thirteen-lined ground squirrel as a model. It analyzes the ChREBP, Ets, and Rb-E2F pathways under euthermic and hibernating conditions.
2. Results show reduced levels of ChREBP and Ets1 proteins and increased phosphorylation during hibernation. Downstream genes like FASN also decrease.
3. The Rb-E2F pathway is suppressed during hibernation as shown by increased levels of silencing proteins like HDACs and SUV39H1, along with decreased E2F1 and increased Rb. This suggests widespread transcriptional
The document summarizes the history and development of PCR technology. It describes key events like the concept of PCR being presented in 1984, the first PCR device called Mr. Cycle in 1985, the isolation of Taq polymerase in 1985 which enabled PCR without manual addition of reagents, and the licensing of PCR by Roche in 1991 for commercial use. It also provides details on the basic components and process of PCR.
This document discusses the process of translation and protein synthesis. It covers topics like the genetic codon, tRNA, amino acid activation, and the roles of the ribosome. It also discusses inhibitors of protein and RNA synthesis that can act on prokaryotes, both prokaryotes and eukaryotes, or just eukaryotes. Finally, it briefly touches on protein folding, molecular chaperones, protein quality control, and triggering sister chromatid separation. The document is authored by Qurat-ul-Ain, who has a Ph.D. in molecular biology and genetics.
This document discusses apoptosis analysis tools from Enzo Life Sciences. It describes their products for monitoring the intrinsic and extrinsic apoptosis pathways from the cell membrane to the nucleus. Their product lines include modulators and screening assays, immunoassays and antibodies, and live cell analysis tools for detecting hallmarks of apoptosis like phosphatidylserine exposure, chromatin condensation, DNA damage, and caspase activation. The document provides examples of specific products for analyzing apoptotic pathways.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The document summarizes research investigating the function of the RGG box domain in the fragile X mental retardation protein (FMRP). Key findings include:
1) Methylation of specific arginine residues in the RGG box inhibits FMRP's ability to bind certain RNAs in vitro.
2) These arginine residues are required for FMRP to properly associate with polysomes.
3) The RGG box and specific arginine residues differentially affect FMRP's ability to bind different RNAs.
4) Protein arginine methyltransferases PRMT1 and PRMT3 methylate the RGG box arginines in FMRP in cells.
The document discusses prion diseases and the protein-only hypothesis of pathogenesis. It summarizes the structures of cellular and scrapie prion protein and describes techniques used to study prion protein aggregates, including EPR spectroscopy. The document outlines research showing recombinant prion protein forms amyloid fibrils with a parallel in-register beta-sheet structure between residues 160-220. Both denaturing and native conditions produce similar amyloid fibrils, but buffer conditions can lead to structurally distinct fibrils. Substitution of single residues is also shown to produce different amyloid structures.
This thesis studied the regulation of alternative splicing of the apoptotic gene bcl-x. The author identified two proteins, hnRNP F and H, that bind to an exon element and promote the production of the pro-apoptotic Bcl-xs isoform. Subsequent work found that hnRNP K binds antagonistic elements near the Bcl-xs splice site, repressing Bcl-xs production. Finally, a large intronic region was shown to inhibit Bcl-xs under basal conditions, but this inhibition is lost when protein kinase C activity is blocked, leading to increased Bcl-xs. This suggests protein kinase C signaling controls bcl-x splicing. Defects in this pathway
Presentation made by Dr. Simon Alberti on October 30, 2015 at the Alzforum-hosted live webinar titled "Fluid Business: Could “Liquid” Protein Herald Neurodegeneration?"
More information and the recording of the session available at http://www.alzforum.org/webinars/fluid-business-could-liquid-protein-herald-neurodegeneration
Pten and eph b4 regulate the establishment of perisomatic inhibition in mouse...Taruna Ikrar
Perisomatic inhibition of pyramidal neurons is established by fast-spiking, parvalbuminexpressing interneurons (PV cells). Failure to assemble adequate perisomatic inhibition is thought to underlie the aetiology of neurological dysfunction in seizures, autism spectrum disorders and schizophrenia. Here we show that in mouse visual cortex, strong perisomatic inhibition does not develop if PV cells lack a single copy of Pten. PTEN signalling appears to drive the assembly of perisomatic inhibition in an experience-dependent manner by suppressing the expression of EphB4; PVcells hemizygous for Pten show an B2-fold increase in expression of EphB4, and over-expression of EphB4 in adult PV cells causes a dismantling of perisomatic inhibition. These findings implicate a molecular disinhibitory mechanism driving the establishment of perisomatic inhibition whereby visual experience enhances Pten signalling, resulting in the suppression of EphB4 expression; this relieves a native synaptic repulsion between PV cells and pyramidal neurons, thereby promoting the assembly of perisomatic inhibition.
