Posttranslational modifications (PTMs), such as phosphorylation, acetylation, and methylation regulate cell adhesion and migration. PTMs modify integrin function and the activity of proteins involved in cytoskeletal dynamics like cofilin, alpha-tubulin, cortactin, and EF1a1. Acetylation of cortactin and alpha-tubulin reduces cell migration by decreasing their association with actin and microtubule stability, respectively. Phosphorylation of cofilin regulates its actin binding activity and ability to sever actin filaments. Methylation of EF1a1 is required for neural crest cell migration. Drugs that alter the cell's acetylation state through inhibition of HDACs or modulation of acetyl-
ABSTRACT- The present study was conducted to investigate the effect of cadmium chloride on Histoarchiteceture of head kidney of fresh water fish Heteropneustes fossilis. The fishes were exposed to 0.5 ppm of cadmium chloride for 21 days. The most remarkable changes in head kidney, due to cadmium chloride were lysed condition of interrenal and chromaffin cells. The traces of cytoplasm had dark brown to black coloured cytoplasm. Most of cells are deformed and necrotic condition. Their size was significant at (P< 0.01 and 0.001) increased after cadmium chloride. All these changes will be recovered by herbal compound i.e. Ashwagandha. The damaged tissues were recovered in already treated group.
Key-words- Ashwagandha, Cadmium chloride, Chromaffin cells, Heteropneustes fossilis, Histopathology, Interrenal cells
The document describes an experiment where disulfide bonds were engineered into a1-antitrypsin (a1-AT) to lock the movement of helix F (hF) and the connecting loop (thFs3A) during protease inhibition. Disulfide bonds were introduced between thFs3A and strands 3A or 5A of the beta-sheet. The disulfide between thFs3A and strand 5A, but not 3A, eliminated inhibitory activity, suggesting displacement from strand 5A is required for inhibition. The disulfide between thFs3A and strand 3A slowed polymerization without affecting inhibition. This provides direct evidence that hF/thFs3A displacement from strand 5
This document describes a study that investigated the interaction between nick-directed DNA loop repair and mismatch repair in human cells. The study constructed DNA substrates containing combinations of mismatches and loops. It was demonstrated that a nick 3' to a large loop can direct loop repair in human cell extracts in a bidirectional manner. However, when a mismatch was near a loop, the efficiency of nick-directed mismatch repair was reduced. This suggests interference between loop repair and mismatch repair when sites are adjacent to avoid double-stranded DNA breaks.
3DSIG 2014 Presentation: Systematic detection of internal symmetry in proteinsSpencer Bliven
These slides are from 3DSIG 2014, presented on July 11.
I describe our investigation of internal symmetry in protein structures. This is quite common (24% of domains), and has many implications for function, folding, and evolution.
I introduce the CE-Symm method, described in
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic Detection of Internal Symmetry in Proteins Using CE-Symm. Journal of Molecular Biology, 426(11), 2255–2268. doi:10.1016/j.jmb.2014.03.010
I discuss the results from running CE-Symm across the PDB, as well as some particularly compelling examples.
See also my poster by the same title for more details.
1) The study analyzed insertions of accessory domains in the haloalkanoic dehalogenase superfamily (HADSF) to understand the effects on the core Rossmann fold structure.
2) Structural similarity networks revealed that sequences with the same inserted domain type shared greater core structure similarity compared to different domain types.
3) Variation in the core structure occurred in alpha helices flanking the central beta sheet, rather than at the core-domain interface, suggesting independent divergence of core and inserted domains during evolution.
This study investigated whether supplementing glutathione (GSH) could attenuate lipopolysaccharide (LPS)-induced mitochondrial dysfunction and apoptosis in a mouse model of acute lung injury (ALI). The researchers found that LPS increased oxidative stress, mitochondrial dysfunction, and apoptosis in mouse lung tissue. However, pre-treating the mice with GSH-ethyl ester prevented the LPS-induced increases in oxidative stress, preserved mitochondrial function, and reduced apoptosis. Thus, GSH supplementation may protect against LPS-induced mitochondrial damage and cellular apoptosis in ALI.
Apaf-1 and Apoptosome Activation in H. sapiensCorbett Hall
Mitochondrial stress triggers cytochrome C-mediated activation of Apaf-1, cleaving Caspase 9 and leading to Apoptosome formation in a second-order, "induced proximity" mechanism
The document discusses how the SUMO E3-ligase PIAS1 couples reactive oxygen species (ROS)-dependent JNK activation to oxidative cell death in human endometrial stromal cells (HESCs). It finds that ROS-dependent JNK activation converges on the SUMO pathway via PIAS1. Knockdown of PIAS1 prevents ROS-dependent hypersumoylation but enhances JNK signaling in HESCs. PIAS1 determines the level of JNK activity, couples ROS signaling to the SUMO pathway, and promotes oxidative cell death. PIAS1 knockdown attenuates ROS-dependent caspase activation and apoptosis.
ABSTRACT- The present study was conducted to investigate the effect of cadmium chloride on Histoarchiteceture of head kidney of fresh water fish Heteropneustes fossilis. The fishes were exposed to 0.5 ppm of cadmium chloride for 21 days. The most remarkable changes in head kidney, due to cadmium chloride were lysed condition of interrenal and chromaffin cells. The traces of cytoplasm had dark brown to black coloured cytoplasm. Most of cells are deformed and necrotic condition. Their size was significant at (P< 0.01 and 0.001) increased after cadmium chloride. All these changes will be recovered by herbal compound i.e. Ashwagandha. The damaged tissues were recovered in already treated group.
Key-words- Ashwagandha, Cadmium chloride, Chromaffin cells, Heteropneustes fossilis, Histopathology, Interrenal cells
The document describes an experiment where disulfide bonds were engineered into a1-antitrypsin (a1-AT) to lock the movement of helix F (hF) and the connecting loop (thFs3A) during protease inhibition. Disulfide bonds were introduced between thFs3A and strands 3A or 5A of the beta-sheet. The disulfide between thFs3A and strand 5A, but not 3A, eliminated inhibitory activity, suggesting displacement from strand 5A is required for inhibition. The disulfide between thFs3A and strand 3A slowed polymerization without affecting inhibition. This provides direct evidence that hF/thFs3A displacement from strand 5
This document describes a study that investigated the interaction between nick-directed DNA loop repair and mismatch repair in human cells. The study constructed DNA substrates containing combinations of mismatches and loops. It was demonstrated that a nick 3' to a large loop can direct loop repair in human cell extracts in a bidirectional manner. However, when a mismatch was near a loop, the efficiency of nick-directed mismatch repair was reduced. This suggests interference between loop repair and mismatch repair when sites are adjacent to avoid double-stranded DNA breaks.
3DSIG 2014 Presentation: Systematic detection of internal symmetry in proteinsSpencer Bliven
These slides are from 3DSIG 2014, presented on July 11.
I describe our investigation of internal symmetry in protein structures. This is quite common (24% of domains), and has many implications for function, folding, and evolution.
I introduce the CE-Symm method, described in
Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, Z. K., Youkharibache, P., Bourne, P. E., & Prlić, A. (2014). Systematic Detection of Internal Symmetry in Proteins Using CE-Symm. Journal of Molecular Biology, 426(11), 2255–2268. doi:10.1016/j.jmb.2014.03.010
I discuss the results from running CE-Symm across the PDB, as well as some particularly compelling examples.
See also my poster by the same title for more details.
1) The study analyzed insertions of accessory domains in the haloalkanoic dehalogenase superfamily (HADSF) to understand the effects on the core Rossmann fold structure.
2) Structural similarity networks revealed that sequences with the same inserted domain type shared greater core structure similarity compared to different domain types.
3) Variation in the core structure occurred in alpha helices flanking the central beta sheet, rather than at the core-domain interface, suggesting independent divergence of core and inserted domains during evolution.
This study investigated whether supplementing glutathione (GSH) could attenuate lipopolysaccharide (LPS)-induced mitochondrial dysfunction and apoptosis in a mouse model of acute lung injury (ALI). The researchers found that LPS increased oxidative stress, mitochondrial dysfunction, and apoptosis in mouse lung tissue. However, pre-treating the mice with GSH-ethyl ester prevented the LPS-induced increases in oxidative stress, preserved mitochondrial function, and reduced apoptosis. Thus, GSH supplementation may protect against LPS-induced mitochondrial damage and cellular apoptosis in ALI.
Apaf-1 and Apoptosome Activation in H. sapiensCorbett Hall
Mitochondrial stress triggers cytochrome C-mediated activation of Apaf-1, cleaving Caspase 9 and leading to Apoptosome formation in a second-order, "induced proximity" mechanism
The document discusses how the SUMO E3-ligase PIAS1 couples reactive oxygen species (ROS)-dependent JNK activation to oxidative cell death in human endometrial stromal cells (HESCs). It finds that ROS-dependent JNK activation converges on the SUMO pathway via PIAS1. Knockdown of PIAS1 prevents ROS-dependent hypersumoylation but enhances JNK signaling in HESCs. PIAS1 determines the level of JNK activity, couples ROS signaling to the SUMO pathway, and promotes oxidative cell death. PIAS1 knockdown attenuates ROS-dependent caspase activation and apoptosis.
This document summarizes a study that investigated cryopreserving hepatocyte cell monolayers using trehalose. The researchers found that trehalose preincubation improved cell viability after cryopreservation in dimethyl sulfoxide. Specifically, they found that incubating hepatocyte monolayers in 100 mM trehalose for 24 hours before freezing in medium containing 10% dimethyl sulfoxide resulted in 42% viability after thawing, compared to only 6-13% viability without trehalose preincubation. Additionally, Raman spectroscopy showed that trehalose reduced ice crystallization during freezing, which could decrease cell injury. The results suggest that trehalose-based approaches may help preserve tissues and organs through cryopreservation.
This presentation describes an evolutionarily based approach to identify wheat genes that may confer resistance to the wheat stem rust pathogen Ug99. The approach uses pairwise comparisons of wheat transcriptomes to detect genes undergoing positive selection, which may have recently evolved in response to selection pressure from Ug99. Two candidate genes have been identified so far - a Bowman-Birk type trypsin inhibitor (Serpin 1) and a metallothionein type-2 protein (MT2). Serpin 1 shows signatures of positive selection localized in regions that code for binding sites. The presentation seeks potential partners to help validate these candidate genes.
