I. Maxadilan insertion into GALV and KoRV-B env generally reduced infectivity, except when inserted after the signal peptide with Linker2 sequences, which allowed infection through native receptors.
II. No Maxadilan constructs could infect via PAC1 receptors alone, suggesting a fusion block.
III. In cells expressing both native and PAC1 receptors, Maxadilan env constructs showed lower titers, indicating interaction with PAC1 is deleterious to infectivity, likely by blocking fusion.
The NFkB pathway was identified as important for high CCL2 expression in the glioma cell line U105MG. Using a transcription factor siRNA array to knock down 42 transcription factors, RELA (a subunit of NFkB) was found to significantly lower CCL2 expression levels. Knocking down RELA also enhanced the effect of BCNU (carmustine) treatment, indicating that targeting the NFkB pathway may help sensitize tumor cells to chemotherapy in glioma.
Chemically ligated gRNAs for CRISPR applications.Minghong Zhong
lgRNA (Chemically ligated gRNA) is designed to improve the functions and selectivity of gRNA, particularly its efficacy, less off-target effect and stability, and the cost-effectiveness in its industrial production.
lgRNAs are very useful for therapeutic and biotechnological applications of CRISPR, particularly for multiplexing and genome scale screening with its convenience for constructing evenly distributed gRNA libraries, by bypassing carcinogenesis and immunogenicity, limits in packaging capacities, random integration into host genomes, and the complicacy and tissue infection tropisms of viral vectors and plasmids.
Rin-like (Rinl) is a novel member of the RIN family of proteins that serve as guanine nucleotide exchange factors (GEFs) for Rab GTPases. Rinl preferentially binds and catalyzes GDP/GTP exchange on Rab5a and Rab22, implicating it in endocytic processes regulated by these Rab proteins. Rinl localizes to neuromuscular synapses and interacts with the receptor tyrosine kinase MuSK, a key regulator of neuromuscular synapse development. Overexpression of Rinl affects both fluid-phase and EGFR receptor-mediated endocytosis. Rinl is closely associated with the actin cytoskeleton and thus may recruit Rab5
The document summarizes a thesis defense presentation on the role of focal adhesion kinase (FAK) in vascular smooth muscle cell (SMC) migration. The results showed that FAK mediates SMC migration toward platelet-derived growth factor (PDGF) by regulating cell polarization. FAK depletion attenuated myosin activation without affecting other signaling pathways. The presentation explored how FAK interacts with Dia2 and cortactin to control SMC migration and proposed future studies on these interactions and their signaling regulation.
Will Jackson presented his Master's defense talk on identifying interactions between the transcription factor Lhx2 and other neocortical proteins. He used a yeast two-hybrid screen to identify interacting proteins, finding that Lhx2 interacts with the RNA helicase Ddx50 and exonuclease Eri3. Further experiments showed the LIM domain of Lhx2 is necessary for binding to Eri3. These interactions may regulate transcription and mRNA stability during neocortical development. Future work will aim to clarify the functional roles and pathways of Lhx2 with its interacting partners.
This document reports on a laboratory project investigating the role of the non-coding RNA rli60 in Listeria monocytogenes. The student constructed an rli60 knockout strain of L. monocytogenes and examined gene expression and metabolism compared to the wild type strain when grown in different media. Quantitative PCR results showed that rli60 is involved in down-regulating the ilv operon, which encodes for branched amino acid biosynthesis. Growth curve and luminescence assays indicated normal bacterial growth and hly virulence gene expression in the rli60 mutant strain. In summary, this project found that the non-coding RNA rli60 regulates metabolic gene expression but does not affect growth or a key virulence factor in L. monocytogenes
This document summarizes a study investigating the oncoprotein EVI1 and its regulation of the carbonic anhydrase 3 (CA3) gene. Microarray analysis identified CA3 as a major target of EVI1. The study aims to validate changes in CA3 expression and determine the mechanism and significance of EVI1-mediated transcriptional regulation of CA3. Results show that EVI1 suppresses CA3 expression at both the mRNA and protein levels by decreasing CA3 promoter activity. This suppression of the antioxidant CA3 gene leads to increased caspase activity and apoptosis in cancer cells expressing EVI1.
The NFkB pathway was identified as important for high CCL2 expression in the glioma cell line U105MG. Using a transcription factor siRNA array to knock down 42 transcription factors, RELA (a subunit of NFkB) was found to significantly lower CCL2 expression levels. Knocking down RELA also enhanced the effect of BCNU (carmustine) treatment, indicating that targeting the NFkB pathway may help sensitize tumor cells to chemotherapy in glioma.
Chemically ligated gRNAs for CRISPR applications.Minghong Zhong
lgRNA (Chemically ligated gRNA) is designed to improve the functions and selectivity of gRNA, particularly its efficacy, less off-target effect and stability, and the cost-effectiveness in its industrial production.
lgRNAs are very useful for therapeutic and biotechnological applications of CRISPR, particularly for multiplexing and genome scale screening with its convenience for constructing evenly distributed gRNA libraries, by bypassing carcinogenesis and immunogenicity, limits in packaging capacities, random integration into host genomes, and the complicacy and tissue infection tropisms of viral vectors and plasmids.