Johannes Friedrich Miescher (1844-1895) was a Swiss physician and biologist who was the first researcher to isolate and identify nucleic acid. He discovered that nucleic acid is a phosphate-nitrogenous base molecule that produces protons in water, making it an acid. The document discusses DNA and RNA nucleotides and bases, transcription, translation, genes, and proteins.
This document discusses Polycomb group (PcG) proteins, which are important repressor proteins that regulate gene expression during development. It describes two main PcG complexes, PRC1 and PRC2, and their mechanisms of action, including histone modifications and chromatin compaction. The document also examines a case study on the interaction between the PcG protein LHP1 and deubiquitinating enzymes UBP12 and UBP13 in Arabidopsis thaliana. The study found that UBP12 and UBP13 interact with and help recruit LHP1 to target genes, and are involved in histone deubiquitination, which impacts gene silencing by PcG proteins.
This document summarizes several research publications on neuroscience topics:
1. One study found that acetaminophen affects central monoaminergic neurotransmission in rats, increasing serotonin levels in various brain regions and decreasing dopamine metabolites, suggesting monoamines may be involved in its analgesic action.
2. Another study showed that the benzodiazepine triazolam suppresses the induction of long-term potentiation in hippocampal neurons, consistent with its positive modulation of GABA-A receptor function.
3. A third study found that chronic treatment with either a substance P receptor antagonist or conventional antidepressant increases burst firing of neurons in the locus coeruleus, similarly to how imipramine works.
Bacteria regulate their gene expression through operon systems that turn genes on and off in response to environmental conditions. Operons group genes encoding enzymes in the same metabolic pathway under a single promoter. In repressible operons like the tryptophan operon, the presence of an end product like tryptophan causes it to bind a repressor protein and block transcription. In inducible operons like the lactose operon, the presence of a nutrient like lactose causes it to bind the repressor protein and induce transcription. This allows bacteria to efficiently regulate their metabolism and only produce necessary enzymes.
The document discusses several topics related to DNA and genetics including DNA replication, restriction enzymes, gel electrophoresis, PCR, DNA sequencing, cloning, and gene expression. It provides figures to illustrate key concepts and techniques such as how restriction enzymes cut DNA, how gel electrophoresis separates DNA fragments by size, how PCR amplifies a target DNA sequence, and the process of cloning a gene into a bacterial plasmid.
The document discusses DNA replication. It describes how DNA replication is semiconservative, with each parental DNA strand serving as a template to produce two new double-stranded DNA molecules. The key steps involve helicase unwinding the DNA, topoisomerase managing supercoils, single-stranded binding proteins coating the exposed strands, primase synthesizing RNA primers, and DNA polymerase extending the primers to replicate the new strands.
Presentation made by Dr. Paul Taylor on October 30, 2015 at the Alzforum-hosted live webinar titled "Fluid Business: Could “Liquid” Protein Herald Neurodegeneration?"
More information and the recording of the session available at http://www.alzforum.org/webinars/fluid-business-could-liquid-protein-herald-neurodegeneration
Traditionally the gene expression pathway was regarded as being composed of independent steps, from RNA transcription to protein translation. To-date there is increasing evidence for coupling between the different processes of the pathway, specifically between transcription and splicing. Given the extensive cross-talk between these processes, we derived a transcription-splicing integrated network. The nodes of the network included experimentally verified human proteins belonging to three groups of regulators: Transcription factors (TFs), splicing factors (SFs) and kinases. The nodes were wired by instances of predicted transcriptional and alternative splicing regulation. Analysis of the network indicated a pervasive cross-regulation among the nodes, specifically; SFs were significantly more often regulated by alternative splicing relative to the two other subgroups, while TFs were more extensively controlled by transcriptional regulation. In particular, we found a significant preference of specific pairs of TF-TF and SF-SF to regulate their target genes, SFs being the most regulated group via independent and combinatorial binding of SFs. Consistent with the extensive cross-regulation among the splicing and transcription factors, the subgroup of kinases within the network had the highest density of predicted phosphorylation sites. The prevalent regulation of the regulatory proteins was further supported by computational analysis of the protein sequences, demonstrating the propensity of these proteins to be highly disordered relative to other proteins in the human proteome. Overall, our systematic study reveals that an organizing principle in the logic of integrated networks favor the regulation of regulatory proteins by the specific regulation they conduct. Based on these results we propose a new regulatory paradigm, postulating that fine-tuned gene expression regulation of the master regulators in the cell is commonly achieved by cross-regulation.
This document describes a proposed method to map neural circuits in the Drosophila olfactory system using chemical control of flp-frt recombination. The researchers plan to fuse the flippase gene to a destabilizing domain, allowing chemical control of flippase activity and recombination through the stabilizing ligand trimethoprim. This would enable sparse labeling of individual neurons using a GFP reporter to trace their projections, avoiding issues with current heat shock methods. The proposed method involves cloning a UAS-flp-DD construct, transfecting Drosophila, and predicting the system would allow mapping neuronal projections by varying ligand levels to control the number of labeled neurons.