Pells et al [2015] PLoS ONE 10[7] e0131102Steve Pells
This research article identifies novel human embryonic stem cell regulators based on their conserved and distinct CpG island methylation patterns. The researchers analyzed CpG island methylation in four human embryonic stem cell lines using a CpG island array and identified 1,111 CpGs that were methylated in all stem cell lines. They compared the methylation profiles to somatic tissues and mRNA expression data to identify stem cell-specific methylation patterns associated with gene expression. Genes related to transcriptional repression and activation were overrepresented among genes associated with methylated or unmethylated CpGs specifically in stem cells. Knockdown experiments confirmed that some candidate regulators induced stem cell differentiation, while overexpression modulated induced pluripotent stem cell formation
The document summarizes research investigating the effects of (-)-epicatechin, a flavanol antioxidant found in cocoa, on gene expression in the yeast Saccharomyces cerevisiae. Yeast were exposed to increasing concentrations of (-)-epicatechin and changes in expression of genes related to longevity and oxidative stress were analyzed. Preliminary results found that a longevity gene (HST2) was upregulated at higher concentrations, while an oxidative stress gene (GSH1) was downregulated, supporting the hypotheses. Future research is proposed to test additional genes and a higher concentration range to better understand how (-)-epicatechin impacts longevity and oxidative stress.
1) Mice were orally administered gold-core/silver-shell nanoparticles (Au/AgNPs) or a control over 7 days to examine genotoxicity.
2) Peripheral blood was collected at 7 days, 14 days, and 21 days and analyzed using biomarkers for DNA damage (γ-H2AX foci and 8-oxoG) and chromosomal damage (micronuclei).
3) Results showed an increase in γ-H2AX foci, a marker for double-strand DNA breaks, in treated mice at 14 days, but no differences in the other biomarkers between treated and control mice.
Omar Quintero-Monzon has over 20 years of experience in biochemistry, protein purification and characterization, antibody drug development, and assay development. He has worked at multiple biotech companies leading projects and developing novel techniques. His experience includes developing assays for glycoprotein analysis, antibody and protein purification methods, and biomarker assays with improved sensitivity.
Discussion of latest work on simulating "evolve and resequence" experiments. Covers issues brought up by Burke et al.'s 2010 paper and how the simulations in Baldwin-Brown et al. (2014) address them.
Effect of stemregenin1 and sb431542 small molecules on ex vivo expansion of u...Liberty University (LU)
This study investigated the ex vivo expansion of umbilical cord blood hematopoietic stem cells (HSCs) using three-dimensional (3D) polyethersulfone (PES) nanofiber scaffolds and two small molecules, Stemregenin1 (SR1) and SB431542. Isolated HSCs were cultured in 3D PES scaffolds or 2D conditions with SR1 and/or SB431542 and growth factors. On days 5 and 10, the cells were analyzed for marker expression, colony formation ability, and gene expression of stemness genes. SR1 increased HSC expansion while SB431542 induced more lineage-committed cells. SR1 upregulated stemness genes and
Rosehip extracts were tested on A-172 human glioblastoma (GBM) cell lines to determine their effects on cell death. The cell lines were treated with 250 μg/ml of rosehip extracts for 48 hours. As a positive control, some cells were also treated with staurosporine. The amount of cell death was measured using a live/dead colorimetric assay. The results showed that exposure to rosehip extracts did not result in cell death of the GBM cell lines.
The document summarizes information about the apolipoprotein E (APOE) gene, including its location, alleles, and association with various health conditions. It discusses how the APOE gene codes for a protein involved in lipid transport, with different alleles (e2, e3, e4) producing slightly different proteins and phenotypes. Studies have shown the e4 allele increases Alzheimer's risk and earlier onset, while the rarer e2 allele may protect against or delay Alzheimer's. The e4 and e2 alleles also impact cardiovascular disease risk. The document aims to study the distribution of APOE alleles in the population of Hotchkiss School and any differences among demographics.
This document summarizes a study investigating the epigenetic changes that occur during the transdifferentiation of pancreatic acinar cells (HPACs) to hepatocyte-like cells. The study found that DNA methylation in HPACs peaks at 24 hours after treatment with dexamethasone, and the cells display phenotypic changes associated with hepatocytes after 7 days. The study also examined the promoter sequence of the SGK1 gene, which is involved in the transdifferentiation process. The results suggest therapeutic potential for producing hepatocytes from pancreatic cells to treat liver disease in a more cost-effective manner than current alternatives.
Comparing Residual Integration Levels of Some IntegrationDeficient Lentiviral...inventionjournals
Lentiviral vectors (LVs) have many advantageous characteristics making them a good choice in the field of gene therapy. Nevertheless, their integration may lead to detrimental effects. To overcome this problem, lentiviral integration can be targeted through using integration-deficient lentiviral vectors (IDLVs). In this study, an integration-proficient lentiviral vector (IPLV) and a battery of IDLVs with single or multiple mutations affecting integration were produced and their integration levels were compared. eGFP time-course experiment and clonogenic assay were used to make these comparisons. It was found that there was not any significant difference between the residual integration of any of the IDLVs used in this study and that of the standard IDLV; D64V-IDLV. It can be concluded that most IDLV integration is mediated by integraseindependent mechanisms.
Sarcar B et al.,-Mol Cancer Ther-2011-Sarcar-Bhaswati Sarcar
This study examined the ability of the Wee-1 inhibitor MK-1775 to enhance the radiosensitivity of glioblastoma cell lines and modulate the radiation-induced G2 checkpoint. The results showed that MK-1775 abrogated the radiation-induced G2 checkpoint and increased radiosensitivity in established glioblastoma cell lines in vitro and in vivo, without affecting the radiation response of normal human astrocytes. MK-1775 appeared to attenuate the early-phase G2 checkpoint arrest in glioblastoma neural stem cell lines, but the arrest was not sustained and radiosensitivity was not increased. Further investigation is needed to understand the role of Wee-1 in the checkpoint response of glioblastoma neural stem cells
This document discusses mutations, which are heritable changes in an organism's genome. Mutations can occur spontaneously during DNA replication due to errors, or can be induced by mutagens like UV radiation or chemicals. Mutations provide genetic variation and are the raw material for evolution, though they are generally harmful. They can result in the formation of new alleles and allow organisms to evolve and adapt to their environments. The document covers different types of mutations and their molecular basis.
This study identified and characterized a new collagenase, ColAh, produced by Aeromonas piscicola AH-3. The researchers identified a gene in A. hydrophila ATCC 7966 that encodes a putative collagenase. They constructed a knockout mutant of this gene (colAh) in A. piscicola AH-3. Tests showed the mutant had significantly lower collagenolytic activity and cytotoxic effects compared to the wild type, demonstrating the colAh gene encodes an active collagenase. Further analysis found ColAh is a ~100kDa metalloprotease that can cleave and bind collagen. This contributes to A. piscicola's collagen degradation and cytotoxicity. ColAh contains the conserved HEXX
The document summarizes a webinar presentation about telomere shortening and its relationship to human disease and cancer. The presentation discusses how telomeres shorten with cell division, potentially leading to diseases like dyskeratosis congenita and acquired aplastic anemia. It shows that some patients with acquired aplastic anemia have mutations in the telomerase gene TERT that cause shorter telomeres, increased chromosomal instability, and worse outcomes. Telomere length may be a predictor of relapse and survival in aplastic anemia patients.
Male and female rats were exposed to mercury (0.5, 1.0 and 1.5mg/kg) for 12 weeks to investigate the effects on antioxidant enzymes. Mercury exposure inhibited antioxidant enzymes like catalase and superoxide dismutase in a gender-specific manner. In female rats, mercury inhibited catalase and superoxide dismutase in the plasma, erythrocytes, liver and kidneys. In male rats, mercury inhibited superoxide dismutase in the liver and catalase in the kidneys. Mercury levels in tissues correlated negatively with antioxidant enzyme levels, specifically in females. The findings support that mercury exposure affects antioxidant defenses differently between males and females.
Cytogenetic effects of benzene on human blood cellsAlexander Decker
This document summarizes a study that investigated the cytogenetic effects of benzene on human blood cells in vitro. Different concentrations of benzene were added to human blood cultures. The results showed that benzene caused increased mitotic index levels and various chromosomal abnormalities that increased with higher benzene concentrations. Specifically, benzene exposure resulted in chromosomal breaks, deletions, ring chromosomes, end-to-end associations, and other irregularities. This supports that benzene is a human clastogen that can induce genetic damage even at low concentrations.
V79C cells were derived from V79 cell line by through chronic oxidative stress that was found to be radio-resistant. These cells had demonstrated transformation–like stable changes and could be used as model system to study oxidant induced carcinogenesis. Our objective was to understand mechanism of radiation-resistance in these cells. Apoptotic cell death was inhibited in these cells as visualized microscopically by Hoechst staining and nucleosomal ladder formation in agarose gel. Release of cytochrome c in cytoplasm and Apoptosis Inducing Factor in the mitochondrial and nuclear fraction of cells were determined by Western blotting. The caspase 9 and caspase 3 activities in these cells were estimated from fluorimetric assays. These results revealed that the radiation resistance was due to inhibition of caspase-dependent apoptotic death pathways although Apoptosis Inducing Factor mediated pathway remained unaffected. These findings may aid in understanding the mechanism of radiation resistance in tumors arising from oxidative stress.
The document discusses protein synthesis and post-translational modification. It describes how translation involves mRNA, ribosomes, tRNA, and release factors to synthesize proteins. The process involves initiation, elongation, and termination. After synthesis, the peptide undergoes folding, modification like phosphorylation, and can be transported to organelles. Post-translational modifications are important for diversity and regulating protein function, and involve processes like methylation, ubiquitination, and glycosylation. Diseases like atherosclerosis and fibrosis are related to disorders of collagen deposition and modification.
post translational modifications of proteinAnandhan Ctry
Post-translational modifications (PTMs) are chemical modifications of proteins that occur after translation. PTMs play a key role in regulating protein function by modifying activity, localization, and interactions. The main types of PTMs discussed are phosphorylation, glycosylation, ubiquitination, S-nitrosylation, methylation, N-acetylation, lipidation, and proteolysis. These modifications are identified through techniques like mass spectrometry, HPLC, radioactive labeling, and gel electrophoresis. PTMs are important for processes like cell signaling, growth, and apoptosis.
