This document discusses extracting protein interactions from biomedical literature. It notes that while databases contain some known interactions, much information remains in unstructured text across millions of published articles. The document presents an example Medline abstract describing interactions between cyclin A, cyclin D1, CDK subunits, and the Rb protein. It aims to develop automated methods to locate and structure such interaction information at scale from literature.
1) The study investigates how localized protein translation in axons regulates presynaptic development at synapses.
2) The researchers developed a method to selectively repress cap-dependent translation in axons using a targeted translational repressor.
3) They found that repressing axonal translation enlarged synaptic vesicle recycling pools, and this effect was partly due to decreased levels of p35, a protein involved in regulating vesicle recycling pools. Local translation of p35 mRNA in axons normally helps regulate vesicle recycling.
Glypican and Biglycan in the Nuclei of Neurons and Glioma CellsYu Liang
This document describes a study that found glypican and biglycan, two proteoglycans, localized to the nuclei of neurons and glioma cells. The researchers identified nuclear localization signals in the amino acid sequences of both proteoglycans. They demonstrated that these signals were functional by showing nuclear localization of beta-galactosidase fusion proteins containing the sequences. Nuclear localization was reduced or abolished when the basic amino acids in the signals were mutated. Dynamic changes in glypican immunoreactivity in the nucleus of glioma cells were also observed during cell division and different phases of the cell cycle. The findings suggest glypican and biglycan may be involved in regulating cell division and survival by participating in nuclear processes in
This document summarizes a study that used computational methods to predict the low-energy conformations of the CCR5 receptor and the binding sites for various ligands. It found that different ligands bind to different receptor conformations. It then validated the predictions by experimentally testing the effects of 11 single point mutations on ligand binding. The predicted binding energies from the mutant receptor conformations matched well with experimental results, supporting the concept that each ligand can stabilize a different receptor conformation.
N-acetyl-D-glucosamine kinase (NAGK) interacts with dynein light-chain roadblock type 1 (DYNLRB1) at dendritic branch points in neurons. Immunocytochemistry and proximity ligation assays showed colocalization of NAGK and DYNLRB1 on microtubule fibers at dendritic branches. NAGK was also found to interact with Golgi outposts and DYNLRB1 at branch points, indicating a tripartite interaction between NAGK, dynein, and Golgi that regulates dendritic growth and branching. Introduction of a peptide derived from DYNLRB1 stunted dendrite development in cultured neurons.
I presented two fascinating stories where Molecular Dynamics simulations contributed to enhancing our understanding of immunodeficiencies. In one of the projects, the treatment of patients could be improved. These slides were presented at the Basler Modeller Stammtisch, 26.02.2021
Milap Thaker - Biology Powerpoint: Harvard University - DNA Damage Checkpointsmilapthaker
The document discusses two mechanisms by which DNA damage checkpoints inhibit mitotic exit in yeast cells. First, the Rad53 checkpoint kinase prevents mitotic exit by inhibiting the Mitotic Exit Network (MEN). Second, the FEAR pathway promotes limited release of the phosphatase Cdc14 from the nucleolus early in anaphase. The study finds that Rad53 acts through the Dun1 kinase to regulate the MEN more directly, while FEAR provides an alternate mechanism for temporary Cdc14 release and a delay in full mitotic exit. Experiments visualize budding, Cdc14 localization, and DNA content in various yeast strains to illustrate the two inhibitory mechanisms.
This study characterized the Dvilp7 gene from Drosophila virilis through a series of experiments. RNA was purified from D. virilis and used to construct cDNA. RACE experiments were used to amplify the 5' and 3' ends of the Dvilp7 cDNA sequence. The full Dvilp7 cDNA sequence was assembled and found to encode a putative protein with a signal peptide. Genomic DNA was also sequenced and compared to determine intron sequences. Characterizing the Dvilp7 gene expands understanding of the genetic mechanisms regulating insulin signaling in Drosophila.
This study examined the association between genetic variants in the human netrin G1 gene and schizophrenia. The researchers identified 10 single nucleotide polymorphisms in the netrin G1 gene and genotyped them in 180 schizophrenia patients and 180 healthy controls. One polymorphism, IVS8-1467C>T, showed a significant allelic association with schizophrenia, with the C allele being overrepresented in patients. Haplotype analysis also found a multi-SNP haplotype in high linkage disequilibrium with IVS8-1467C>T that was significantly associated with schizophrenia. These findings suggest that netrin G1 or a nearby gene may contribute to genetic risk for schizophrenia.