Sex determination in fruit flies is controlled through alternative splicing of pre-mRNAs. The sex lethal (Sxl) protein determines whether splicing produces functional proteins that develop the fly as male or female. In females, Sxl allows splicing that produces functional transformer (Tra) and doublesex (Dsx) proteins, directing female development. In males without Sxl, Tra and Dsx are spliced to nonfunctional forms, resulting in male development. This mechanism involves different promoters, exon skipping, and alternative splice site selection to ultimately generate either male or female flies through their gene expression patterns.
1. The document presents research on transcription factor regulation during mammalian hibernation using the thirteen-lined ground squirrel as a model. It analyzes the ChREBP, Ets, and Rb-E2F pathways under euthermic and hibernating conditions.
2. Results show reduced levels of ChREBP and Ets1 proteins and increased phosphorylation during hibernation. Downstream genes like FASN also decrease.
3. The Rb-E2F pathway is suppressed during hibernation as shown by increased levels of silencing proteins like HDACs and SUV39H1, along with decreased E2F1 and increased Rb. This suggests widespread transcriptional
The document summarizes the history and development of PCR technology. It describes key events like the concept of PCR being presented in 1984, the first PCR device called Mr. Cycle in 1985, the isolation of Taq polymerase in 1985 which enabled PCR without manual addition of reagents, and the licensing of PCR by Roche in 1991 for commercial use. It also provides details on the basic components and process of PCR.
This document discusses the process of translation and protein synthesis. It covers topics like the genetic codon, tRNA, amino acid activation, and the roles of the ribosome. It also discusses inhibitors of protein and RNA synthesis that can act on prokaryotes, both prokaryotes and eukaryotes, or just eukaryotes. Finally, it briefly touches on protein folding, molecular chaperones, protein quality control, and triggering sister chromatid separation. The document is authored by Qurat-ul-Ain, who has a Ph.D. in molecular biology and genetics.
This document discusses apoptosis analysis tools from Enzo Life Sciences. It describes their products for monitoring the intrinsic and extrinsic apoptosis pathways from the cell membrane to the nucleus. Their product lines include modulators and screening assays, immunoassays and antibodies, and live cell analysis tools for detecting hallmarks of apoptosis like phosphatidylserine exposure, chromatin condensation, DNA damage, and caspase activation. The document provides examples of specific products for analyzing apoptotic pathways.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
This document provides information about Nanosyn, a contract research organization that offers various drug discovery services including high throughput screening, assay development, and medicinal chemistry services. It describes Nanosyn's microfluidic-based detection technology which allows simultaneous detection of enzyme substrates and products in a single sample run. This provides accurate and reproducible results. The technology also tolerates autofluorescent compounds and enables identification of both inhibitors and activators.
The document is a reference guide for pathway maps and related QIAGEN products. It includes a table of contents listing over 40 signaling pathways. For each pathway, it lists related RT2 Profiler PCR Arrays and Cignal Reporter Assay Kits from QIAGEN that can be used to study gene expression and transcription factor activity for that pathway. It also provides brief descriptions of the PCR array and reporter assay products and directs readers to QIAGEN websites for more information.
This document discusses several genes related to stem cell pluripotency, including OCT4, SOX2, NANOG, and LIN28. It provides information on the functions of these genes obtained from searches of PubMed, NCBI Gene, and other bioinformatics databases. Details include OCT4's role in maintaining pluripotency, SOX2's interaction with OCT4 and DNA binding structure, alignments of NANOG mRNA and protein sequences between human and mouse, and conserved domains identified in human and mouse LIN28 proteins through BLAST and CDD searches.
Fruit breedomics workshop wp6 from marker assisted breeding to genomics assis...fruitbreedomics
The document discusses strategies for genotyping using single nucleotide polymorphisms (SNPs). It describes different types of molecular markers that have been used over time, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs), amplified fragment length polymorphisms (AFLPs) and SNPs. It also provides details on different SNP genotyping techniques ranging from low to high throughput, such as gel electrophoresis, fluorescent PCR, mass spectrometry and various array-based methods. The document outlines the process of developing a high density 480K SNP array for apple, including SNP discovery by resequencing accessions and filtering SNPs for the array design.
Next Generation Sequencing & Transcriptome AnalysisBastian Greshake
This document discusses next generation sequencing methods like 454 sequencing, Illumina sequencing, and SOLiD sequencing. It then describes how the large amounts of sequencing data generated can be used for transcriptome analysis to study gene expression, identify new genes, and analyze non-model organisms. Finally, it outlines some of the common bioinformatics tools used for assembling sequencing reads, detecting SNPs, finding homologous genes, identifying open reading frames, and annotating genes.