This document summarizes a study that investigated cryopreserving hepatocyte cell monolayers using trehalose. The researchers found that trehalose preincubation improved cell viability after cryopreservation in dimethyl sulfoxide. Specifically, they found that incubating hepatocyte monolayers in 100 mM trehalose for 24 hours before freezing in medium containing 10% dimethyl sulfoxide resulted in 42% viability after thawing, compared to only 6-13% viability without trehalose preincubation. Additionally, Raman spectroscopy showed that trehalose reduced ice crystallization during freezing, which could decrease cell injury. The results suggest that trehalose-based approaches may help preserve tissues and organs through cryopreservation.
This presentation describes an evolutionarily based approach to identify wheat genes that may confer resistance to the wheat stem rust pathogen Ug99. The approach uses pairwise comparisons of wheat transcriptomes to detect genes undergoing positive selection, which may have recently evolved in response to selection pressure from Ug99. Two candidate genes have been identified so far - a Bowman-Birk type trypsin inhibitor (Serpin 1) and a metallothionein type-2 protein (MT2). Serpin 1 shows signatures of positive selection localized in regions that code for binding sites. The presentation seeks potential partners to help validate these candidate genes.
Pells et al [2015] PLoS ONE 10[7] e0131102Steve Pells
This research article identifies novel human embryonic stem cell regulators based on their conserved and distinct CpG island methylation patterns. The researchers analyzed CpG island methylation in four human embryonic stem cell lines using a CpG island array and identified 1,111 CpGs that were methylated in all stem cell lines. They compared the methylation profiles to somatic tissues and mRNA expression data to identify stem cell-specific methylation patterns associated with gene expression. Genes related to transcriptional repression and activation were overrepresented among genes associated with methylated or unmethylated CpGs specifically in stem cells. Knockdown experiments confirmed that some candidate regulators induced stem cell differentiation, while overexpression modulated induced pluripotent stem cell formation
The document summarizes research investigating the effects of (-)-epicatechin, a flavanol antioxidant found in cocoa, on gene expression in the yeast Saccharomyces cerevisiae. Yeast were exposed to increasing concentrations of (-)-epicatechin and changes in expression of genes related to longevity and oxidative stress were analyzed. Preliminary results found that a longevity gene (HST2) was upregulated at higher concentrations, while an oxidative stress gene (GSH1) was downregulated, supporting the hypotheses. Future research is proposed to test additional genes and a higher concentration range to better understand how (-)-epicatechin impacts longevity and oxidative stress.
1) Mice were orally administered gold-core/silver-shell nanoparticles (Au/AgNPs) or a control over 7 days to examine genotoxicity.
2) Peripheral blood was collected at 7 days, 14 days, and 21 days and analyzed using biomarkers for DNA damage (γ-H2AX foci and 8-oxoG) and chromosomal damage (micronuclei).
3) Results showed an increase in γ-H2AX foci, a marker for double-strand DNA breaks, in treated mice at 14 days, but no differences in the other biomarkers between treated and control mice.
Omar Quintero-Monzon has over 20 years of experience in biochemistry, protein purification and characterization, antibody drug development, and assay development. He has worked at multiple biotech companies leading projects and developing novel techniques. His experience includes developing assays for glycoprotein analysis, antibody and protein purification methods, and biomarker assays with improved sensitivity.
Discussion of latest work on simulating "evolve and resequence" experiments. Covers issues brought up by Burke et al.'s 2010 paper and how the simulations in Baldwin-Brown et al. (2014) address them.
Effect of stemregenin1 and sb431542 small molecules on ex vivo expansion of u...Liberty University (LU)
This study investigated the ex vivo expansion of umbilical cord blood hematopoietic stem cells (HSCs) using three-dimensional (3D) polyethersulfone (PES) nanofiber scaffolds and two small molecules, Stemregenin1 (SR1) and SB431542. Isolated HSCs were cultured in 3D PES scaffolds or 2D conditions with SR1 and/or SB431542 and growth factors. On days 5 and 10, the cells were analyzed for marker expression, colony formation ability, and gene expression of stemness genes. SR1 increased HSC expansion while SB431542 induced more lineage-committed cells. SR1 upregulated stemness genes and
Rosehip extracts were tested on A-172 human glioblastoma (GBM) cell lines to determine their effects on cell death. The cell lines were treated with 250 μg/ml of rosehip extracts for 48 hours. As a positive control, some cells were also treated with staurosporine. The amount of cell death was measured using a live/dead colorimetric assay. The results showed that exposure to rosehip extracts did not result in cell death of the GBM cell lines.
The document summarizes information about the apolipoprotein E (APOE) gene, including its location, alleles, and association with various health conditions. It discusses how the APOE gene codes for a protein involved in lipid transport, with different alleles (e2, e3, e4) producing slightly different proteins and phenotypes. Studies have shown the e4 allele increases Alzheimer's risk and earlier onset, while the rarer e2 allele may protect against or delay Alzheimer's. The e4 and e2 alleles also impact cardiovascular disease risk. The document aims to study the distribution of APOE alleles in the population of Hotchkiss School and any differences among demographics.
This document summarizes a study investigating the epigenetic changes that occur during the transdifferentiation of pancreatic acinar cells (HPACs) to hepatocyte-like cells. The study found that DNA methylation in HPACs peaks at 24 hours after treatment with dexamethasone, and the cells display phenotypic changes associated with hepatocytes after 7 days. The study also examined the promoter sequence of the SGK1 gene, which is involved in the transdifferentiation process. The results suggest therapeutic potential for producing hepatocytes from pancreatic cells to treat liver disease in a more cost-effective manner than current alternatives.
Comparing Residual Integration Levels of Some IntegrationDeficient Lentiviral...inventionjournals
Lentiviral vectors (LVs) have many advantageous characteristics making them a good choice in the field of gene therapy. Nevertheless, their integration may lead to detrimental effects. To overcome this problem, lentiviral integration can be targeted through using integration-deficient lentiviral vectors (IDLVs). In this study, an integration-proficient lentiviral vector (IPLV) and a battery of IDLVs with single or multiple mutations affecting integration were produced and their integration levels were compared. eGFP time-course experiment and clonogenic assay were used to make these comparisons. It was found that there was not any significant difference between the residual integration of any of the IDLVs used in this study and that of the standard IDLV; D64V-IDLV. It can be concluded that most IDLV integration is mediated by integraseindependent mechanisms.
Sarcar B et al.,-Mol Cancer Ther-2011-Sarcar-Bhaswati Sarcar
This study examined the ability of the Wee-1 inhibitor MK-1775 to enhance the radiosensitivity of glioblastoma cell lines and modulate the radiation-induced G2 checkpoint. The results showed that MK-1775 abrogated the radiation-induced G2 checkpoint and increased radiosensitivity in established glioblastoma cell lines in vitro and in vivo, without affecting the radiation response of normal human astrocytes. MK-1775 appeared to attenuate the early-phase G2 checkpoint arrest in glioblastoma neural stem cell lines, but the arrest was not sustained and radiosensitivity was not increased. Further investigation is needed to understand the role of Wee-1 in the checkpoint response of glioblastoma neural stem cells
This document discusses mutations, which are heritable changes in an organism's genome. Mutations can occur spontaneously during DNA replication due to errors, or can be induced by mutagens like UV radiation or chemicals. Mutations provide genetic variation and are the raw material for evolution, though they are generally harmful. They can result in the formation of new alleles and allow organisms to evolve and adapt to their environments. The document covers different types of mutations and their molecular basis.
This study identified and characterized a new collagenase, ColAh, produced by Aeromonas piscicola AH-3. The researchers identified a gene in A. hydrophila ATCC 7966 that encodes a putative collagenase. They constructed a knockout mutant of this gene (colAh) in A. piscicola AH-3. Tests showed the mutant had significantly lower collagenolytic activity and cytotoxic effects compared to the wild type, demonstrating the colAh gene encodes an active collagenase. Further analysis found ColAh is a ~100kDa metalloprotease that can cleave and bind collagen. This contributes to A. piscicola's collagen degradation and cytotoxicity. ColAh contains the conserved HEXX
The document summarizes a webinar presentation about telomere shortening and its relationship to human disease and cancer. The presentation discusses how telomeres shorten with cell division, potentially leading to diseases like dyskeratosis congenita and acquired aplastic anemia. It shows that some patients with acquired aplastic anemia have mutations in the telomerase gene TERT that cause shorter telomeres, increased chromosomal instability, and worse outcomes. Telomere length may be a predictor of relapse and survival in aplastic anemia patients.
Male and female rats were exposed to mercury (0.5, 1.0 and 1.5mg/kg) for 12 weeks to investigate the effects on antioxidant enzymes. Mercury exposure inhibited antioxidant enzymes like catalase and superoxide dismutase in a gender-specific manner. In female rats, mercury inhibited catalase and superoxide dismutase in the plasma, erythrocytes, liver and kidneys. In male rats, mercury inhibited superoxide dismutase in the liver and catalase in the kidneys. Mercury levels in tissues correlated negatively with antioxidant enzyme levels, specifically in females. The findings support that mercury exposure affects antioxidant defenses differently between males and females.
Cytogenetic effects of benzene on human blood cellsAlexander Decker
This document summarizes a study that investigated the cytogenetic effects of benzene on human blood cells in vitro. Different concentrations of benzene were added to human blood cultures. The results showed that benzene caused increased mitotic index levels and various chromosomal abnormalities that increased with higher benzene concentrations. Specifically, benzene exposure resulted in chromosomal breaks, deletions, ring chromosomes, end-to-end associations, and other irregularities. This supports that benzene is a human clastogen that can induce genetic damage even at low concentrations.