1) The study investigates how localized protein translation in axons regulates presynaptic development at synapses.
2) The researchers developed a method to selectively repress cap-dependent translation in axons using a targeted translational repressor.
3) They found that repressing axonal translation enlarged synaptic vesicle recycling pools, and this effect was partly due to decreased levels of p35, a protein involved in regulating vesicle recycling pools. Local translation of p35 mRNA in axons normally helps regulate vesicle recycling.
Glypican and Biglycan in the Nuclei of Neurons and Glioma CellsYu Liang
This document describes a study that found glypican and biglycan, two proteoglycans, localized to the nuclei of neurons and glioma cells. The researchers identified nuclear localization signals in the amino acid sequences of both proteoglycans. They demonstrated that these signals were functional by showing nuclear localization of beta-galactosidase fusion proteins containing the sequences. Nuclear localization was reduced or abolished when the basic amino acids in the signals were mutated. Dynamic changes in glypican immunoreactivity in the nucleus of glioma cells were also observed during cell division and different phases of the cell cycle. The findings suggest glypican and biglycan may be involved in regulating cell division and survival by participating in nuclear processes in
This document summarizes a study that used computational methods to predict the low-energy conformations of the CCR5 receptor and the binding sites for various ligands. It found that different ligands bind to different receptor conformations. It then validated the predictions by experimentally testing the effects of 11 single point mutations on ligand binding. The predicted binding energies from the mutant receptor conformations matched well with experimental results, supporting the concept that each ligand can stabilize a different receptor conformation.
N-acetyl-D-glucosamine kinase (NAGK) interacts with dynein light-chain roadblock type 1 (DYNLRB1) at dendritic branch points in neurons. Immunocytochemistry and proximity ligation assays showed colocalization of NAGK and DYNLRB1 on microtubule fibers at dendritic branches. NAGK was also found to interact with Golgi outposts and DYNLRB1 at branch points, indicating a tripartite interaction between NAGK, dynein, and Golgi that regulates dendritic growth and branching. Introduction of a peptide derived from DYNLRB1 stunted dendrite development in cultured neurons.
I presented two fascinating stories where Molecular Dynamics simulations contributed to enhancing our understanding of immunodeficiencies. In one of the projects, the treatment of patients could be improved. These slides were presented at the Basler Modeller Stammtisch, 26.02.2021
Milap Thaker - Biology Powerpoint: Harvard University - DNA Damage Checkpointsmilapthaker
The document discusses two mechanisms by which DNA damage checkpoints inhibit mitotic exit in yeast cells. First, the Rad53 checkpoint kinase prevents mitotic exit by inhibiting the Mitotic Exit Network (MEN). Second, the FEAR pathway promotes limited release of the phosphatase Cdc14 from the nucleolus early in anaphase. The study finds that Rad53 acts through the Dun1 kinase to regulate the MEN more directly, while FEAR provides an alternate mechanism for temporary Cdc14 release and a delay in full mitotic exit. Experiments visualize budding, Cdc14 localization, and DNA content in various yeast strains to illustrate the two inhibitory mechanisms.
This study characterized the Dvilp7 gene from Drosophila virilis through a series of experiments. RNA was purified from D. virilis and used to construct cDNA. RACE experiments were used to amplify the 5' and 3' ends of the Dvilp7 cDNA sequence. The full Dvilp7 cDNA sequence was assembled and found to encode a putative protein with a signal peptide. Genomic DNA was also sequenced and compared to determine intron sequences. Characterizing the Dvilp7 gene expands understanding of the genetic mechanisms regulating insulin signaling in Drosophila.
This study examined the association between genetic variants in the human netrin G1 gene and schizophrenia. The researchers identified 10 single nucleotide polymorphisms in the netrin G1 gene and genotyped them in 180 schizophrenia patients and 180 healthy controls. One polymorphism, IVS8-1467C>T, showed a significant allelic association with schizophrenia, with the C allele being overrepresented in patients. Haplotype analysis also found a multi-SNP haplotype in high linkage disequilibrium with IVS8-1467C>T that was significantly associated with schizophrenia. These findings suggest that netrin G1 or a nearby gene may contribute to genetic risk for schizophrenia.
a short introduction about deep learning and how we can use deep neural networks in different biological problems such as protein function prediction and gene expression inference.