This document contains information about molecular biology techniques including DNA replication, restriction enzyme digestion of DNA, agarose gel electrophoresis, polymerase chain reaction, DNA sequencing, and cloning of recombinant DNA. It includes diagrams of these processes and concepts such as restriction sites, sticky and blunt ends, plasmids, cloning vectors, and the production of recombinant organisms through transformation. The document also discusses gene regulation examples including operons, transcription factors, epigenetics, and RNA interference.
This presentation summarizes research on characterizing RNA aptamers that recognize Regnase-1. It discusses how aptamers were selected through SELEX to bind Regnase-1 with high affinity. Structural modeling and docking simulations were performed to analyze the tertiary structures of Regnase-1 and identified aptamers, as well as their interactions. The results provide insight into how Regnase-1 regulates immune responses through mRNA decay mediated by aptamer binding.
This document summarizes the sequencing and analysis of the Monascus pilosus genome. Key points include:
- The genome was sequenced using a whole genome shotgun strategy combining EST, BAC/fosmid, and plasmid libraries. The draft assembly resulted in 15.2 Mb arranged in 5 scaffolds.
- A total of 8,887 ESTs were generated and assembled into 4,168 contigs and 2,719 singletons, representing 4,015 tentative unigenes. Highly expressed genes included heat shock proteins and elongation factors.
- Genome analysis identified 9,997 predicted genes, 513 genes undergoing alternative splicing, and gene clusters involved in lovastatin and polyketide biosynthesis. The genome provides
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PARP-1 inhibitors have shown promise in oncology by potentiating the effects of DNA damaging chemotherapy agents. Cephalon identified a pyrrolocarbazole hit that inhibited PARP-1 but had poor properties. Through structure-based design and SAR studies, they developed CEP-8983, a potent PARP inhibitor. A prodrug, CEP-9722, was synthesized to improve solubility and pharmacokinetics. In preclinical studies, CEP-8983 and its active metabolite CEP-9397 potentiated the effects of temozolomide in tumor cell lines. CEP-9722 advanced to Phase 1 and 2 clinical trials for evaluation as monotherapy and
Reporter assay and q pcr application 2012Elsa von Licy
This document summarizes a presentation on high-performance cell-based assay and qPCR technologies for pathway-focused research. The presentation overview discusses QIAGEN's SABiosciences portfolio, PCR arrays, Cignal and Cignal Lenti pathway reporters, and provides a summary. PCR arrays allow analysis of mRNA expression of up to 84 genes related to biological pathways in a single experiment. Cignal reporter assays use dual-luciferase reporters to study 45 signal transduction pathways. Cignal Lenti reporters use lentiviral delivery of luciferase or GFP reporters to study pathways in difficult to transfect cells like stem cells or primary cells.
This document summarizes Shivendra Kumar's class presentation on SNP genotyping using KASP. It introduces SNP genotyping and the KASP platform. It describes using KASP to genotype a wheat mapping population derived from a cross between an introgression line containing stripe rust resistance genes and a susceptible cultivar. KASP markers were developed and used to map the resistance genes. One candidate resistance gene was identified and further analyzed through expression studies and development of a linked KASP marker. Recombinants were identified and confirmed through additional KASP genotyping.
This document discusses genome resequencing for SNP discovery and genotyping. It describes what SNPs are, their effects, how many exist in the human genome, and the key steps for SNP discovery including sequencing, validation, screening, and mapping. Methods for SNP discovery discussed include Sanger sequencing, Roche 454 sequencing, Illumina sequencing, and Applied Biosystems SOLiD sequencing.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
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
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 skills
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
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Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
5. Progettazione dei primers ALLINEAMENTO
CON Primer-
BLAST
I parametri di temperatura e
lunghezza dei primers voluti sono
stati impostati nel tool «Primer
Blast» e si è proceduto con
l’allineamento della seq. NM_003037
6. SCELTA DELLA
COPPIA DI
PRIMER
Una coppia di primer con
almeno una giunzione
esone -esone
nell’amplicone è stata
scelta e la sue
caratteristiche sono state
riportate nel file Word.
La coppia scelta è la n°1.
Le loro posizioni sono
state riportate sulla
sequenza nel file Word.
7. Analisi di una sequenza: caratteristiche
fisico-chimiche - ProtParam
La seq proteica è stata
recuperata in formato FASTA
e inserita nel database
ProtParam.
Number of amino acids: 335
Molecular weight: 37230.9
Theoretical pI: 8.70
Ext. coefficient 43235Abs 0.1% (=1
g/l) 1.161, assuming all pairs of Cys
residues form cystines
Ext. coefficient 42860Abs 0.1% (=1
g/l) 1.151, assuming all Cys residues
are reduced
Instability index: 46.72; this
classifies the protein as unstable.