V79C cells were derived from V79 cell line by through chronic oxidative stress that was found to be radio-resistant. These cells had demonstrated transformation–like stable changes and could be used as model system to study oxidant induced carcinogenesis. Our objective was to understand mechanism of radiation-resistance in these cells. Apoptotic cell death was inhibited in these cells as visualized microscopically by Hoechst staining and nucleosomal ladder formation in agarose gel. Release of cytochrome c in cytoplasm and Apoptosis Inducing Factor in the mitochondrial and nuclear fraction of cells were determined by Western blotting. The caspase 9 and caspase 3 activities in these cells were estimated from fluorimetric assays. These results revealed that the radiation resistance was due to inhibition of caspase-dependent apoptotic death pathways although Apoptosis Inducing Factor mediated pathway remained unaffected. These findings may aid in understanding the mechanism of radiation resistance in tumors arising from oxidative stress.
The document discusses protein synthesis and post-translational modification. It describes how translation involves mRNA, ribosomes, tRNA, and release factors to synthesize proteins. The process involves initiation, elongation, and termination. After synthesis, the peptide undergoes folding, modification like phosphorylation, and can be transported to organelles. Post-translational modifications are important for diversity and regulating protein function, and involve processes like methylation, ubiquitination, and glycosylation. Diseases like atherosclerosis and fibrosis are related to disorders of collagen deposition and modification.
post translational modifications of proteinAnandhan Ctry
Post-translational modifications (PTMs) are chemical modifications of proteins that occur after translation. PTMs play a key role in regulating protein function by modifying activity, localization, and interactions. The main types of PTMs discussed are phosphorylation, glycosylation, ubiquitination, S-nitrosylation, methylation, N-acetylation, lipidation, and proteolysis. These modifications are identified through techniques like mass spectrometry, HPLC, radioactive labeling, and gel electrophoresis. PTMs are important for processes like cell signaling, growth, and apoptosis.
TRANSLATION & POST - TRANSLATIONAL MODIFICATIONSYESANNA
The document discusses various aspects of translation - the process by which the sequence of nucleotides in mRNA is used to direct the synthesis of a polypeptide chain. It describes how the genetic code is used to translate mRNA into a protein via tRNA and the ribosome. Key points covered include codon-anticodon interactions, the roles of initiation and elongation factors, and termination of protein synthesis.
This document discusses approaches to diagnosing and treating tumors through physics. It summarizes research on the spread of tumor cells through invasion and migration in tissues and blood vessels to form secondary tumors. Graphs and images show mechanisms of cell crawling, the balance of forces during invasion, strain energy in invaded cells, and mean squared displacement measurements. Automatic analysis of invasion profiles can classify tumor cell lines. Gene expression profiles correlate with invasiveness and processes like matrix adhesion, deadhesion, and focal adhesion. Cell invasion assays study the effects of drugs and genes on the metastatic mechanism.
- The document discusses the endothelium and how it becomes dysfunctional during chronic kidney disease (CKD).
- The endothelium normally regulates vasodilation, coagulation, inflammation, and regeneration, but during CKD it exhibits defects in these functions due to the accumulation of uremic toxins.
- Uremic toxins like indoxyl sulfate and p-cresol sulfate increase oxidative stress and damage endothelial cells, impairing nitric oxide production and promoting a proinflammatory phenotype.
- Reducing the levels of these toxins through dietary changes or toxin-binding therapies may help restore healthy endothelial function and reduce cardiovascular risk in CKD patients.
- The study generated a monoclonal polyreactive antibody (pAb 2C3) that can bind various cellular and extracellular antigens.
- pAb 2C3 inhibits but does not block cell adhesion to extracellular matrix proteins by interfering with integrin clustering and aggregation rather than blocking individual integrin binding. This partial inhibition of cell adhesion results in increased random cell migration.
- Malignant cells showed a higher increase in motility and similar decrease in adhesion compared to normal cells in the presence of pAb 2C3. The effects of pAb on cell adhesion and migration differ from other factors like PDGF or urokinase.
1) Cell adhesion molecules (CAMs) allow cells to adhere to other cells and to the extracellular matrix. The main CAM families are cadherins, integrins, the immunoglobulin superfamily, and selectins.
2) Cadherins are calcium-dependent CAMs that mediate homophilic adhesion between cells of the same type. They link to the actin cytoskeleton via catenins. Cadherins play important roles in tissue formation and embryogenesis.
3) Integrins are heterodimeric CAMs composed of alpha and beta subunits. They mediate calcium-dependent adhesion between cells and the extracellular matrix by binding ligands like fibronectin and laminin. Integrins also
Biomembranes separate cell interiors from the external environment, participate in cell functions, and mediate cell-cell and cell-environment interactions. Biomembranes are composed of a phospholipid bilayer with embedded and peripheral proteins. The phospholipid bilayer forms a semipermeable barrier through self-assembly of phospholipid molecules with hydrophobic tails and hydrophilic heads. Membrane proteins have hydrophobic regions that extend through the bilayer and hydrophilic regions exposed to the aqueous environment on either side. Additional structures like the glycocalyx, extracellular matrix, basal lamina, and focal adhesions further facilitate cellular interactions and processes like migration.
1. Lymphocyte trafficking involves migration between lymphoid and non-lymphoid tissues through a multi-step process of tethering, rolling, activation, arrest, and diapedesis.
2. Specific adhesion molecules and chemokines mediate the homing of naive and memory T cells to different tissues. Naive T cells enter lymph nodes through L-selectin and PNAd, while memory T cells home to sites of infection through integrins like α4β7 and CLA.
3. Precise control of lymphocyte trafficking is important for mounting effective immune responses, as it allows antigen-experienced cells to return to places they have previously encountered pathogens.
This document summarizes different families of adhesion molecules that are important for cell-cell interactions and immune cell migration. The four main families discussed are cadherins, integrins, immunoglobulin superfamily proteins, and selectins. Integrins in particular play key roles in processes like platelet aggregation, inflammation, wound healing, and tissue migration. Dysregulation of adhesion molecules can also contribute to diseases.
The document discusses the concept of morphogens, which are soluble molecules that form concentration gradients to specify different cell fates at varying distances from the source. Morphogens were originally proposed to explain regeneration in flatworms and hydras, where body fragments regenerate complete organisms based on concentration gradients. Examples of identified morphogens discussed include the nodal protein in zebrafish, which specifies dorsal cell fates in a concentration-dependent manner, and retinoic acid in vertebrates, which alters Hox gene expression and positional values in a dose-dependent way to pattern the anterior-posterior axis. For a molecule to be considered a morphogen, cells must respond directly to it and differentiation must depend on its concentration.
The document discusses cell adhesion and migration. It outlines four classes of cell junctions: anchoring junctions, occluding junctions, channel-forming junctions, and signal-relaying junctions. Anchoring junctions like adherens junctions and desmosomes connect cells to each other and transmit stresses through connections to the cytoskeleton. Tight junctions form seals between cells and separate membrane domains. Cadherins are important cell adhesion molecules that mediate calcium-dependent cell-cell adhesion through homophilic binding. Regulation of cadherins and other cell adhesion molecules controls processes like epithelial-mesenchymal transition that are important for tissue development and cancer metastasis.
This document summarizes cellular adhesion molecules that are involved in the inflammatory process. It discusses selectins, integrins, and their roles and ligands in leukocyte trafficking and extravasation from blood vessels into tissues during inflammation. Selectins such as L-selectin, E-selectin, and P-selectin mediate initial tethering and rolling of leukocytes on endothelial cells, while integrins such as LFA-1 and VLA-4 are involved in tight adhesion and transmigration. Diseases associated with deficiencies in these adhesion molecules and attempts to target them therapeutically in human allergic inflammation and diseases like asthma are also summarized.
Neutrophils, or polymorphonuclear leukocytes (PMNs), are the most abundant type of white blood cell and play a key role in the innate immune system. PMNs are produced continuously in the bone marrow and circulate in the bloodstream before migrating to sites of infection or inflammation. PMN migration involves rolling, firm adhesion, and transmigration through the endothelium and epithelium guided by cellular adhesion molecules and chemoattractants such as interleukin-8 and leukotriene B4. Upon activation at sites of infection, PMNs phagocytose pathogens and release toxic granule contents and reactive oxygen species to fight infection.
This document summarizes several major families of cell adhesion molecules (CAMs) and adhesion receptors. It discusses cadherins, which form homophilic bonds between adjacent cells and link to the cytoskeleton. Integrins are heterodimeric receptors that bind extracellular matrix proteins and require calcium or magnesium. Selectins contain lectin domains that recognize sugar structures on neighboring cells. Neural cell adhesion molecules are single-pass transmembrane proteins important for neural tissue formation.
2. inflammation cellular events dr ashutosh kumarDrAshutosh Kumar
The document discusses the process of acute inflammation and the cellular events involved. It describes how leukocytes are recruited to the site of injury through a process called chemotaxis. It then outlines the steps of phagocytosis - adherence, ingestion, digestion. It discusses the mechanisms used by phagocytes to kill and degrade microbes, including both oxygen-dependent and oxygen-independent processes. Finally, it briefly mentions some genetic defects and acquired conditions that can cause defects in leukocyte function.
Cell adhesion molecules and matrix proteinsUSmile Ï Ṩṃïlệ
Cell adhesion molecules are proteins located on cell surfaces that are involved in binding between cells or between cells and the extracellular matrix. The three main types are cadherins, integrins, and selectins. Cadherins are calcium-dependent proteins that mediate cell-cell adhesion. Integrins are transmembrane receptors that bind to components of the extracellular matrix and mediate cell-matrix adhesion as well as cell signaling. Selectins mediate the initial capture and rolling of leukocytes along vascular surfaces. Cell adhesion molecules play important physiological roles in processes like leukocyte trafficking, blood coagulation, and morphogenesis. They also have applications as therapeutic targets in areas such as cancer, osteoporosis, and inflammatory diseases.
Kupffer Cells Mediate Leptin-Induced Liver Fibrosis.