Does RNA avoidance dictate protein expression level?Paul Gardner
Selection against mRNA:ncRNA interactions is observed across bacterial and archaeal genomes. Stochastic interactions between abundant ncRNAs and mRNAs may influence protein expression levels by inhibiting translation. Analysis of highly conserved genes in over 1,500 bacterial and 100 archaeal genomes provides evidence that mRNA and ncRNA sequences have evolved to avoid stable interactions, suggesting such interactions are selectively avoided to prevent inaccurate regulation of protein levels.
Dougherty Reeves Lucas Gamble Lesort Cowell 2012Elizabeth Lucas
This study investigated Purkinje cell dysfunction in an animal model of Huntington's disease (HD). The study found:
1) Reductions in expression of calcium-binding proteins and GABA enzymes in the cerebellum of HD model mice, specifically in the Purkinje cell layer, as shown by gene expression analysis and immunohistochemistry.
2) No loss of Purkinje cells in presymptomatic HD model mice, but significant Purkinje cell loss by end-stage, as shown by stereological analysis.
3) Impaired Purkinje cell firing in presymptomatic HD model mice, prior to accumulation of huntingtin protein and cell loss, indicating early Purkinje cell
This study investigated the effects of knocking down neuroligin genes on planarian regeneration abilities. Planarians were separated into four groups - a control group with an unc22 gene knockdown and three experimental groups with neuroligin 1A/1B, 2, or 1B/2 gene knockdowns. The worms were cut and imaged over 10 days to observe eyespot regeneration and blastema tissue re-pigmentation. Results showed that single neuroligin knockdowns caused 1-2 day delays in regeneration, while the double 1B/2 knockdown caused more severe 4 day delays. This supports the hypothesis that neuroligins are important for synaptic signaling required for normal planarian regeneration.
This document discusses RNA bioinformatics and RNA structure prediction. It begins by asking why RNA is important and notes that non-coding RNAs are as numerous as protein-coding genes. It then discusses RNA structure, including primary, secondary and tertiary structure. Key methods for RNA structure prediction include Nussinov's algorithm, which maximizes base pairing, and Zuker's algorithm, which predicts minimum free energy structures using a nearest neighbor model. Comparative sequence analysis can also help predict RNA structure by identifying covarying base pairs that are evolutionarily conserved.
This document discusses checkpoints in the cell cycle and mutations. It describes the four phases of the cell cycle and two major checkpoints - G1/S and G2/M. Progression through the cell cycle is controlled by cyclins and cyclin-dependent kinases (Cdks). Mutations can occur spontaneously or be induced by mutagens like radiation and chemicals. They can cause changes in DNA sequences and structures. Checkpoint genes and tumor suppressor genes normally prevent mutations from causing cancer, but their mutation allows uncontrolled cell growth.
STRING - Prediction of a functional association network for the yeast mitocho...Lars Juhl Jensen
The document discusses predicting functional associations between proteins in the yeast mitochondrial system using the STRING database. It summarizes how STRING integrates genomic context, experimental data, and evidence from other species to infer functional links. It then describes applying these methods to predict mitochondrial proteins in yeast and build an association network for the yeast mitochondrial system, identifying functional modules within it.
- Dopamine plays an important role in motor control and Parkinson's disease is characterized by degeneration of dopaminergic neurons.
- Previous models of Parkinson's disease in C. elegans observed neuronal degeneration via fluorescent microscopy at day 9 of development, which was time-consuming.
- This study developed a new assay to detect behavioral defects in C. elegans correlated with dopamine neuron degeneration at an earlier time point (day 3), allowing faster screening of factors that contribute to Parkinson's disease onset.
Effects of knockout of antioxidant genes on spermatogenesisxsonixs
1) The study examined the effects of knocking out antioxidant genes Gclm and Nrf2 on sperm production and morphology in mice.
2) For Nrf2 knockout mice, results showed significantly decreased testicular and epididymal sperm counts compared to wild type mice, but no significant effects on sperm morphology.