Aliphatic index: 91.61
Grand average of hydropathicity
(GRAVY): -0.202
COMPOSIZIONE
IN AA
vs
FREQUENZA
NORMALIZZATA
DEGLI AA
Ala (A) 15 4.5%
Arg (R) 13 3.9%
Asn (N) 17 5.1%
Asp (D) 9 2.7%
Cys (C) 7 2.1%
Gln (Q) 14 4.2%
Glu (E) 20 6.0%
Gly (G) 21 6.3%
His (H) 6 1.8%
Ile (I) 18 5.4%
Leu (L) 39 11.6%
Lys (K) 21 6.3%
Met (M) 8 2.4%
Phe (F) 7 2.1%
Pro (P) 22 6.6%
Ser (S) 29 8.7%
Thr (T) 27 8.1%
Trp (W) 4 1.2%
Tyr (Y) 14 4.2%
Val (V) 24 7.2%
Pyl (O) 0 0.0%
Sec (U) 0 0.0%
= frequenza
< di 3% rispetto alla
frequenza normalizzata
= frequenza
> di 3% rispetto alla
frequenza normalizzata
Amino acid composition
8,7%
8,5%
8. Ricerche ed analisi usando pattern e
profili: ProSite
1 hit (by 1 profile)
on 1 sequence
Nessun pattern
Un ponte disolfuro
INPUT: seq.
proteica
DATABASE:
patten/profili
9. Ricerche ed analisi usando pattern e
profili: rps - BLAST INPUT: seq.
proteica
DATABASE:
profili PSSM
10. Ricerche ed analisi usando pattern e
profili: InterPro APPLICAZIONE
DEI PHMM
Detailed signature
matches
Signaling lymphocytic
activation molecule, N-
terminal
Immunoglobulin-like
domain
Unintegrated signatures
Lo stesso risultato di
Pfam/rps-BLAST
11. Informazioni della ricerca di
pattern/profili
SLAM superfamily (rps-BLAST)
Signaling lymphocytic activation molecule, N-terminal
(ProSite)
Immunoglobulin-like domain (ProSite, Interpro)
Disulfide bond (ProSite)
INFORMAZIONI
INTEGRATE
NELLA
SEQUENZA
PROTEICA
12. Predizione della localizzazione delle
proteine: Psort PREDIZIONE
DEI SITI DI
LOCALIZZAZIO
NE DELLA
PROTEINA
NELLA CELLULA
Position of the most N-terminal TMS: 5 at i=2
INTEGRAL Likelihood =-12.37 Transmembrane 242 - 258 ( 237 - 264)
INTEGRAL Likelihood = -4.78 Transmembrane 5 - 21 ( 3 - 23)
Type IIIa or IIIb is favored for ER memb. proteins Memb.protein
with uncleavable signl is often at ER
KDEL Count: 0
apolar signal for intramitochondrial sorting (Gavel position 53) from:
5 to: 21
Type III proteins may be localized at Golgi
13. Predizione della localizzazione delle
proteine: SignalIP PREDIZIONE SITI
DI CLIVAGGIO E
EVENTUALE
PRESENZA DI
PEPTIDI
SEGNALE
C-score= raw-cleavage site score
S-score= signal peptide score
Y-score = combined cleavage site score
15. Predizione della localizzazione
delle proteine INFORMAZIONI
INTEGRATE
NELLA
SEQUENZA
PROTEICA
= dominio transmembrana Psort
= dominio transmembrana Psort + TMHMM
= sito di clivaggio SignalIP
= dominio transmembrana TMHMM
16. Parametri:
Expected Threshold: 0,001
Word size: 3
Ricerca per confronto di
sequenze: BLASTP INPUT: seq.
proteica
DATABASE:
RefseqPrimo risultato salvato in html
Taxonomy reports specie in
cui trovo la mia proteina:
primati,
conigli & lepri,
roditori,
balene & delfini,
ungulati,
carnivori,
pipistrelli,
placentati
7 sequenze simili
in uomo
17. Seconda ricerca BLASTP
Le sequenze sono state riportate nel file word e rese più leggibili
INPUT: seq.