Rin-like (Rinl) is a novel member of the RIN family of proteins that serve as guanine nucleotide exchange factors (GEFs) for Rab GTPases. Rinl preferentially binds and catalyzes GDP/GTP exchange on Rab5a and Rab22, implicating it in endocytic processes regulated by these Rab proteins. Rinl localizes to neuromuscular synapses and interacts with the receptor tyrosine kinase MuSK, a key regulator of neuromuscular synapse development. Overexpression of Rinl affects both fluid-phase and EGFR receptor-mediated endocytosis. Rinl is closely associated with the actin cytoskeleton and thus may recruit Rab5
The document summarizes a thesis defense presentation on the role of focal adhesion kinase (FAK) in vascular smooth muscle cell (SMC) migration. The results showed that FAK mediates SMC migration toward platelet-derived growth factor (PDGF) by regulating cell polarization. FAK depletion attenuated myosin activation without affecting other signaling pathways. The presentation explored how FAK interacts with Dia2 and cortactin to control SMC migration and proposed future studies on these interactions and their signaling regulation.
Will Jackson presented his Master's defense talk on identifying interactions between the transcription factor Lhx2 and other neocortical proteins. He used a yeast two-hybrid screen to identify interacting proteins, finding that Lhx2 interacts with the RNA helicase Ddx50 and exonuclease Eri3. Further experiments showed the LIM domain of Lhx2 is necessary for binding to Eri3. These interactions may regulate transcription and mRNA stability during neocortical development. Future work will aim to clarify the functional roles and pathways of Lhx2 with its interacting partners.
This document reports on a laboratory project investigating the role of the non-coding RNA rli60 in Listeria monocytogenes. The student constructed an rli60 knockout strain of L. monocytogenes and examined gene expression and metabolism compared to the wild type strain when grown in different media. Quantitative PCR results showed that rli60 is involved in down-regulating the ilv operon, which encodes for branched amino acid biosynthesis. Growth curve and luminescence assays indicated normal bacterial growth and hly virulence gene expression in the rli60 mutant strain. In summary, this project found that the non-coding RNA rli60 regulates metabolic gene expression but does not affect growth or a key virulence factor in L. monocytogenes
This document summarizes a study investigating the oncoprotein EVI1 and its regulation of the carbonic anhydrase 3 (CA3) gene. Microarray analysis identified CA3 as a major target of EVI1. The study aims to validate changes in CA3 expression and determine the mechanism and significance of EVI1-mediated transcriptional regulation of CA3. Results show that EVI1 suppresses CA3 expression at both the mRNA and protein levels by decreasing CA3 promoter activity. This suppression of the antioxidant CA3 gene leads to increased caspase activity and apoptosis in cancer cells expressing EVI1.
Honors thesis overview: Katie Amberg-JohnsonPhilip Johnson
The document discusses using molecular tweezers to investigate the fracture point of the σ54 core binding domain during transcription initiation. The experiment involves generating DNA handles, attaching them to the purified core binding domain protein, and then using molecular tweezers to apply force and simulate the "tugging" by the activator binding domain. This could reveal if the two subdomains of the core binding domain unfold separately or together under stress.
This document summarizes an RNA project focused on inhibition of Dipeptidyl peptidase-IV (DPP-IV), a treatment for Type 2 Diabetes. Key components included:
1) An Internal Ribosome Entry Site (IRES) to allow translation of multiple protein coding regions. Two IRES sequences from EMCV and NKRF were characterized.
2) A neomycin gene to confer antibiotic resistance for selection.
3) An aptazyme as an RNA "kill switch" activated by theophylline.
4) siRNA targeting the 3' untranslated region of DPP-IV mRNA for cleavage.
5) An RNA-dependent RNA polymerase (
Molecular characterizacion and Functional Analysis of the PilQ 380-706: a No...Anamariagaravito
This document summarizes a study that aimed to characterize and analyze the function of the PilQ380-706 protein from Pseudomonas aeruginosa. The researchers cloned the pilQ380-706 gene into an expression vector and overexpressed the protein in E. coli. They then isolated and refolded the inclusion bodies to purify the recombinant PilQ380-706 protein. Western blot analysis confirmed the protein was biologically active. The study concludes that PilQ380-706 plays an important role in type 4 pili biogenesis in P. aeruginosa and could be a potential candidate for a new vaccine or adjuvant against this pathogen.
Next generation biotherapeutics production system Trichoderma reeseiChristopher Landowski
The project aimed to develop Trichoderma reesei as a cost-effective platform for producing therapeutic proteins like antibodies. Major barriers were protease degradation and incorrect glycosylation. Through protease gene deletions and fermentation optimization, production levels were increased from 50 mg/L to over 7 g/L for antibodies and interferon. Glycoengineering was used to modify T. reesei's glycosylation pathway to produce mammalian-like Man5 and G0 glycoforms important for antibody functionality. Deletions of genes like alg3, pmt1, and additions like Stt3, GlsII, MnsI, GnTI/II altered glycosylation for therapeutic protein production.
This document outlines the development of a pipeline to characterize novel small RNAs discovered in clinical blood samples via next generation sequencing. Eight novel sequences were chosen as a pilot set. The pipeline involves verifying the sequences with qPCR, cloning and sequencing the products, and performing further analysis including transfection with inhibitors to determine functional significance. Two sequences, Cad 3 and Cad 7, were analyzed in more depth through the initial steps to help establish the pipeline. The goal is to ultimately understand the functional roles of these novel small RNAs.
1) The document summarizes research into genetic interactors of the BRCA2 tumor suppressor gene, which is linked to hereditary breast cancer. A retroviral screening identified BRE as a genetic interactor that rescues lethality in BRCA2-deficient cells.
2) Further experiments showed that BRE overexpression in BRCA2-deficient cells leads to increased levels of the Cdc25A cell cycle regulator after DNA damage, preventing cell cycle arrest.