3) For Gclm knockout mice, results found no significant effects on sperm morphology but a trend of higher percentages of immature sperm compared to wild type mice.
The document discusses the cause of Fragile X syndrome, which is a genetic condition associated with intellectual disabilities and certain physical characteristics. There has been some debate around whether deletion or expansion of the CGG trinucleotide in the FMR1 gene causes the syndrome. Some research has found that a substitution of G>C in the CGG trinucleotide leads to gene silencing and causes the syndrome. However, other research from a study of a healthy family found that a CGG>CCG substitution is a non-coding polymorphism and does not affect gene expression or cause the syndrome. The purpose is to analyze which findings are correct regarding the molecular basis of Fragile X syndrome.
1) LAR is a receptor for chondroitin sulfate proteoglycans (CSPGs), which are inhibitory to axon growth in the central nervous system.
2) CSPGs bind to LAR with high affinity and stimulate its phosphatase activity. Blocking LAR reverses CSPG-mediated growth inhibition.
3) In mouse models of spinal cord injury, peptides targeting LAR promote axon growth, functional recovery, and behavioral improvements by overcoming the inhibitory effects of CSPGs. LAR blockade may be a promising therapeutic approach for central nervous system axon injury.
Austin Neurology & Neurosciences is an open access, peer reviewed, scholarly journal dedicated to publish articles covering all areas of Neurology & Neurological Sciences.
The journal aims to promote research communications and provide a forum for doctors, researchers, physicians and healthcare professionals to find most recent advances in all areas of Neurology & Neurological Sciences. Austin Neurology & Neurosciences accepts original research articles, reviews, mini reviews, case reports and rapid communication covering all aspects of neurology & neurosciences.
Austin Neurology & Neurosciences strongly supports the scientific up gradation and fortification in related scientific research community by enhancing access to peer reviewed scientific literary works. Austin Publishing Group also brings universally peer reviewed journals under one roof thereby promoting knowledge sharing, mutual promotion of multidisciplinary science.
Gene editing application for cancer therapeuticsNur Farrah Dini
The application of TALENs as one of the gene editing tools in order to modify a specific targeted sites on a genome. This method shows a tremendous benefits especially in cancer research.
This document describes a new bioinformatic procedure for identifying the genetic basis of physiological processes in non-model species. The procedure is illustrated by identifying genes involved in cold-induced angiogenesis in carp, a non-model species. The strategy uses ortholog prediction between carp, zebrafish and human to link carp DNA sequences to known angiogenic genes. Conditioned stepped reciprocal best hit BLAST analysis was found to be the most effective ortholog assignment method. Applying this strategy to carp gene expression data identified 135 candidate genes involved in cold-induced angiogenesis, 12 of which were examined in more detail.
This document summarizes a study that analyzed genomic CpG islands (CGIs) across 34 animal genomes to understand their evolutionary context and relationships to other genomic features. The study found that genome size had the strongest correlation with CGI number and density across species, rather than the hypothesized relationships to unique transcription factors or protein-coding sequences. Additionally, average CpG/expected ratio of CGIs and background genomic GC content displayed phylogenetic signal, suggesting these features have been maintained in animal phylogeny. The ratio of unique transcription factors to protein-coding sequences also showed phylogenetic signal.
Lack of association between CD45 C77G polymorphism and multiple sclerosis in ...ijtsrd
Multiple sclerosis (MS) is a severe disabling and demyelinating disease of the nervous system. Its etiology involves profound genetic component. The latest contender known to have been correlated with MS is protein tyrosine phosphatase receptor-type C (PTPRC or CD45); however, to date its role remains contentious. The aim of the current study was to examine the association of functionally significant exon 4 C77G polymorphism of CD45 with MS in Kashmiri population from Indian subcontinent. The preliminary findings of our study revealed absence of C77G in majority of the cases as well as controls. These findings strongly suggest that the alterations in CD45 are sporadically associated with the genesis of MS. In conclusion, results from our study are in accordance with some of the international studies; however, more studies with large datasets from Kashmir as well as other ethnic populations are warranted to validate the above preliminary findings and demonstrate the role of CD45 C77G polymorphism in MS pathogenesis. Insha Zahoor | Amrina Shafi | Mudasir A Mir"Lack of association between CD45 C77G polymorphism and multiple sclerosis in Kashmir" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-1 | Issue-6 , October 2017, URL: http://www.ijtsrd.com/papers/ijtsrd5813.pdf http://www.ijtsrd.com/biological-science/biotechnology/5813/lack-of-association-between-cd45-c77g-polymorphism-and--multiple-sclerosis-in-kashmir/insha-zahoor
Slides from my talk describing CE-Symm and my research on internal symmetry. It was given for jLBR, the weekly seminar series for our department at PSI.