proteica
DATABASE:
Refseq
18. Analisi filogenetica - MEGA5
ALLINEAMENTO
MULTIPLO TRA
SEQ RECUPERATE
E SEQ DI
INTERESSE
19. OUTPUT ALBERO
BOOTSTRAP
CONSENSO –
MEGA5
Albero consenso
Myseq Prim signalinglymphocyticactivationmoleculeprecursor Homosapiens NP 003028.1
Prim signalinglymphocyticactivationmoleculeprecursor Homosapiens NP 003028.1
Prim signalinglymphocyticactivationmolecule Gorillagorilla XP 004027768.1
Prim signalinglymphocyticactivationmolecule Macacamulatta XP 001117605.1
Prim signalinglymphocyticactivationmoleculeisoformX1 Homosapiens XP 005245513.1
Prim signalinglymphocyticactivationmoleculeisoformX3 Homosapiens XP 011508207.1
Mamm signalinglymphocyticactivationmolecule Vicugnapacos XP 015104492.1
Mamm signalinglymphocyticactivationmoleculeprecursor Canislupusfamiliaris NP 001003084.1
Mamm signalinglymphocyticactivationmoleculeprecursor Feliscatus NP 001265755.1
Mamm signalinglymphocyticactivationmoleculeprecursor Rattus norvegicus NP 001102548.1
Mamm signalinglymphocyticactivationmoleculeisoformX2 Mus musculus XP 006496936.1
Mamm signalinglymphocyticactivationmoleculeprecursor Mus musculus NP 038758.2
Mamm signalinglymphocyticactivationmoleculeisoformX1 Mus musculus XP 006496935.1
Ucc signalinglymphocyticactivationmolecule Gallus gallus XP 423077.3
Ucc naturalkillercellreceptor2B4isoformX13 Gallusgallus XP 003643429.2
Ucc naturalkillercellreceptor2B4isoformX10 Gallusgallus XP 015153958.1
Ucc naturalkillercellreceptor2B4isoformX9 Gallusgallus XP 015153957.1
Ucc naturalkillercellreceptor2B4isoformX12 Gallusgallus XP 004950235.2
Ucc naturalkillercellreceptor2B4isoformX8 Gallusgallus XP 015153956.1
Ucc naturalkillercellreceptor2B4isoformX4 Gallusgallus XP 004950229.2
Ucc naturalkillercellreceptor2B4isoformX6 Gallusgallus XP 015153954.1
Ucc naturalkillercellreceptor2B4isoformX1 Gallusgallus XP 015153951.1
Ucc naturalkillercellreceptor2B4isoformX7 Gallusgallus XP 015153955.1
Ucc naturalkillercellreceptor2B4isoformX3 Gallusgallus XP 015153952.1
20. Albero originale OUTPUT ALBERO
ORIGINALE –
MEGA5
Myseq Prim signalinglymphocyticactivationmoleculeprecursor Homosapiens NP 003028.1
Prim signalinglymphocyticactivationmoleculeprecursor Homosapiens NP 003028.1
Prim signalinglymphocyticactivationmolecule Gorillagorilla XP 004027768.1
Prim signalinglymphocyticactivationmolecule Macacamulatta XP 001117605.1
Prim signalinglymphocyticactivationmoleculeisoformX1 Homosapiens XP 005245513.1
Prim signalinglymphocyticactivationmoleculeisoformX3 Homosapiens XP 011508207.1
Mamm signalinglymphocyticactivationmolecule Vicugnapacos XP 015104492.1
Mamm signalinglymphocyticactivationmoleculeprecursor Canislupusfamiliaris NP 001003084.1
Mamm signalinglymphocyticactivationmoleculeprecursor Feliscatus NP 001265755.1
Mamm signalinglymphocyticactivationmoleculeprecursor Rattus norvegicus NP 001102548.1
Mamm signalinglymphocyticactivationmoleculeprecursor Mus musculus NP 038758.2
Mamm signalinglymphocyticactivationmoleculeisoformX1 Mus musculus XP 006496935.1
Mamm signalinglymphocyticactivationmoleculeisoformX2 Mus musculus XP 006496936.1
Ucc signalinglymphocyticactivationmolecule Gallus gallus XP 423077.3
Ucc naturalkillercellreceptor2B4isoformX13 Gallusgallus XP 003643429.2
Ucc naturalkillercellreceptor2B4isoformX10 Gallusgallus XP 015153958.1
Ucc naturalkillercellreceptor2B4isoformX9 Gallusgallus XP 015153957.1
Ucc naturalkillercellreceptor2B4isoformX12 Gallusgallus XP 004950235.2
Ucc naturalkillercellreceptor2B4isoformX8 Gallusgallus XP 015153956.1
Ucc naturalkillercellreceptor2B4isoformX4 Gallusgallus XP 004950229.2
Ucc naturalkillercellreceptor2B4isoformX6 Gallusgallus XP 015153954.1
Ucc naturalkillercellreceptor2B4isoformX1 Gallusgallus XP 015153951.1
Ucc naturalkillercellreceptor2B4isoformX7 Gallusgallus XP 015153955.1
Ucc naturalkillercellreceptor2B4isoformX3 Gallusgallus XP 015153952.1
21. OUTPUT ALBERO
BOOTSTRAP
CONSENSO –
MEGA5
SENZA
RIPETIZIONE
Myseq Prim signalinglymphocyticactivationmoleculeprecursor Homosapiens NP 003028.1
Mamm signalinglymphocyticactivationmoleculeprecursor Feliscatus NP 001265755.1
Prim signalinglymphocyticactivationmoleculeisoformX3 Homosapiens XP 011508207.1
Ucc naturalkillercellreceptor2B4isoformX12 Gallusgallus XP 004950235.2
Ucc naturalkillercellreceptor2B4isoformX13 Gallusgallus XP 003643429.2
Mamm signalinglymphocyticactivationmoleculeisoformX1 Mus musculus XP 006496935.1
Ucc signalinglymphocyticactivationmolecule Gallus gallus XP 423077.3
Ucc naturalkillercellreceptor2B4isoformX4 Gallusgallus XP 004950229.2
Ucc naturalkillercellreceptor2B4isoformX7 Gallusgallus XP 015153955.1
Ucc naturalkillercellreceptor2B4isoformX1 Gallusgallus XP 015153951.1
27. = dominio di transmembrana+sito di clivaggio
OUTPUT DI
MAST
(MEME) DA
FILE html
I motivi 2+5+6 sono presenti solo nel cluster Gallus gallus
Il motivo 1 è presente in tutte le sequenze, tranne nelle sequenze di Homo Sapiens
(la sequenza 7 e la 8) e in una di Gallus gallus, la sequenza 10
I motivi 3 e 4 sono condivisi da tutte le sequenze.