3) BRE was found to interact with the transcription factor ATF3 and induce transcription of Cdc25A. Reporter assays aim to identify the role of ATF3 binding sites on the Cdc25A promoter in regulating its transcription
This document summarizes research on NF-kB signaling in cancer, specifically gastric cancer. It describes the background, structure and activation processes of NF-kB. Experiments show that NF-kB1 and RELA are upregulated in gastric cancer cell lines and tumors, and their knockdown inhibits tumor growth in vitro and in vivo. Furthermore, miR-508-3p is identified as a tumor suppressor that directly targets and downregulates NF-kB1 in gastric cancer. Re-expression of NF-kB1 partly reverses the tumor suppressive effects of miR-508-3p overexpression. In conclusion, downregulation of miR-508-3p contributes to canonical NF-kB activation in gastric tumorigenesis.
This document discusses the role of NF-κB in regulating apoptosis. It describes how NF-κB is a transcription factor that regulates the expression of many anti-apoptotic genes. The regulation of NF-κB involves its interaction with the inhibitory protein IκB and transport between the cytoplasm and nucleus. Phosphorylation of IκB leads to its degradation and the release of NF-κB to enter the nucleus and activate gene transcription. This tight regulation of NF-κB activity and localization determines whether a cell survives or undergoes apoptosis.
Signal transduction in plant defense responsesVINOD BARPA
Signal transduction a Process by which a cell converts one kind of signal into another. Plant disease resistance and susceptibility are gov¬erned by the combined genotypes of host and pathogen and depend on a complex exchange of signals and responses occurring under given environmental con¬ditions. During the long process of host-pathogen co-evolution, plants have developed various elaborate mechanisms to ward off pathogen attack. Whereas some of these defense mechanisms are preformed and provide physical and chemical barriers to hinder pathogen infection, others are induced only after pa¬thogen attack. Similar to animal immune responses, induced plant defense responses involve a network of signal transduction and the rapid activation of gene expression following pathogen infection. They do not have immune system and locomotary organs to escape environmental challenges and biotic stresses. In plant, nature has provided them some preformed and inducible defense resistance. Host recognition of invading pathogen is often determined by the so called “gene for gene” interaction between avirulence (avr) gene of pathogen and corresponding resistance (R) gene of host (Flor, 1971) which encode receptor for the recognition of specific elicitor or ligand encoded directly or indirectly by pathogen avr gene. Recent studies have revealed intriguing parallels between animal and plant defense responses as demonstrated by the structural and functional conservation of some of their signal transduction processes. Furthermore, signaling components such as G proteins, NADPH oxidase, H202, salicylic acid (SA, and aspirin), mitogen-activated protein kinases (MAPK), and transcription factors have been shown to be associated with or participate in both animal and plant defense responses, suggesting the presence of con¬served signaling pathways for host defenses in diverse higher eukaryotes.
1) When the elongation rate of RNA polymerase II is decreased via a mutation in the Rpb2 subunit, levels of the histone methyltransferase Set2 and methylation of histone H3 at lysine 36 (H3K36) both increase.
2) Genetic interactions between set2 and other genes change depending on whether the wild type or mutant form of Rpb2 is present.
3) Deletion of the SRI domain of Set2, but not mutations affecting its catalytic activity, is necessary for the synthetic sick growth phenotype seen when set2 is deleted in the Rpb2 mutant strain. This provides a novel view of Set2's functions.
Recombinant Fab fragments specific for the pfHRPII and pfHSP72 : implications for malaria diagnosis - Parole de junior de la 7e édition du Cours international « Atelier Paludisme » - Ravaoarisoa Elisabeth - Madagascar - elisa@pasteur.mg
By constructing a plasmid containing flanking sequences of the adenylate cyclase gene and a tryptophan marker gene, researchers aim to knockout the adenylate cyclase gene in Schizophyllum commune via homologous recombination. The plasmid would replace the adenylate cyclase sequence with the tryptophan gene in the genome, allowing only cells without adenylate cyclase to grow in media lacking tryptophan. Using a ku80 knockout strain of S. commune increases the likelihood of homologous recombination during transformation. Primers and restriction enzymes were used to amplify flanking sequences and insert them into a vector plasmid to ultimately construct the adenylate cyclase knockout plasmid.
TransVax, a therapeutic DNA vaccine targeting cytomegalovirus (CMV), showed promising results in a Phase 2 trial involving 80 hematopoietic cell transplant recipients. The vaccine significantly reduced CMV reactivation rates, increased the time to initial viral reactivation, and decreased the duration of viremia compared to placebo. No significant safety concerns were observed. The trial provides evidence that TransVax can control CMV reactivation in high-risk transplant patients in a manner superior to preemptive antiviral therapy alone.
Los días 20 y 21 de octubre de 2016, la Fundacion Ramón Areces organizó un simposio internacional para analizar las 'Enfermedades raras de la piel: de la clínica al gen y viceversa'. El doctor Fernando Larcher Laguzzi, del CIEMAT-Universidad Carlos III de Madrid-IIS Fundación Jiménez Díaz, ejerció de coordinador.
1) The study found that deletion of the protein cIAP1 in mice alters actin cytoskeleton organization, preventing the formation of filopodia in response to TNF.
2) cIAP1 was shown to directly interact with and regulate the activity of the small GTPase cdc42, which controls filopodia formation. Specifically, cIAP1 promotes the stabilization of cdc42 by facilitating its interaction with RhoGDIa in the cytosol.