GASTROENTEROLOGY 2009;137:713–723
JIANHUA WANG,* ISABELLE LECLERCQ,‡ JOANNE M. BRYMORA,* NING XU,* MEHDI RAMEZANI–MOGHADAM,* ROSLYN M. LONDON,* DAVID BRIGSTOCK,§ and JACOB GEORGE*
*Storr Liver Unit, Westmead Millennium Institute, University of Sydney and Westmead Hospital, Westmead, Australia; ‡Laboratory of Gastroenterology, Faculty of
Medicine, Université Catholique de Louvain, Brussels, Belgium; and §Center for Cell and Vascular Biology, Children’s Research Institute, Columbus, Ohio
瘦素(Leptin)是一由脂肪細胞(Adipocyte)所分泌之荷爾蒙,是調控體重及新陳代謝之重要因子。過去研究發現病態肥胖(Obese)、脂肪肝(Nonalcoholic steatohepatitis)及酒精性肝炎(Alcoholic liver disease)等病患之血液循環中,Leptin量有明顯增加。而近期研究報告指出leptin具有促進肝臟纖維化(Liver fibrosis)之能力,當中分子機理並未明確。
在肝纖維化過程中,肝臟星狀細胞(HSC)會被活化增生及促進胞外基質(ECM)產生,而鄰近之Kupffer細胞(KC)則已知可透過促發炎因子(Proinflammatory factor)和促纖維化因子(Profibrogenic factors)例如TGF-β1和ROS影響HSC表現。雖然HSC是肝纖維化過程中重要角色,前人研究卻發現leptin似對HSC無任何調控作用。故本篇作者針對Leptin是否透過間接作用於HSC鄰近之KC,刺激其產生促纖維化因子,以活化HSC。
為探討leptin直接或間接影響HSC之分子機理,本篇作者透過RT-PCR、Immunoblot等分子生物學方法,分別測定leptin刺激後HSC及KC中Collagen I、TIMP1等促纖維化因子基因及蛋白表現,發現leptin雖可促使HSC增生,但對其纖維化能力之影響甚微。而leptin可刺激KC中TGF-β1及CTGF/CCN2等肝纖維化中重要之cytokines表現。另發現Leptin-treated KC-conditioned培養液可刺激HSC增生及增加其中Collagen I、TIMP1等表現,得出了leptin是透過刺激KC來活化HSC之推論。作者亦於後續實驗中,透過磷酸化測定、EMSA等方法探討leptin訊號傳遞作用,發現leptin可活化KC中STAT3、ERK1/2、AKT等路徑,及下游因子AP-1、NF-κB,而此兩種蛋白具有增強TGF-β1及CTGF/CCN2基因表現之能力。
Pathophysiological mechanisms and consequences of gut edema (Annika Reintam W...WSACS
Gut edema in acute illness is not yet sufficiently studied and existing knowledge is largely based on experimental animal studies or small studies in healthy volunteers. However, increasing evidence confirms that gut edema impairs intestinal motility and healing of bowel anastomoses, being therefore an important contributor to outcome.
Current presentation focuses mainly on the role of fluids in development of intestinal edema.
Mahra Nourbakhsh's presentation, Hepatitis C Virus #1Mahra Nourbakhsh
The document summarizes information about hepatitis C virus (HCV) infection globally and in Canada. It provides statistics showing that an estimated 169.7 million people worldwide have HCV infection, with the highest prevalence rates in Africa, Southeast Asia, and the Eastern Mediterranean. In Canada, an estimated 242,500 people have HCV infection, with 7,900 new cases estimated in 2007. The document then outlines various aspects of HCV including transmission routes, natural history, diagnostic tools, viral life cycle, immunopathogenesis, progression of liver disease, and potential mechanisms of hepatic steatosis associated with HCV.
Cirrhosis results from different mechanisms of liver injury that lead to necroinflammation and fibrogenesis; Patients
with liver cirrhosis often require liver transplantation but it is affected by many problems, including relative operative
damage, high costs, lack of donors, and risk of rejection. Currently studies are shown the Stem cell therapy has the
potential to provide a valuable adjunct to the management of disease, Stem cell should be the natural candidates to
provide a renewable source of cells for transplantation.
The main mechanism of stem cell therapy is that stem cell capacity to differentiate into any of the hundreds of distinct
cell types that comprise the human body. In addition to their potential in therapeutics can be used to study the earliest
stages of human development and disease modeling using human cells.
Keywords: Cell Therapy; Liver Cirrhosis; Stem Cell; Transplantation. limitlessly, and often play the principal role in
liver regeneration
Hepatitis B virus X protein (HBx) plays a critical role in mediating cell growth and apoptosis. This study investigated the role of HBx in disrupting stress fiber formation and triggering apoptosis. The results showed that HBx expression increased phosphorylated myosin light chain and myosin light chain kinase levels. HBx disrupted stress fiber formation and regulated focal adhesion kinase and integrin-linked kinase through phosphatase and tensin homolog. Inhibiting myosin light chain kinase or phosphatase and tensin homolog restored effects caused by HBx, suggesting HBx triggers apoptosis through a myosin light chain kinase and phosphatase and tensin homolog dependent pathway by disrupting stress fiber formation.
This document summarizes a presentation on uremic toxins. It begins with an overview of current classifications of uremic toxins and the effects of some important toxins. It then discusses therapeutic approaches, including classifications of toxins, specific toxins like indoxyl sulfate and p-cresol, clinical outcomes associated with toxin levels, and dialytic and non-dialytic removal methods like gut modulation and adsorption. The document provides detail on classifications, toxin effects, and a range of therapeutic strategies for removing uremic toxins.
This document summarizes research on sperm cell motility, viability, and calcium regulation. It discusses how sperm motility is regulated by calcium levels, which are controlled by ion channels such as CATsper. Modulating calcium channels and reducing motility may increase sperm cell viability by decreasing reactive oxygen species production. The document also reviews the roles of factors like temperature, membrane potential, and ion currents in modulating calcium concentrations and sperm cell functions like capacitation and the acrosome reaction.
Bosche et al. - A differential impact of lithium on endothelium-dependent but...Dr. Bert Bosche
This document summarizes a study that investigated the effects of lithium on endothelium-dependent and endothelium-independent vessel relaxation. The study found that at lower therapeutic lithium concentrations (0.4 mmol/L), acetylcholine-induced endothelium-dependent vessel relaxation was slightly increased. However, at higher therapeutic and supratherapeutic lithium concentrations (0.8-100 mmol/L), endothelium-dependent vessel relaxation diminished in a concentration-dependent manner. In contrast, endothelium-independent vasorelaxation remained unaltered at any lithium concentration tested. Therefore, lithium has opposing effects on the endothelium depending on concentration, improving endothelium-dependent functions at lower levels but impairing them at
Oncology: Spatial Localization of Ras proteinsNachiket Vartak
This is a presentation of work done at the MPI Dortmund from 2008-2013 on the mechanism through with localization of the Ras protein in generated in cells. It presents the inhibiton Palmostatin-B, which inhibits this mechanism, leading to reveral of oncogenic signaling and cancerous phenotypes.
The repeated inflammation caused by monthly ovulation exposes the fallopian tube epithelium to oxidative stress, leading to transcription-associated mutations in the TP53 gene. This is believed to be the first step in the development of high grade serous ovarian carcinoma (HGSC). Estrogen and inflammatory cytokines generated during ovulation cause DNA damage in the fallopian tube cells through reactive oxygen species. Mutation of the TP53 gene prevents the cells from undergoing apoptosis in response to this damage, allowing genetic changes to accumulate and cancer to develop.
Alpha-1 Antitrypsin (α-1 AT) deficiency is a common genetic disorder that affects 1 in 2,000 individuals in the USA. Additionally, over 20 million people have been identified as carriers for this genetic disorder. In severe cases, α-1 AT deficiency can cause substantial lung and liver damage, which if left untreated could result in death and there are no current available treatments. Alpha-1 protein is produced in the liver, travels in the bloodstream and utilized in the lungs to protect healthy lung tissue from harmful destruction by elastase. A common single amino acid substitution, located at E342K (ATZ) was identified in α-1 AT deficient humans. When this specific mutation occurs two phenotypes can result: 1) ATZ can polymerize in the liver causing cellular toxicity 2) inhibits alpha-1 antitrypsin from inhibiting elastase which can result in lung disease. Currently; little is known about the cellular mechanisms that clear the accumulated proteins in the liver. Therefore, an investigative study utilizing C. elegans model of ATZ was performed in order to help determine the cellular mechanisms that dispose of accumulated proteins. Specifically RNA interference was utilized to knockdown expression of specific genes. This investigation examined genes involved in the heat-shock pathway (HSP), unfolded protein response (UPR), and insulin signaling pathway (IS). Phenotypic analysis including: embryonic lethality, protein aggregation expression, and longevity, was completed after knockdown of genes to determine effect on ATZ accumulation. Currently with our preliminary data suggests that the heat-shack pathway may play a role in ATZ accumulation. Determining the mechanism of protein accumulation in the investigation of C. elegans may lead to possible drug targets and therefore the development of a treatment which may alleviate those diagnosed with this disorder.
Hypotonic Isotonic And Hypertonic SolutionsKimberly Jones
This experiment aims to determine how solute concentration, particle size, and a membrane's
selective permeability affect diffusion. It is hypothesized that potassium permanganate will diffuse
further than methylene blue in agar due to its smaller molecular mass. Starch will remain in a
dialysis tube while iodine enters due to their size difference. A dialysis tube with higher internal
solute concentration will gain volume via osmosis, while one in a hyperosmotic solution will lose
volume.
This study examines how applied hydrodynamic drag force affects the contractions of live Vorticella by impeding their contractions in a microfluidic channel. As the stall force increased by changing the flow rate and viscosity of the solution, the contracted stalk length increased and maximum contraction speed decreased, while contractions took longer. The time lag in contraction between the zooid and stalk also increased. This implies that the stalk cannot contract until it develops enough force to overcome the stall force. As stall force increased, relaxations took longer and the stalk resumed contraction after the force was removed, showing that the spasmoneme retains contractile force but the stall force extends the stalk.
The document summarizes several key studies from 2011 related to glomerular diseases, polycystic kidney disease, acute kidney injury, and transplantation. Notable findings include identification of bovine serum albumin as a potential antigen in membranous nephropathy, discovery of soluble urokinase receptor as a circulating factor in recurrent focal segmental glomerulosclerosis, and evidence that tolvaptan and metformin may be novel therapeutics for polycystic kidney disease by inhibiting vasopressin and mTOR pathways respectively.
This document summarizes an experiment that investigated the relationship between gamma radiation exposure and cellular senescence in human lymphocytes. 20 samples of lymphocytes were irradiated with doses from 0 to 4 Gray of gamma radiation. The cells' p16 proteins were then analyzed using fluorescent antibodies to identify senescent cells. The results showed a positive quadratic correlation between radiation dose and the occurrence of senescence, indicating more cells underwent senescence at higher doses. More trials are needed to establish a more accurate connection and reduce procedural errors.