This document discusses the global regulation of cholesterol homeostasis. There are two sources of cellular cholesterol: de novo synthesis and uptake from LDL. Endogenous cholesterol synthesis occurs via the mevalonate pathway, where HMG CoA reductase (HMGR) catalyzes the rate-limiting step. HMGR levels and activity are tightly regulated through transcriptional and post-transcriptional feedback mechanisms mediated by sterols and sterol regulatory elements. When cellular sterol levels increase, HMGR levels and activity decrease via regulated intracellular degradation and transcription factor inhibition. This complex regulatory system maintains appropriate cholesterol levels and prevents toxicity.
Teresita Carvajal has over 30 years of accounting experience including positions as Controller for various companies. She has expertise in financial statement preparation, accounts receivable, accounts payable, payroll, budgeting, and human resources. Her experience includes setting up accounting systems, automating processes, and ensuring compliance with internal controls and tax regulations. She is proficient in QuickBooks, ADP, and other accounting software.
Treatment of Effluent from Granite Cutting Plant by Using Natural Adsorbents ...IJERD Editor
Granite cutting plant is one such industry that releases polluting and turbid effluent. The residue from all these processes is discharged with water as an effluent. The effluent mainly contains many solids that harm the environment. Hence it requires treatment techniques before disposal. Several conventional methods are available for removal of contaminants like coagulation, adsorption, polyelectrolyte methods and biological methods. Most of them are cost prohibitive. The reduction of solids concentration in the effluent before disposal by using the techniques, coagulation followed by adsorption using natural adsorbents, like rice husk carbon and saw dust carbon, in contrast to the usage of activated carbon as it is costly. From a local Granite cutting plant near Anantapur, the effluent is collected and its physico-chemical characteristics are estimated and found to be pH(7.5), TS(4240mg/l), TSS(21560mg/l), TDS(12373mg/l).Effluent obtained is subjected to coagulation by potash alum followed by adsorption using saw dust carbon and rice husk carbon.
a short introduction about deep learning and how we can use deep neural networks in different biological problems such as protein function prediction and gene expression inference.
Does RNA avoidance dictate protein expression level?Paul Gardner
Selection against mRNA:ncRNA interactions is observed across bacterial and archaeal genomes. Stochastic interactions between abundant ncRNAs and mRNAs may influence protein expression levels by inhibiting translation. Analysis of highly conserved genes in over 1,500 bacterial and 100 archaeal genomes provides evidence that mRNA and ncRNA sequences have evolved to avoid stable interactions, suggesting such interactions are selectively avoided to prevent inaccurate regulation of protein levels.
Dougherty Reeves Lucas Gamble Lesort Cowell 2012Elizabeth Lucas
This study investigated Purkinje cell dysfunction in an animal model of Huntington's disease (HD). The study found:
1) Reductions in expression of calcium-binding proteins and GABA enzymes in the cerebellum of HD model mice, specifically in the Purkinje cell layer, as shown by gene expression analysis and immunohistochemistry.
2) No loss of Purkinje cells in presymptomatic HD model mice, but significant Purkinje cell loss by end-stage, as shown by stereological analysis.
3) Impaired Purkinje cell firing in presymptomatic HD model mice, prior to accumulation of huntingtin protein and cell loss, indicating early Purkinje cell
This study investigated the effects of knocking down neuroligin genes on planarian regeneration abilities. Planarians were separated into four groups - a control group with an unc22 gene knockdown and three experimental groups with neuroligin 1A/1B, 2, or 1B/2 gene knockdowns. The worms were cut and imaged over 10 days to observe eyespot regeneration and blastema tissue re-pigmentation. Results showed that single neuroligin knockdowns caused 1-2 day delays in regeneration, while the double 1B/2 knockdown caused more severe 4 day delays. This supports the hypothesis that neuroligins are important for synaptic signaling required for normal planarian regeneration.