3) TNF stimulation disrupts the interaction between cIAP1 and cdc42, allowing cdc42-mediated rearrangement of the actin cytoskeleton and formation of filopodia independently of NF-kB activation
ReedWoyda_Introducing Green Fluorescence Into Homo sapiens And Escherichia Co...Reed Woyda
This study aimed to introduce the green fluorescent protein (GFP) gene into E. coli and human cells. GFP was successfully inserted into E. coli and shown to be expressed under control of the L-arabinose promoter. Addition of restriction sites to GFP was also successful, allowing for digestion of the GFP and pcDNA plasmid. However, ligation of the digested GFP fragment into pcDNA was unsuccessful, likely due to nuclease contamination. Expression of GFP in human cells could not be verified due to a technical error during immunoblotting. While some goals were achieved, such as GFP expression in E. coli, further optimization is needed to fully introduce GFP into human cells via this methodology.
A Novel Sheeppox virus vectored vaccine for Foot-and-Mouth-Disease was developed from scratch. The vaccine was tested in Sheep and found to elicit strong Antibody and Cell mediated Immune response when used in a prime boost regimen with Protein and DNA vaccines.
The document provides instructions for using Gateway cloning technology to construct entry clones and expression clones for protein expression. Key steps include:
1. Constructing entry clones containing the gene of interest using restriction digestion/ligation or BP recombination.
2. Choosing a destination vector for protein expression in E. coli, mammalian cells, or baculovirus based on desired tags and expression system.
3. Transferring the gene of interest from the entry clone to the destination vector using LR recombination to generate an expression clone for protein production.
pBluescript is an example of a combination between plasmids and phages (phagemids).
Phagemids represent a hybrid type of class of vectors that serve to produce single-stranded DNA.
To integrate promoter-GW-lux fragment onto chromosome of E.coliUrja Bhatt
This document describes integrating a promoter-lux fragment onto the chromosome of E. coli to provide more robust results in promoter assays compared to a plasmid. The lux fragment was amplified by PCR and ligated into the destination vector pGRG25. This new plasmid, pGRG25-pDEW201GWlux, was transformed into E. coli. The promoter sequence was then integrated onto the chromosome using Gateway Technology. Promoter activity was tested under different conditions to evaluate strain backgrounds and DNA damage.
Honors thesis overview: Katie Amberg-JohnsonPhilip Johnson
The document discusses using molecular tweezers to investigate the fracture point of the σ54 core binding domain during transcription initiation. The experiment involves generating DNA handles, attaching them to the purified core binding domain protein, and then using molecular tweezers to apply force and simulate the "tugging" by the activator binding domain. This could reveal if the two subdomains of the core binding domain unfold separately or together under stress.
This document summarizes an RNA project focused on inhibition of Dipeptidyl peptidase-IV (DPP-IV), a treatment for Type 2 Diabetes. Key components included:
1) An Internal Ribosome Entry Site (IRES) to allow translation of multiple protein coding regions. Two IRES sequences from EMCV and NKRF were characterized.
2) A neomycin gene to confer antibiotic resistance for selection.
3) An aptazyme as an RNA "kill switch" activated by theophylline.
4) siRNA targeting the 3' untranslated region of DPP-IV mRNA for cleavage.
5) An RNA-dependent RNA polymerase (
Molecular characterizacion and Functional Analysis of the PilQ 380-706: a No...Anamariagaravito
This document summarizes a study that aimed to characterize and analyze the function of the PilQ380-706 protein from Pseudomonas aeruginosa. The researchers cloned the pilQ380-706 gene into an expression vector and overexpressed the protein in E. coli. They then isolated and refolded the inclusion bodies to purify the recombinant PilQ380-706 protein. Western blot analysis confirmed the protein was biologically active. The study concludes that PilQ380-706 plays an important role in type 4 pili biogenesis in P. aeruginosa and could be a potential candidate for a new vaccine or adjuvant against this pathogen.
Next generation biotherapeutics production system Trichoderma reeseiChristopher Landowski
The project aimed to develop Trichoderma reesei as a cost-effective platform for producing therapeutic proteins like antibodies. Major barriers were protease degradation and incorrect glycosylation. Through protease gene deletions and fermentation optimization, production levels were increased from 50 mg/L to over 7 g/L for antibodies and interferon. Glycoengineering was used to modify T. reesei's glycosylation pathway to produce mammalian-like Man5 and G0 glycoforms important for antibody functionality. Deletions of genes like alg3, pmt1, and additions like Stt3, GlsII, MnsI, GnTI/II altered glycosylation for therapeutic protein production.
This document outlines the development of a pipeline to characterize novel small RNAs discovered in clinical blood samples via next generation sequencing. Eight novel sequences were chosen as a pilot set. The pipeline involves verifying the sequences with qPCR, cloning and sequencing the products, and performing further analysis including transfection with inhibitors to determine functional significance. Two sequences, Cad 3 and Cad 7, were analyzed in more depth through the initial steps to help establish the pipeline. The goal is to ultimately understand the functional roles of these novel small RNAs.
1) The document summarizes research into genetic interactors of the BRCA2 tumor suppressor gene, which is linked to hereditary breast cancer. A retroviral screening identified BRE as a genetic interactor that rescues lethality in BRCA2-deficient cells.
2) Further experiments showed that BRE overexpression in BRCA2-deficient cells leads to increased levels of the Cdc25A cell cycle regulator after DNA damage, preventing cell cycle arrest.