This document presents information on protein folding and mechanisms that conserve protein folding. It discusses how chaperones, such as the GroES/GroEL complex, assist in protein folding. The GroES/GroEL complex uses ATP to encapsulate proteins and release them once folded. Chaperones help prevent protein misfolding and aggregation, which can cause diseases. Clinical examples provided include how protein aggregation can lead to diseases like sickle cell anemia, cystic fibrosis, Huntington's, Alzheimer's, and Parkinson's.
This document summarizes research aiming to determine the role of post-translational modifications like ubiquitination on the lipid binding affinity of the Angiomotin 130 protein. Site-directed mutagenesis was used to induce mutations mimicking or preventing ubiquitination at specific lysine residues in the ACCH domain. Preliminary spot blot assays suggest mutating lysine 87 to glutamate does not decrease lipid binding affinity, but more work is needed to characterize the effects of ubiquitinating specific residues. Future work will confirm mutations, perform lipid binding assays to quantify affinity changes, and identify residues for further study using full-length protein constructs.
This document summarizes a study that characterized double-gene knockout mutants of Escherichia coli. Specifically, it investigated how deleting a second gene, the glyoxylate shunt gene aceA, affected the growth of the E. coli Dpgi mutant. It also examined how the order of gene deletions impacted the growth rates and substrate uptake rates of double mutants. Transcriptomic analysis identified differential expression of the gene aceK, which may explain phenotypic differences between mutants. The study integrated phenotypic analysis, metabolic modeling, and transcriptomics to better understand how latent reactions influence mutant physiology and the implications for microbial genetics and metabolic engineering.
Cystinosis is an autosomal recessive metabolic disease that belongs to the family of lysosomal storage disorders (LSDs).
Cystinosis is a monogenic hereditary disease caused by mutations or deletions in the ubiquitous gene CTNS, encoding the lysosomal transmembrane cystine transporter, cystinosin.
This gene encodes a seven-transmembrane lysosomal protein, which is a proton-driven cystine transporter.
Similar to Presentation format4 posttranslational modification in cell adhesion and migration (20)
Evidence of Jet Activity from the Secondary Black Hole in the OJ 287 Binary S...Sérgio Sacani
Wereport the study of a huge optical intraday flare on 2021 November 12 at 2 a.m. UT in the blazar OJ287. In the binary black hole model, it is associated with an impact of the secondary black hole on the accretion disk of the primary. Our multifrequency observing campaign was set up to search for such a signature of the impact based on a prediction made 8 yr earlier. The first I-band results of the flare have already been reported by Kishore et al. (2024). Here we combine these data with our monitoring in the R-band. There is a big change in the R–I spectral index by 1.0 ±0.1 between the normal background and the flare, suggesting a new component of radiation. The polarization variation during the rise of the flare suggests the same. The limits on the source size place it most reasonably in the jet of the secondary BH. We then ask why we have not seen this phenomenon before. We show that OJ287 was never before observed with sufficient sensitivity on the night when the flare should have happened according to the binary model. We also study the probability that this flare is just an oversized example of intraday variability using the Krakow data set of intense monitoring between 2015 and 2023. We find that the occurrence of a flare of this size and rapidity is unlikely. In machine-readable Tables 1 and 2, we give the full orbit-linked historical light curve of OJ287 as well as the dense monitoring sample of Krakow.
PPT on Alternate Wetting and Drying 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.
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.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
Microbial interaction
Microorganisms interacts with each other and can be physically associated with another organisms in a variety of ways.
One organism can be located on the surface of another organism as an ectobiont or located within another organism as endobiont.
Microbial interaction may be positive such as mutualism, proto-cooperation, commensalism or may be negative such as parasitism, predation or competition
Types of microbial interaction
Positive interaction: mutualism, proto-cooperation, commensalism
Negative interaction: Ammensalism (antagonism), parasitism, predation, competition
I. Mutualism:
It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which mutualist and host are metabolically dependent on each other.
Mutualistic relationship is very specific where one member of association cannot be replaced by another species.
Mutualism require close physical contact between interacting organisms.
Relationship of mutualism allows organisms to exist in habitat that could not occupied by either species alone.
Mutualistic relationship between organisms allows them to act as a single organism.
Examples of mutualism:
i. Lichens:
Lichens are excellent example of mutualism.
They are the association of specific fungi and certain genus of algae. In lichen, fungal partner is called mycobiont and algal partner is called
II. Syntrophism:
It is an association in which the growth of one organism either depends on or improved by the substrate provided by another organism.
In syntrophism both organism in association gets benefits.
Compound A
Utilized by population 1
Compound B
Utilized by population 2
Compound C
utilized by both Population 1+2
Products
In this theoretical example of syntrophism, population 1 is able to utilize and metabolize compound A, forming compound B but cannot metabolize beyond compound B without co-operation of population 2. Population 2is unable to utilize compound A but it can metabolize compound B forming compound C. Then both population 1 and 2 are able to carry out metabolic reaction which leads to formation of end product that neither population could produce alone.
Examples of syntrophism:
i. Methanogenic ecosystem in sludge digester
Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria.
Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane.
ii. Lactobacillus arobinosus and Enterococcus faecalis:
In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone.
The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
Travis Hills of MN is Making Clean Water Accessible to All Through High Flux ...Travis Hills MN
By harnessing the power of High Flux Vacuum Membrane Distillation, Travis Hills from MN envisions a future where clean and safe drinking water is accessible to all, regardless of geographical location or economic status.
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdfSelcen Ozturkcan
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
Presentation format4 posttranslational modification in cell adhesion and migration
1. Posttranslational modification in
cell adhesion and migration
with emphasis on acetylation
Dipl.-Ing. Birgit Kastberger
Department of Cellular Physiology and
Metabolism, University Medical Center,
University of Geneva
Oral exam: November 7, 2014
2. Cell
Extracellular matrix (ECM)
Integrins are involved in cell adhesion and migration
provide a link from the ECM to the actin cytoskeleton
a b1A
Harvard University, BioVisions-The Inner Life Of A Cell, 2011
Integrins
Actin
3. adaptor and b1A integrin PTMs
are involved in cell adhesion & migration
Filopodial contacts
first contact with ECM
spreading
Lamellipodia
adhesion, maturation, signalling
Focal adhesions
ECM remodelling
Fibrillar adhesions
W. Hu et al, Plos One, 2014, Geiger, et al., Nature Reviews Molecular Cell Biology, 2001
Fibrillar adhesions: ↓phospho-Tyrosine, ↑Tensin
Tensin
Focal adhesions: ↑phospho-Tyrosine
pTyr
… integrins
… weblike/remodeling actin
… adaptor proteins
… bundled/contractile
actin stress fibres
4. b1A integrin tail is phosphorylated and acetylated
Extracellular
domain: 21-728 aa
Transmembrane
domain: 729-751 aa
Cytoplasmic
tail: 752-798 aa
β1A LLMIIHDRREFAKFEKEKMNAKWDTGENPIYKSAVTTVVNPKYEGK
What role do PTMs play?
PP P PPP Ac
5. Over 200 distinct covalent PTMs diversify the proteome
KL Vermillion et al, JCB, 2014; Prabakaran et al, Wiley P., 2012, Thermo Scientific: post-translational-modification
Most frequent PTMs
experimentally observed
Khoury et al., Sci. Rep. 1, 2014 (2011)
P h o s p h o ry la tio n
A c e ty la tio n
M e th y la tio n
O th e rs
P
P P
P Ac
Ac
Me AcAc
6. 3 examples of more widely studied reversible PTMs : phosphorylation
t1/2=20min
Donor: ATP
Kinase
Phosphatase
x Okadaic acid, H2O2
x
Imatinib, Dasatinib, Staurosporin
EGF, PDGF
experimental phosphoryl. frequencynorm to aa frequ. pY/pT/pS: 1/1/4
+PO4
-3 provoke charge modification
Kinases > high Kd for ATP > makes them operate close
to independently from ATP concentrations
Arena et al, CMLS, 2005; S. Prabakaran et al., Wiley Periodicals, 2012
phosphorylation modulates
• activity
• conformation
• docking sites
7. Phosphorylation in cell adhesion and migration: Cofilin
K. Rottner et al 2011 Curr. Opin. Cell Biol; Y. Zhang, Genes Dev, 2012, Mizuno, Cellular Signalling, 2013; Moriyama, Genes Cells, 1996; Nagai et al, Genes & Cancer, 2012;
Harvard University, BioVisions-The Inner Life Of A Cell, 2011
Cofilin ↑pSer3 inactive Cofilin does not bind actin
(phospho mimic S3D mutation)
β1 integrin triggers downstream phosphorylation of
pSer3 in Cofilin
↓pSer3 active Cofilin binds to actin
found at the leading edge of mobile cells
is required for directional migration
severs actin filaments
Cofilin
active
Cofilin
Ser-3
P
inactive
Ser-3
↑dephospho mimic S3A mutant >
↑cell migration and invasiveness
invading astrocytoma
brain cancer cell
number through the
matrigel-precoated
membrane
activity regulated by phosphorylation >
local K/P concentration
8. 3 examples of widely studied reversible PTMs: methylation
S. Prabakaran et al., Wiley Periodicals, 2012; S. Lanouette et al, Mol. Syst. B., 2014, Vermillion et al, JCB, 2014
Methyl Donor: SAM
Lysine Methyl-Transferase (HMT)
t1/2= very stable
GSK J4 HCl
x
only small mass change
↑ protein stability
modulates interactions between
protein/DNA, protein/protein: docking site
no change of positive charge
crosstalks with PTMs
x
Demethylase (HDM)
Mono- Di- Tri-methylation
↓ hydrogen bond formation
not erasable by hydrolysis
but via oxidative conversion > into hydrolytically labile imine
methylation
Competitive inhibitors for SAM:
Trifluoroacetate salt, UNC0631 each methyl group > ↑ hydrophobicity of hydrophilic Lys
9. Lysine-Methylation in cell adhesion and migration:
elongation factor 1-a1 (EF1a1) methylation is required for neural crest migration
K.L. Vermillion et al, JCB, 2014
IF
Control chicken embryo
no change in neural crest migration
(at somite 9 stage)
EF1a1 binds to the actin cytoskeleton at the
leading edge of migratory neural crest cells
Sox10: Protein specifically present
in migrating neural crest cells
GFP GFP
GFP GFP
6x di-/tri-methylated K (found by MS)
to methylation resistant A
EF1a1 prevents or promotes
actin polymerization (conc.