All’interno del dominio 4 nella mia sequenza proteica, si riconosce il dominio
transmembrana recuperato dalle informazioni fornitemi da TMHMM e PSort
1
2
3
4
5
6
7
8
9
10
30. Interpretazione funzionale di
dati derivanti da esperimenti
di microarray
J Clin Invest. 2016 Jan;126(1):181-94. doi: 10.1172/JCI83013. Epub 2015 Nov 30.
SLAMF1 regulation of chemotaxis and autophagy determines CLL patient response.
Bologna C, Buonincontri R, Serra S, Vaisitti T, Audrito V, Brusa D, Pagnani A, Coscia M, D'Arena G, Mereu
E, Piva R, Furman RR, Rossi D, Gaidano G,Terhorst C, Deaglio S.
Abstract
Chronic lymphocytic leukemia (CLL) is a variable disease; therefore, markers to identify aggressive forms
are essential for patient management. Here, we have shown that expression of the costimulatory molecule
and microbial sensor SLAMF1 (also known as CD150) is lost in a subset of patients with an aggressive CLL
that associates with a shorter time to first treatment and reduced overall survival. SLAMF1 silencing in CLL-
like Mec-1 cells, which constitutively express SLAMF1, modulated pathways related to cell migration,
cytoskeletal organization, and intracellular vesicle formation and recirculation. SLAMF1 deficiency
associated with increased expression of CXCR4, CD38, and CD44, thereby positively affecting chemotactic
responses to CXCL12. SLAMF1 ligation with an agonistic monoclonal antibody increased ROS
accumulation and induced phosphorylation of p38, JNK1/2, and BCL2, thereby promoting the autophagic
flux. Beclin1 dissociated from BCL2 in response to SLAMF1 ligation, resulting in formation of the
autophagy macrocomplex, which contains SLAMF1, beclin1, and the enzyme VPS34. Accordingly,
SLAMF1-silenced cells or SLAMF1(lo) primary CLL cells were resistant to autophagy-activating
therapeutic agents, such as fludarabine and the BCL2 homology domain 3 mimetic ABT-737. Together, these
results indicate that loss of SLAMF1 expression in CLL modulates genetic pathways that regulate
chemotaxis and autophagy and that potentially affect drug responses, and suggest that these effects underlie
unfavorable clinical outcome experienced by SLAMF1(lo) patients.
RIPORTARE
DUE
ABSTRACT
31. Biochemistry (Mosc). 2014 Dec;79(12):1405-11. doi: 10.1134/S0006297914120165.
Upstream open reading frames regulate translation of the long isoform of SLAMF1
mRNA that encodes costimulatory receptor CD150.
Putlyaeva LV1, Schwartz AM, Korneev KV, Covic M, Uroshlev LA, Makeev VY, Dmitriev
SE, Kuprash DV.
Abstract
More than 40% of human genes contain upstream open reading frames (uORF) in their 5'-
untranslated regions (5'-UTRs) and at the same time express at least one truncated mRNA
isoform containing no uORF. We studied translational regulation by four uORFs found in the
5'-UTR of full-length mRNA for SLAMF1, the gene encoding CD150 membrane protein.
CD150 is a member of the CD2 superfamily, a costimulatory lymphocyte receptor, a receptor
for measles virus, and a microbial sensor on macrophages. The SLAMF1 gene produces at least
two mRNA isoforms that differ in their 5'-UTRs. In the long isoform of the SLAMF1 mRNA
that harbors four uORFs in the 5'-UTR, the stop codon of uORF4 overlaps with the AUG codon
of the main ORF forming a potential termination-reinitiation site UGAUG, while uORF2 and
uORF3 start codons flank a sequence identical to Motif 1 from the TURBS regulatory element.