3) BRE was found to interact with the transcription factor ATF3 and induce transcription of Cdc25A. Reporter assays aim to identify the role of ATF3 binding sites on the Cdc25A promoter in regulating its transcription
This document summarizes research on NF-kB signaling in cancer, specifically gastric cancer. It describes the background, structure and activation processes of NF-kB. Experiments show that NF-kB1 and RELA are upregulated in gastric cancer cell lines and tumors, and their knockdown inhibits tumor growth in vitro and in vivo. Furthermore, miR-508-3p is identified as a tumor suppressor that directly targets and downregulates NF-kB1 in gastric cancer. Re-expression of NF-kB1 partly reverses the tumor suppressive effects of miR-508-3p overexpression. In conclusion, downregulation of miR-508-3p contributes to canonical NF-kB activation in gastric tumorigenesis.
This document discusses the role of NF-κB in regulating apoptosis. It describes how NF-κB is a transcription factor that regulates the expression of many anti-apoptotic genes. The regulation of NF-κB involves its interaction with the inhibitory protein IκB and transport between the cytoplasm and nucleus. Phosphorylation of IκB leads to its degradation and the release of NF-κB to enter the nucleus and activate gene transcription. This tight regulation of NF-κB activity and localization determines whether a cell survives or undergoes apoptosis.
Signal transduction in plant defense responsesVINOD BARPA
Signal transduction a Process by which a cell converts one kind of signal into another. Plant disease resistance and susceptibility are gov¬erned by the combined genotypes of host and pathogen and depend on a complex exchange of signals and responses occurring under given environmental con¬ditions. During the long process of host-pathogen co-evolution, plants have developed various elaborate mechanisms to ward off pathogen attack. Whereas some of these defense mechanisms are preformed and provide physical and chemical barriers to hinder pathogen infection, others are induced only after pa¬thogen attack. Similar to animal immune responses, induced plant defense responses involve a network of signal transduction and the rapid activation of gene expression following pathogen infection. They do not have immune system and locomotary organs to escape environmental challenges and biotic stresses. In plant, nature has provided them some preformed and inducible defense resistance. Host recognition of invading pathogen is often determined by the so called “gene for gene” interaction between avirulence (avr) gene of pathogen and corresponding resistance (R) gene of host (Flor, 1971) which encode receptor for the recognition of specific elicitor or ligand encoded directly or indirectly by pathogen avr gene. Recent studies have revealed intriguing parallels between animal and plant defense responses as demonstrated by the structural and functional conservation of some of their signal transduction processes. Furthermore, signaling components such as G proteins, NADPH oxidase, H202, salicylic acid (SA, and aspirin), mitogen-activated protein kinases (MAPK), and transcription factors have been shown to be associated with or participate in both animal and plant defense responses, suggesting the presence of con¬served signaling pathways for host defenses in diverse higher eukaryotes.
1) When the elongation rate of RNA polymerase II is decreased via a mutation in the Rpb2 subunit, levels of the histone methyltransferase Set2 and methylation of histone H3 at lysine 36 (H3K36) both increase.
2) Genetic interactions between set2 and other genes change depending on whether the wild type or mutant form of Rpb2 is present.
3) Deletion of the SRI domain of Set2, but not mutations affecting its catalytic activity, is necessary for the synthetic sick growth phenotype seen when set2 is deleted in the Rpb2 mutant strain. This provides a novel view of Set2's functions.
Recombinant Fab fragments specific for the pfHRPII and pfHSP72 : implications for malaria diagnosis - Parole de junior de la 7e édition du Cours international « Atelier Paludisme » - Ravaoarisoa Elisabeth - Madagascar - elisa@pasteur.mg
By constructing a plasmid containing flanking sequences of the adenylate cyclase gene and a tryptophan marker gene, researchers aim to knockout the adenylate cyclase gene in Schizophyllum commune via homologous recombination. The plasmid would replace the adenylate cyclase sequence with the tryptophan gene in the genome, allowing only cells without adenylate cyclase to grow in media lacking tryptophan. Using a ku80 knockout strain of S. commune increases the likelihood of homologous recombination during transformation. Primers and restriction enzymes were used to amplify flanking sequences and insert them into a vector plasmid to ultimately construct the adenylate cyclase knockout plasmid.
TransVax, a therapeutic DNA vaccine targeting cytomegalovirus (CMV), showed promising results in a Phase 2 trial involving 80 hematopoietic cell transplant recipients. The vaccine significantly reduced CMV reactivation rates, increased the time to initial viral reactivation, and decreased the duration of viremia compared to placebo. No significant safety concerns were observed. The trial provides evidence that TransVax can control CMV reactivation in high-risk transplant patients in a manner superior to preemptive antiviral therapy alone.
Los días 20 y 21 de octubre de 2016, la Fundacion Ramón Areces organizó un simposio internacional para analizar las 'Enfermedades raras de la piel: de la clínica al gen y viceversa'. El doctor Fernando Larcher Laguzzi, del CIEMAT-Universidad Carlos III de Madrid-IIS Fundación Jiménez Díaz, ejerció de coordinador.
1) The study found that deletion of the protein cIAP1 in mice alters actin cytoskeleton organization, preventing the formation of filopodia in response to TNF.
2) cIAP1 was shown to directly interact with and regulate the activity of the small GTPase cdc42, which controls filopodia formation. Specifically, cIAP1 promotes the stabilization of cdc42 by facilitating its interaction with RhoGDIa in the cytosol.