dep.)
methylation resistant EF1a1 expression > ↓ cell migration distance
10. 3 examples of more widely studied reversible PTMs: acetylation
t1/2= 1-60min
Acetyl transferase (HAT)
or equilibrium reaction
Deacetylase (HDAC)
Glucose, EtOH
x
SBHA, TSA, SAHA
Anacardic acid
Resveratrol, SRT-501
(are well tolerated in humans)
Lundby et al, Cell Reports, 2012; Friis et al, Nucleic Acids Research 2009; Walsh et al,
Angew. Chem. Int. Ed., 2005; Okanishi et al, J. proteome research, 2013; S. Prabakaran
et al., Wiley Periodicals, 2012
Lys-e amine acetylation neutralizes its positive charge
• alters hydrogen bonds
• alters stability
• docking site
• hampers electrostatic interaction
• increases hydrophobicity of hydrophilic Lys
• tissue-type acetylation pattern
• cell compartment specific Lys acetylation
x
Donor: AcCoA
11. Lysine is the most heavily modified amino acid
• Lys acetylation blocks other PTMs
• lengthens protein’s lifetime (e.g. p53)
XJ Yang, Mol. Cell., 2008
12. 18 human HDAC enzymes classified into 4 groups
based on yeast homology
Kelly et al, Ashley Publications, 2002; Kim et al, Am J Transl Res, 2011; Sadoul et al, J. Biomed. and Biotech., 2011;
Grant, Academic Press, p89, 2012; Michishita et al, MBC, 2005
HDACs class III
SIRT 1/2cytop/3/4/5/6/7
NAD+
ubiquitously expressed
high expression in brain, testis
HDACs class I
1/2/3cytop/8cytop
Zn2+
ubiquitously expressed
TSA HDACs class II
IIa: 4cytop/5cytop/7cytop/9cytop
IIb: 6cytop/10cytop
Zn2+
predominant in heart,
smooth muscle, brain, kidney
TSA
HDACs class IV
11cytop
Zn2+
predominant in heart,
smooth muscle, brain, kidney
TSA
13. Acetylation can mingle with other PTMs to form complex regulatory
programs
XJ Yang, Mol. Cell., 2008; Rao et al, BMC Bioinformatics, 2013; Z. Lu et al, Plos One, 2011; Latham et al, Nat Struct Mol Biol, 2007
46.0% of studied Ac-Lys are
predicted to have an effect on
phosphorylation sites:
• creation/destruction of a
phosphorylation site
• alterations in kinase binding
Z. Lu et al, Plos One, 2011
#ofalteredphosphorylationsites
Distance from K-Ac
Distance distribution of altered phosphorylation site to K-Ac (Q)
in silico perturbation of the microenvironment
through substitution of Lys (K) (+) with Glu (Q) (neutral), mimicking a neutral Ac-Lys
14. autophagy
amino acid
degradation
Acetyl-CoA: the crossroads of fat, sugar and protein catabolism
J. Patel et al., Nutrition & Metabolism, 2011; Choudhary et al, Nature reviews, 2014; Wellen et al, Nature reviews, 2012; Mariño et al, cell press, 2014
acetate can be produced by
• deacetylation reactions
• ethanol metabolism in the liver
• by bacteria in the colon
Citrate-Shuttle
nutrient starvation > depletes AcCoA
provokes autophagy
caloric intake elevates Acetyl-CoA concentrations
acetyl-CoA concentration influences
• HAT activity
• overall acetylation level
↑↓
15. 2 examples of protein acetylation in cell adhesion and migration:
a-tubulin acetylation reduces cell motility
XJ Yang et al, cell press, 2008; Joo et al, nature communications, 2014; Glozak, science direct, 2005; Harvard University, BioVisions-The Inner Life Of A Cell, 2011
welkescience
Microtubles
• α- and β-tubulin dimers form long, hollow cylinders
• component of cytoskeleton
• platforms for intracellular transport (secretory vesicles, organelles)
Microtubules
Deacetylation: HDAC6, SIRT2
↑microtubule acetylation
• ↓reduces cell migration
• ↑increased stability
↓ microtubule acetylation
• found at leading edge
• prone to ↑depolymerization
• ↑HDAC6 >↓microtubule acetylation >
↑cell migration speed
16. 2 examples of protein acetylation in cell adhesion and migration:
Cortactin acetylation reduces cell motility
X. Zhang et al, Cell Press, 2007; Y. Zhang et al, Oncogene, 2009; XJ Yang et al, cell press, 2008; Kirkbridge et al, Cell Adhesion and Migration, 2011;p ;
Harvard University, BioVisions-The Inner Life Of A Cell, 2011
Cortactin
Cortactin
• cytoplasmic, monomeric
• regulates branched actin assembly & stabilization at leading edge
• abnormally expressed in many human tumours
↑ overexpression > ↑invasiveness and ↑migration
↓ depletion > ↓ impairs cell migration
Acetylation: p300
Deacetylation: HDAC6 and Sirt1
deacetylated cortactin
• ↑ cells migrate faster
• translocates to cell periphery
• ↑ actin binding
• ↑ high levels of SIRT1
• observed in tumours
hyperacetylated cortactin (up to 10 residues)
• ↓ translocation to the cell periphery
• ↓ association with actin
• ↓cell motility
17. Drug effects on cell acetylation state and disease: HDAC inhibitors
Singh et al, ERAT, 2010; Choudhary et al, Science, 2009; Wikipedia: SAHA, 2014; stocan.weebly.com, 2014; penn-medicine-lung-transplant.blogspot.ch, 2014
SAHA (Vorinostat)
• FDA approved
• treatment for cutaneous T-cell lymphoma (CTCL)
• anti-cancer drug with low toxicity
• competes with Zn2+ > blocks active site of HDACs
• affects growth/survival of tumor cells
• ↑ overall protein acetylation
• provokes tumour selective
↑ pro-apoptotic gene
↓ pro-survival gene
HDAC-1
gastric cancer
lung cancer
HDAC-5/10
HDAC inhibitors are anticancer drugs
• ↑ cell cycle arrest/apoptosis/autophagy
• ↓ metastasis/angiogenesis
• ↑ acetylation mediated p53 activation > ↑ p53’s half life
SAHA
HDACs are often deregulated in cancer
18. Drug effects on cell acetylation state and disease: Glucose
Miller et al, MBoC, 2014; Choudhary et al; Nature reviews, 2014
↑SIRT1
consequences of high glucose conditions for adhesion/matrix
↑ increase integrin cell adhesion
↑ stimulate FN polymerization
diabetics > ↑ higher plasma glucose concentrations > may entail
greater ↑overall protein acetylation
E.g. diabetic nephropathy comes with ECM expansion
↓glucose restriction
↑ provokes glucose production from fatty acids > maintains
blood glucose levels
↑ SIRT1 > ↓ acetylation of proteins?
↑high concentrations of glucose
↑ acetyl-CoA levels
↑ overall protein acetylation
↑ fatty acid production
19. Drug effects on cell acetylation state and disease: EtOH
Blythe et al, alcoholism: Clinical and Experimental research, 2010; Kannarkat, Journal of Hepatology, 2006; Lieberman et al, Wolters Kluwer, 2012
3 male rats fed 5 weeks with 36% ETOH
containing diet
Arrows: 2 fold or greater increase of acetylation
Acetyl-CoA
liver’s EtOH
metabolism
EtOH transformed into acetate (liver) > acetate metabolized to AcCoA
Anti-acetyl Lysine antibody of rat livers
highly reactive
with Lys
not toxic
treatment chronic liver disease > ↓ overall acetylation
HDAC activator Resveratrol attenuates fatty liver in alcohol-exposed mice
• chronic EtOH consumption provokes liver protein
↑hyperacetylation (3x ↑): tubulin, actin, cortactin, p53
• key factor in liver injury
mitochondrial dysfunction, altered protein trafficking
• after EtOH withdrawal > acetylation remains
• 0.04 ‰ endogenous EtOH in human blood
bacterial fermentation
caloric intake > 0.06 ‰
• EtOH exposure to cells > ↑protein acetylations, phosphorylations,
methylations
20. Conclusion: cell adhesion and migration are crucial for organisms
• structural organization
embryogenesis
body growth
• body function
immune responses
repair after injury
• constant dynamics
tissue remodelling
tissue renewal (adult’s cell age: 7-10 years)
• maintain body structure
connective tissue
epithelial tissue
• allow cell movement
matrix modelling
adhesion making/breaking
Spalding et al, Cell, 2005; Alberts, 2008
Cell-Matrix adhesions: via integrins
Cell migration: via cytoskeleton
PTMs drive integrin function
PTMs drive the function of
cofilin, a-tubulin, cortactin, EF1a1
Cell adhesion and migration are essential for the structure and maintenance of
multicellular organisms & PTMs are involved in their regulation
21. Thank you for your attention!
Now it’s time for questions..
22. PTMs crosstalking evidence: the p53 example
DNA damage> p53 activation
• via methylation-acetylation-phosphorylation cascade
• Lys372 methylation required for p53 acetylation
• Lys370 and Lys372 acetylation on p53
change DNA binding specificity
forms docking sites for transcriptional co-activators
enhances nuclear localization
impairs methylation, ubiquitination > ↑ p53 half-life
• impacts on phosphorylation of Ser371
contributes to p53 stabilization
cell cycle arrest through targeted protein expression
Acetyltransferases (HAT): p300
Deacetylases (HDACs) : HDAC1, HDAC3, SIRT1, SIRT7
p53-transcription factor, tumour suppressor
• very unstable
• may be ac, p, m, ub,..