TURBS was shown to be required for a coupled termination-reinitiation event during
translation of polycistronic RNAs of some viruses. In a model cell system, reporter mRNA
based on the 5'-UTR of SLAMF1 short isoform, which lacks any uORF, is translated 5-6 times
more efficiently than the mRNA with 5'-UTR from the long isoform. Nucleotide substitutions
disrupting start codons in either uORF2-4 result in significant increase in translation efficiency,
while substitution of two nucleotides in TURBS Motif 1 leads to a 2-fold decrease in activity.
These data suggest that TURBS-like elements can serve for translation control of certain
cellular mRNAs containing uORFs.
PMID: 25716736 DOI: 10.1134/S0006297914120165
RIPORTARE
DUE
ABSTRACT
32. Utilizzo di String 9.1
RICERCA DI
INTERAZIONI
FRA PROTEINE
NOTE E
PREDETTE
33. Controllo sul foglio <<gene list up-dn>>. Il gene SLAMF1 è DOWN
REGOLATO.
Collegamento: link all’esperimento (geni down):
http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetN
ame=GSE13411_NAIVE_VS_IGM_MEMORY_BCELL_UP
Resting human memory B cells are intrinsically programmed for enhanced survival and
responsiveness to diverse stimuli compared to naive B cells.
Good KL1, Avery DT, Tangye SG.
Abstract
Enhanced secondary Ab responses are a vital component of adaptive immunity, yet little is
understood about the intrinsic and extrinsic regulators of naive and memory B cells that result in
differences in their responses to Ag. Microarray analysis, together with surface and intracellular
phenotyping, revealed that memory B cells have increased expression of members of the TNF
receptor, SLAM (signaling lymphocytic activation molecule), B7, and Bcl2 families, as well as the
TLR-related molecule CD180 (RP105). Accordingly, memory B cells exhibited enhanced survival,
proliferation, and Ig secretion, and they entered division more rapidly than did naive B cells in
response to both T cell-dependent and T cell-independent stimuli. Furthermore, both IgM and
isotype-switched memory B cells, but not naive B cells, costimulated CD4+ T cells in vitro
through a mechanism dependent on their constitutive expression of CD80 and CD86. This study
demonstrates that up-regulation of genes involved in activation, costimulation, and survival
provides memory B cells with a unique ability to produce enhanced immune responses and
contributes to the maintenance of the memory B cell pool.
RECUPERO
DELL’ABSTRACT
DA GENE
EXPRESSION
OMNIBUS [ DA
GSEA]
35. Tools di Enrichment Analysis:
KEGG Analysis
Wikipathways Analysis
Drug association Analysis
Analisi funzionale dei risultati di
microarray - Webgesalt
La mia proteina non è presente né in
KEGG, né in Wikipathway Scelta dei
pathway più significativi
WEBGESALT
CLASSE I
43. Lista dei geni dei termini /
pathway di DAVID in cui è
presente il mio termine
KLF6
BAK1
PKNOX1
FYN
BCL6
LIG4
SLAMF1
LTB
SYK
Analisi funzionale dei risultati di
microarray – STRING 9.1 multiple
names RICERCA DI
INTERAZIONI
FRA PROTEINE
CON UNA LISTA
SELEZIONATA
44. SLAMF1 è un membro della famiglia delle molecole attivanti i segnali dei linfociti. E’
un componente della CD2 superfamily,un recettore linfocitico costimulatorio, un
recettore per il virus del morbillo e un sensore microbico sulla superficie dei
macrofagi.
È presente in due isoforme, di cui una troncata(differiscono nel loro 5’ UTR).
Dimostra un’alta affinità nel self-ligand, importante nella stimolazione bidirezionale
tra cellule T e cellule B.
Il profilo di espressione genica di SLAMF1 è molto diverso tra cellule immunitarie
(PCs, naϊve e cellule di memoria) Ciò è probabilmente dovuto ad un cambiamento
nella fisiologia; inoltre ha un ruolo nella differenziazione e nella funzione delle cellule
durante la risposta immunitaria all’antigene. A questo proposito, SLAM1 è collegato ai
pathways di signaling dei Toll- like receptor e delle Chemochine
E’ associato a diversi fattori di trascrizione, tra cui anche stimolatori linfoidi (anche
collegati all’insorgenza di linfomi)
La down-regolazione di SLAMF1 è fisiologica nelle cellule di memoria (che up-
regolano geni per una veloce divisione cellulare), ma può essere anche patologica,
poichè strettamente collegata all’insorgenza di leucemie [Chronic lymphocytic
leukemia (CLL)]
CONCLUSIONI
CONCLUSIONI
BASATE SU:
-ABSTRACT
-ENRICHMENT
ANALYSIS
-NETWORK