3) TNF stimulation disrupts the interaction between cIAP1 and cdc42, allowing cdc42-mediated rearrangement of the actin cytoskeleton and formation of filopodia independently of NF-kB activation
ReedWoyda_Introducing Green Fluorescence Into Homo sapiens And Escherichia Co...Reed Woyda
This study aimed to introduce the green fluorescent protein (GFP) gene into E. coli and human cells. GFP was successfully inserted into E. coli and shown to be expressed under control of the L-arabinose promoter. Addition of restriction sites to GFP was also successful, allowing for digestion of the GFP and pcDNA plasmid. However, ligation of the digested GFP fragment into pcDNA was unsuccessful, likely due to nuclease contamination. Expression of GFP in human cells could not be verified due to a technical error during immunoblotting. While some goals were achieved, such as GFP expression in E. coli, further optimization is needed to fully introduce GFP into human cells via this methodology.
A Novel Sheeppox virus vectored vaccine for Foot-and-Mouth-Disease was developed from scratch. The vaccine was tested in Sheep and found to elicit strong Antibody and Cell mediated Immune response when used in a prime boost regimen with Protein and DNA vaccines.
The document provides instructions for using Gateway cloning technology to construct entry clones and expression clones for protein expression. Key steps include:
1. Constructing entry clones containing the gene of interest using restriction digestion/ligation or BP recombination.
2. Choosing a destination vector for protein expression in E. coli, mammalian cells, or baculovirus based on desired tags and expression system.
3. Transferring the gene of interest from the entry clone to the destination vector using LR recombination to generate an expression clone for protein production.
pBluescript is an example of a combination between plasmids and phages (phagemids).
Phagemids represent a hybrid type of class of vectors that serve to produce single-stranded DNA.
To integrate promoter-GW-lux fragment onto chromosome of E.coliUrja Bhatt
This document describes integrating a promoter-lux fragment onto the chromosome of E. coli to provide more robust results in promoter assays compared to a plasmid. The lux fragment was amplified by PCR and ligated into the destination vector pGRG25. This new plasmid, pGRG25-pDEW201GWlux, was transformed into E. coli. The promoter sequence was then integrated onto the chromosome using Gateway Technology. Promoter activity was tested under different conditions to evaluate strain backgrounds and DNA damage.
Transcriptomics of RKN resitance in Upland CottonSameer Khanal
This study performed a comparative transcriptomic analysis of resistant and susceptible cotton genotypes at early and late stages of infection by the root-knot nematode Meloidogyne incognita. RNA sequencing of infected and uninfected root samples identified differentially expressed genes between resistant and susceptible lines. Two genes involved in defense against the nematode were found to be overexpressed at a resistance quantitative trait locus (qMi-C11), and two plant receptor genes were overexpressed at another locus (qMi-C14). Ongoing work includes time-series analysis of gene expression in resistant, susceptible, and near-isogenic lines to identify genes responsible for resistance mechanisms.
a) Describe two ways the researcher could minimise experimenter bias i.docxbickerstaffinell
a) Describe two ways the researcher could minimise experimenter bias in this study.
b) Describe a way the researchers could minimise sample bias in this study. (distinct from your answers in part a)
Nuclear import of SARS-CoV-2 nucleocapsid (N) protein is not inhibited by overmectin B.A. Loney* and M.A. Larkey* *Bundoora Institute for Applied Medical Research. Introduction The causative agent of the current COVID-19 pandemic, SARS-CoV-2, is a single stranded positive sense RNA virus that is closely related to severe acute respiratory syndrome coronavirus (SARS-CoV). It has been previously shown that SARS-CoV-2 nucleocapsid (N) is present in the cytoplasm but can also actively localize to the nucleolus where it can interact with host proteins and also bind to viral RNA. It has also been previously shown that nuclear import of similar nucleocapsid proteins (including the HIV-1 nucleocapsid protein, NC) from other RNA viruses can be inhibited by the drug overmectin resulting in decreased viral replication efficiency. There are multiple nuclear import pathways mediated by different receptors. The two most common nuclear import pathways are mediated by the importin / heterodimer or by the importin homodimer. Overmectin has previously been demonstrated to inhibit nuclear import by disrupting the importin / pathway. In this study SARS-CoV-2 nucleocapsid (N) was transfected into Hela cells and the effectiveness of overmectin at inhibiting its nuclear import was determined. Methods Expression of N protein in the absence of other viral proteins. To investigate the nuclear import of SARS-CoV-2 N protein three constructs were created. 1. pEGFP-NCov2. The N gene (from SARS-CoV-2, isolate BJ04) was cloned into the eukaryotic expression vector pEGFP-C1 (Promega) such that expression of the N gene was under the control of a cytomegalovirus (CMV) polymerase Il promoter to express an N protein fusion with the C-terminal of EGFP. 2. pEGFP. The pEGFP-C1 expression vector alone. 3. EEGFP-TRF1. A positive control for nuclear import. The human TRF1 gene was cloned into the eukaryotic expression vector pEGFP-C1 to express an N protein fusion with the C-terminal of EGFP. TRF1 nuclear localisation has shown to be mediated by the importin homodimer. Hela cells were cultured in 12 separate culture plates at a density of 1 0 5 cells per 9.6 cm 2 plate with each plate containing 2 coverslips. Cells were cultured using Cell Biologics' Culture Complete Growth Medium with 5\% foetal calf serum at 3 7 C and 5% CO 2 . Cells were transfected with 2 g of either pEGFPNCov2 (plates 1,4,7 and 10), pEGFP (plates 2, 5, 8 and 11) or pEGFP-TRF1 (3, 6, 9 and 12) and 50 g of Lipofectamine (GibcoBRL). 12 hours post-transfection, even numbered plates were treated with 5 M overmectin in DMSO and odd numbered plates were left untreated. After 24 hours coverslips were removed, and the cells fixed. DAPI was added to visualise the nuclei and the localisation of GFP determined by fluorescent mic.