• gene mutated in 50% of human cancers (eg Lys 120)
• in nucleus/cytoplasm at low levels (unstressed cells)
• activated p53 protein induces cell-cycle arrest/apoptosis
mice with 7xKR mutations at the C-term
including Lys370/372:
viable and phenotypically normal
Patel et al, Nutrition & Metabolism, 2011; XJ Yang
et al, Cell, 2008; Walsh et al, Angew. Chem., 2005;
Ashcroft, et al Mol. Cell. Biol., 1999
Editor's Notes
May I list the functions of integrins with the help of this scheme
Integrins serve as mechanical link to ECM & provide signalling in response to mechanical tension
b1A Integrin
-b1A synthesises (fibrillogenesis) and migrates on the fibronectin scaffold
knock out of b1A is lethal in mice embryos (Baudoin et al, 1998)
Since integrin signaling is also bidirectional (outside the cell to inside the cell and vice versa)
Filopodia are spike like projections of the plasma membrane that allow a cell explore its environment
which HDACs are involved
siRNA: small interfering RNA, =transient
46 aa in tail
Within the last few decades, scientists have discovered that the human proteome is vastly more complex than the human genome. While it is estimated that the human genome comprises between 20,000 and 25,000 genes (1), the total number of proteins in the human proteome is estimated at over 1 million (2). These estimations demonstrate that single genes encode multiple proteins. Genomic recombination, transcription initiation at alternative promoters, differential transcription termination, and alternative splicing of the transcript are mechanisms that generate different mRNA transcripts from a single gene
phosphoryl frequency: pY/pT/pS: 1/2/8 ; aa frequency: Y/T/S: 1/2/2
ILK: pseudo kinase; FAK functions without kinase activity, ckit has also kinase unrelated functions
perphosphate group
SH2 +PTB domain binds pTyrosine; 14-3-3 +WD40 domain binds pS/pT
Protein Kinases constitute the largest single enzyme family in the human genome
1/3 of all proteins in mammalian cells can undergo phosphorylation
Kinases have a big variety spectrum of substrates> reflecting the true complexity of signal transduction cascades.
Of the hundreds of PTMs identified, the most intensively studied is protein phosphorylation, in which protein kinases (PK) attach phosphate moieties to Ser, Thr, or Tyr residues. Protein phosphorylation appears to play an essential role in many diverse and critical cellular processes, and inhibitors of their function have emerged as important modes of therapy for malignant diseases.
Phosvitin is one of the egg (commonly hen’s egg) yolk[1][2] phosphoproteins known for being the most phosphorylated protein found in nature.[3][4][5] Phosvitin isolation was first described by Mecham and Olcott in the year 1949
Casein (/ˈkeɪs.ɪn/ or /ˈkeɪˌsiːn/, from Latin caseus, "cheese") is the name for a family of related phosphoproteins (αS1, αS2, β, κ). These proteins are commonly found in mammalian milk, making up 80% of the proteins in cow milk and between 20% and 45% of the proteins in human milk
NaVO4: Sodium orthovanadate
NaF: Sodium Fluoride
EGF: epidermal growth factor
PDGF: platelet-derived growth factor
tyrosine-kinase inhibitors (TKIs) operate by four different mechanisms: they can compete with adenosine triphosphate (ATP), the phosphorylating entity, the substrate or both or can act in an allosteric fashion, namely bind to a site outside the active site, affecting its activity by a conformational change
Left panel: Protein kinases mediate phosphorylation at serine, threonine and tyrosine side chains, and phosphatases reverse protein phosphorylation by hydrolyzing the phosphate group. Right panel: Phosphorylation causes conformational changes in proteins that either activate (top) or inactivate (bottom) protein function.
How to increase phosphorylation: activating drugs from Masspec England
Phosphorylation in cancers
PIP2 regulates cofilin activity by binding cofilin and inhibiting cofilin from binding to F-actin
Serine residue at position 3
Aspartic acid (S3D)
(B) Results of cell migration assays. EV, WT, S3A, and S3D cells were seeded through a cell sedimentation manifold to establish a
circular confluent monolayer on substrate-coated wells (bovine serum albumin [BSA] or laminin [LN]). The cells were allowed to migrate for 24 hours, and photographs were taken before and after migration. Bar graphs show average migration rate calculated as the change in the diameter of the circle circumscribing the cell population over a 24-hour period. Asterisks indicate statistically significant differences (*P = 0.006, **P = 0.005). (C) Results of cell
invasion assay. (Left) Bar graphs showing the average invading cell number through the Matrigel-precoated membrane with 8-mm pores within 24 hours
in 6 random light microscopic fields magnified at 200 times. Asterisk indicates statistically significant difference (*P = 0.011). (Right) Photomicrographs of
the membranes with the invading cells stained with 0.5% crystal violet. Original magnification 200×.
Chromo domain binds methyl Lys
Methylation is a regulator of ubiquitination
SAM: S-adenosylmethionine made out of ATP and aa methionine
HMT do not only methylate Histones but alsol nonhistone proteins
How to increase methylation: traumata, decrease: Psychopharmaca, histones (acetylation, methylation but in cytoplasmic proteins)?
All evidence suggests that EF1a1 methylation is not required for translation (Sherman et al, 1989; Cavalius et al, 1997; Polevoda et al, 2007)
EF1a1 is primarily known as a component of the translational machinery: it shuttles tRNA into the ribosomal position; it binds both actin and actin mRNA at the leading edge, is thought to enable localized actin translation to facilitate actin polymerization for motility
EF1a1 can either prevent or promote actin polymerization depending on its cellular concentration, EF1a1 levels are developmentally regulated
At 4-6 somites the EF1a1 6mm mutant elicited a similar range of neural crest specification> so the mutant does not disrupt EF1a1 activity during specification much as a methylation-resistant EF1a1 does not affect translation in yeast.
Methylation is a regulator of ubiquitination
SAM: S-adenosylmethionine
HMT do not only methylate Histones but alsol nonhistone proteins
How to increase methylation: traumata, deacrease : Psychopharmaca, histones (acetylation, methylation but in cytoplasmic proteins)?
for Bromo domains
SAHA: suberoylanilide hydroxamic acid
transcription factor/ tumour suppressor protein: p53
E/Glu: Glutamic acid, D/Asp: Aspartic acid
The acetylation of histone neutralizes the positive charge of
lysine residues resulting in a decrease in the binding affinity for
the negatively charged phosphate groups of DNA.
require a zinc molecule as cofactor in their active site
10 cytoplasmic found HDACs
Q: Glutamine
Cartoon illustrating crosstalk between phosphorylation and acetylation. Different signals act on Ser (S), Thr (T) or Tyr (Y) phosphorylation, which in turn affects acetylation of a neighboring Lys. Acetylation might also regulate phosphorylation. The Lys can be adjacent to or far away from the phosphorylation site, which can be either N-terminal or C-terminal from the acetylation site.
from citrate ATP citrate lyase (ACL): Citrat shuttle: Ac-CoA+Oxalacetat
from acetate by acetyl-CoA synthetase (ACS)
from pyruvate by the pyruvate dehydrogenase complex (PDC)
tricarboxylic acid (TCA) cycle (also known as the citric acid cycle).
In mammalian cells, Ac-coA is synthesized in two pathways. In the first pathway, Ac-coA synthetase condenses acetate and coenzyme A into Ac-coA. In mammals, acetate can be produced by deacetylation reactions, by ethanol metabolism in the liver and by bacteria residing in the colon; acetate can then be used to produce acetyl-CoA
In the second pathway, energy from hydrolyzed ATP is utilized by ATP-citrate lyase (ACL) to convert citrate, a TCA cycle intermediate, and coenzyme A into Ac-coA and oxaloacetate.
Compartmentalized synthesis of acetyl-CoA. a | In mammalian cells, mitochondrial acetyl-coenzyme A (acetyl-CoA) is produced from pyruvate by the pyruvate dehydrogenase complex (PDC) or by the β-oxidation of fatty acids, and then feeds into the tricarboxylic acid (TCA) cycle (also known as the citric acid cycle). Citrate can be exported from mitochondria into the cytoplasm, where it freely diffuses into and out of the nucleus. The extra-mitochondrial pool of acetyl-CoA, which is used for protein acetylation or for lipogenesis, is synthesized from citrate by ATP citrate lyase (ACL) or from acetate by acetyl-CoA synthetase (ACS). ACS is localized in the cytoplasm and ACL is localized in the cytoplasm and the nucleus60, which implies that acetyl-CoA is produced in both compartments. Because these enzymes use different substrates for generating acetyl-CoA, the relative importance of ACL and ACS in non-mitochondrial acetylation may depend on differences in carbon source utilization.
Microtubulin, Yamada paper, which HDACs are involved
which HDACs are involved
which HDACs are involved
Cutaneous T cell lymphoma (CTCL) is a type of cancer of the immune system. Unlike most non-Hodgkin's lymphomas (which are generally B-cell related), CTCL is caused by a mutation of T cells. The malignant T cells in the body initially migrate to the skin, causing various lesions to appear. These lesions change shape as the disease progresses, typically beginning as what appears to be a rash which can be very itchy and eventually forming plaques and tumors before metastasizing to other parts of the body.
Occlusion of the arterioles
↑ provokes glucose production from fatty acids (gluconeogenesis)
which HDAC, in vitro fertilisation s are involved
Mesangial cells are specialized cells around blood vessels in the kidneys, at the mesangium.
which HDACs are involved
Connective tissue (plentiful ECM-sparsely distributed cells, rare cell-cell contacts)
Epithelial tissue (close-lined up cells bound to basement membrane by hemidesmosomes a6b4 integrin (Laminin las ECM ligand)
Immune system: Macrophages, Neutrophils
For their great support
-proteins regulating kinase signalling are enriched for acetylation (MS data) > suggesting crosstalk between acetylation and phosphorylation
-Acetylation of histone H3 at Lys9 and Lys27 crosstalks with phosphorylation of Ser10 and Ser28, respectively (Latham and Dent, 2007) Positive crosstalk has been reported between acetylation of Lys14 and phosphorylation of Ser10 in histone H3, and our findings correctly predict this interaction. multiple enzymes appear to phosphorylate histone protein H3 at residue Ser10 which appears to stimulate acetylation at Lys14 (positive crosstalk). Conversely, this phosphorylation blocks acetylation and methylation at Lys9 in the same protein (negative crosstalk) (Latham et al, Nat Struct Mol Biol, 2007)