MULTIPLE CLONING SITE and BACTERIOPHAGE LAMBDA (λ - phage ) Amany Elsayed
This document summarizes key aspects of cloning vectors and techniques. It discusses multiple cloning sites that contain unique restriction enzyme sites used to insert DNA fragments. Both plasmid vectors and bacteriophage lambda can be used for cloning, with lambda able to accommodate larger inserts up to 25kb. The document compares features of plasmid and lambda cloning, such as circular vs. linear DNA, transformation vs. transfection, and plating methods. It also explains the transformation process, including factors that influence efficiency like calcium chloride treatment and host bacterial strain.
The document describes the RheoSwitch Mammalian Inducible Expression System which provides precise control of gene expression in mammalian cells. It contains three plasmids - pNEBR-R1 encodes a nuclear receptor heterodimer for regulating transcription of genes cloned into pNEBR-X1. pNEBR-X1 is used to clone the gene of interest and contains response elements regulated by the receptor. pNEBR-X1GLuc is a control plasmid expressing Gaussia luciferase. The system allows inducible expression of a gene of interest in the presence of a small molecule ligand.
1. SARS-CoV-2 infects alveolar epithelial cells expressing ACE2 and RAGE. Cell death releases HMGB1, a ligand of RAGE.
2. HMGB1 binding to RAGE activates signaling pathways like NFkB and increases inflammation. The virus may also mimic HMGB1 to bind RAGE.
3. Soluble RAGE produced from membrane RAGE can bind to Fcgbp and reduce inflammation in the lungs. Genetic variations in RAGE expression impact COVID-19 severity and outcomes like ARDS.
1. SARS-CoV-2 infects alveolar cells expressing ACE2 and RAGE, causing cell death and release of the damage signal HMGB1.
2. HMGB1 binds RAGE and activates signaling pathways increasing inflammation. SARS-CoV-2 may also bind and activate RAGE.
3. Activated RAGE is cleaved to soluble sRAGE which binds ligands and anchors to Fcgbp, reducing inflammation. Insufficient sRAGE or Fcgbp may lead to complications like cytokine storm or death.
Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine ...
Maxadilan poster
1. Retargeting gammaretroviruses for
gene delivery using Maxadilan
Specific delivery of curative genes to cell types of choice is an ongoing
challenge in gene therapy. We explore one strategy to re-target a gamma-retroviral
vector to neurons, by inserting a Maxadilan peptide into different regions of Gibbon
Ape Leukemia Virus (GALV) and a newly identified GALV-related koala retrovirus B
(KoRV-B) envelope protein env.
Various Maxadilan-GALV or KoRV-B env constructs were made and tested for
their ability to recognize, bind and mediate entry into PAC1 expressing cells via
binding and infectivity assays. We found that Maxadilan, flanked with ‘hinge’
sequences and inserted right after the signaling peptide of the GALV or KoRV-B env
did not disrupt the function of GALV or KoRVB env to infect susceptible cells that
express their receptors. Insertion of Maxadilan in KoRV-B allowed the env to bind
strongly to PAC1 receptors, but failed to mediate virus entry. Our data suggests that
the use of PAC1 to mediate entry, by KoRV-B env with Maxadilan inserted, is
blocked at the fusion step.
Background
Jan Clement Santiago, Wenqin Xu, Jill Russ & Maribeth V. Eiden
Section on Directed Gene Transfer,
National Institute of Mental Health, Bethesda, MD 20892
Abstract
Results
Conclusion
Methods
I. Maxadilan insertion generally reduces or neutralizes the infectivity of vectors
bearing GALV and KoRV-B env.
II. Maxadilan inserted after the signal peptide and flanked with Linker2 allows GALV
and KoRV-B to infect through their native receptors.
III. The infectivity of Maxadilan env constructs are reduced in susceptible cells
expressing PAC1 receptors.
IV. Since binding assays show that Maxadilan env constructs bind to PAC1, the block to
cell entry through PAC1 must be at the fusion step.
A. Virus particles binding to PAC1 and remaining “stuck” outside the cell could
account for the lower titers of Maxadilan env constructs in susceptible cells
expressing PAC1 receptors compared to cells that do not.
B. Although GALV-Maxadilan-Linker2 enveloped particles are infectious (Table 1),
GALV-MaxadilanV5-Linker2 was not binding to PAC1 (Fig 1). The V5 may be
affecting its functional conformation. We assumed previously that adding the
relatively small V5 tag would not drastically affect its properties. We may have to
compare infectious titers between GALV-Max2 and GALV-Max2-V5.
1
2
3
4
5
• GALV or KoRV-B env vectors with Maxadilan inserted all produced titers at least 1-
log lower than wild type (not shown), or none.
• Among the constructs though, B and E (Maxadilan+Linker2 inserted right after
signaling peptide) has the least detrimental effect on infectivity.
Ø They are still functional in mediating entry through their native receptors.
• No Maxadilan constructs could infect MDTF with PAC1 receptors only.
Ø Maxadilan inserts cannot mediate entry through PAC1.
• B and E are infectious, but their titers are significantly less in MDTF expressing also
PAC1. No titer reduction is seen in MDTF-PAC1 from envelopes without Maxadilan
(see A and D).
Ø Co-expression of PAC1 reduced susceptibility of MDTF cells to B and E,
suggesting the interaction of PAC1 with Maxadilan is deleterious to infectivity.
Gibbon Ape Leukemia Virus envelope Mean
&ters
on
MDTF
with
receptors:
Insert
Loca&on
PiT1
PiT1
&
PAC1
PAC1
A
V5+Linker2
5'
end
a/er
signaling
pep4de
2.60
x
105
5.89
x
105
<
10
B
Maxadilan+Linker2
5'
end
a/er
signaling
pep4de
2.53
x
105
2.10
x
104
<
10
C
Maxadilan+Linker2
replaces
Variable
Region
B
<
10
<
10
<
10
Koala Retrovirus B envelope Mean
&ters
on
MDTF
with
receptors:
Insert
Loca&on
THTR1
THTR1
&
PAC1
PAC1
D
V5+Linker2
5'
end
a/er
signaling
pep4de
3.12
x
104
3.33
x
104
<
10
E
Maxadilan+Linker2
5'
end
a/er
signaling
pep4de
1.78
x
105
7.04
x
103
<
10
F
Maxadilan
near
5'
end
a/er
signaling
pep4de
<
10
<
10
<
10
G
Maxadilan
replaces
Variable
Region
A
<
10
<
10
<
10
H
Maxadilan
replaces
Variable
Region
B1
1.00
x
101
3.12
x
102
<
10
I
Maxadilan
replaces
Variable
Region
B2
5.55
x
102
1.39
x
102
<
10
J
Maxalidan
+
Linker
2
replaces
H
of
PHQ
region
<
10
<
10
<
10
Binding of Env constructs to
MDTF-PAC1
K-MaxV5∆H
K-MaxV5-L2
KB-V5-L2
G-MaxV5-L2
Cellcounts
Intensity of bound probe (FL2-H)
To test if the Maxadilan insert
and PAC1 receptors are
indeed interacting, binding
assays were done. The
Maxadilan inserts were
tagged with V5 to allow for
anti-V5 antibody staining for
the envelopes that bound to
PAC1 receptors.
• KoRV-B V5-Linker2 is the negative control, because MDTF-PAC1 do not express the
corresponding KoRV-B receptor THTR1
• KoRV-B MaxadilanV5-Linker2 & KoRV-B MaxadilanV5∆H bind to MDTF-PAC1
• GALV-MaxadilanV5-Linker2 does not bind to MDTF-PAC1
Tables 2 & 3.
Infectious titers of GALV & KoRV-B envelopes with Maxadilan inserted at various sites
Table 3
GALV
env
inserts
Titers
in
MDTF-‐PiT1
V5
8.03
x
105
V5
+
Linker1
3.62
x
105
V5
+
Linker2
1.18
x
106
V5
+
Linker3
7.05
x
105
Table 1. Infectious titers of GALV env with V5 peptide tag and linkers inserted
Adding Linker2 produced GALV env
insert construct with the highest titers.
Consequently, most env insertions later
will incorporate Linker2.
References6
Maxadilan1
– a potent 61 amino acid vasodilator peptide isolated from
sand fly salivary glands
– specifically activates the mammalian PAC1 receptor
– 500X more potent than the next most potent PAC1 agonist
GALV (Gibbon Ape Leukemia Virus) env
– widely used in gene therapy for its relative safety and efficacy
– receptor is PiT1 (phosphate transporter 1)
sand fly
Envelopes (env)
Env (envelope protein):
Enveloped Virus
Linker sequences2
– give space for an inserted epitope to “hinge” out and not inhibit the native
conformation of the envelope protein
– based on a published GALV construct
KoRV-B (Koala Retrovirus B) env
– closely related to GALV
– receptor is THTR1 (thiamine transporter 1)
1. Generate insert with overlapping
homologous regions to vector via PCR
2. Expose 5’ overhangs in insert & cut vector
by incubating each with T4 polymerase
• In absence of dNTPs, T4 polymerase have 3’
exonuclease activity that is stopped by adding dCTP
3. Incubate vector and insert together (with
Recombinase A)
• overlapping regions anneal to each other
4. Transform into E.coli
• cell repairs nicks and gaps in recombinant plasmid
Env constructs made via Sequence & Ligation Independent Cloning
1.) Transfect env to 293T cells
+ gag/pol
+ genome
(encodes β-galactosidase)
2.) Harvest viral
supernatant 48 hrs
post transfection
3.) Infect MDTF cells
4.) 48 - 72 hrs post infection,
stain then count β-gal -
expressing cells
Making virus particles for infectivity assays
40x magnification of β-gal transduced
MDTF (blue cells), using KoRVB-V5 env.
Binding assays
MDTF cell
PAC1 receptors
V5 tag
3.) Incubate MDTF-PAC1 with env supernatant for
30 mins at 37˚C
env
Maxadilan
ligand
4.) Probe with anti-V5 1˚ antibody
5.) Probe with 2˚ fluorescent antibody
6.) Detect fluorescing cells with FACS
1.) Transfect V5-tagged env only to 293T cells
2.) Collect supernatant 48 hrs after, concentrate 2X
Env surface unit
signal peptideN terminus variable
region A
variable
region B
1Lerner, E. A., Iuga, A. O., and Reddy, V. B. (2007). Maxadilan, a PAC1 receptor agonist from sand flies. Peptides 28, 1651-1654.
2Bahrami, S., Pagh K.,Ejegod, D., et al (2012). Construction of a Gammaretrovirus with a Novel Tropism and Wild-Type Replication Kinetics Capable of Using Human APJ as Entry Receptor. Journal of virology
86(19): 10621-106272012
variable regions are major determinants of receptor specificity