This document discusses RNA bioinformatics and RNA structure prediction. It begins by asking why RNA is important and notes that non-coding RNAs are as numerous as protein-coding genes. It then discusses RNA structure, including primary, secondary and tertiary structure. Key methods for RNA structure prediction include Nussinov's algorithm, which maximizes base pairing, and Zuker's algorithm, which predicts minimum free energy structures using a nearest neighbor model. Comparative sequence analysis can also help predict RNA structure by identifying covarying base pairs that are evolutionarily conserved.
This document discusses checkpoints in the cell cycle and mutations. It describes the four phases of the cell cycle and two major checkpoints - G1/S and G2/M. Progression through the cell cycle is controlled by cyclins and cyclin-dependent kinases (Cdks). Mutations can occur spontaneously or be induced by mutagens like radiation and chemicals. They can cause changes in DNA sequences and structures. Checkpoint genes and tumor suppressor genes normally prevent mutations from causing cancer, but their mutation allows uncontrolled cell growth.
STRING - Prediction of a functional association network for the yeast mitocho...Lars Juhl Jensen
The document discusses predicting functional associations between proteins in the yeast mitochondrial system using the STRING database. It summarizes how STRING integrates genomic context, experimental data, and evidence from other species to infer functional links. It then describes applying these methods to predict mitochondrial proteins in yeast and build an association network for the yeast mitochondrial system, identifying functional modules within it.
- Dopamine plays an important role in motor control and Parkinson's disease is characterized by degeneration of dopaminergic neurons.
- Previous models of Parkinson's disease in C. elegans observed neuronal degeneration via fluorescent microscopy at day 9 of development, which was time-consuming.
- This study developed a new assay to detect behavioral defects in C. elegans correlated with dopamine neuron degeneration at an earlier time point (day 3), allowing faster screening of factors that contribute to Parkinson's disease onset.
Effects of knockout of antioxidant genes on spermatogenesisxsonixs
1) The study examined the effects of knocking out antioxidant genes Gclm and Nrf2 on sperm production and morphology in mice.
2) For Nrf2 knockout mice, results showed significantly decreased testicular and epididymal sperm counts compared to wild type mice, but no significant effects on sperm morphology.
3) For Gclm knockout mice, results found no significant effects on sperm morphology but a trend of higher percentages of immature sperm compared to wild type mice.
The document discusses the cause of Fragile X syndrome, which is a genetic condition associated with intellectual disabilities and certain physical characteristics. There has been some debate around whether deletion or expansion of the CGG trinucleotide in the FMR1 gene causes the syndrome. Some research has found that a substitution of G>C in the CGG trinucleotide leads to gene silencing and causes the syndrome. However, other research from a study of a healthy family found that a CGG>CCG substitution is a non-coding polymorphism and does not affect gene expression or cause the syndrome. The purpose is to analyze which findings are correct regarding the molecular basis of Fragile X syndrome.
1) LAR is a receptor for chondroitin sulfate proteoglycans (CSPGs), which are inhibitory to axon growth in the central nervous system.
2) CSPGs bind to LAR with high affinity and stimulate its phosphatase activity. Blocking LAR reverses CSPG-mediated growth inhibition.
3) In mouse models of spinal cord injury, peptides targeting LAR promote axon growth, functional recovery, and behavioral improvements by overcoming the inhibitory effects of CSPGs. LAR blockade may be a promising therapeutic approach for central nervous system axon injury.
Austin Neurology & Neurosciences is an open access, peer reviewed, scholarly journal dedicated to publish articles covering all areas of Neurology & Neurological Sciences.
The journal aims to promote research communications and provide a forum for doctors, researchers, physicians and healthcare professionals to find most recent advances in all areas of Neurology & Neurological Sciences. Austin Neurology & Neurosciences accepts original research articles, reviews, mini reviews, case reports and rapid communication covering all aspects of neurology & neurosciences.
Austin Neurology & Neurosciences strongly supports the scientific up gradation and fortification in related scientific research community by enhancing access to peer reviewed scientific literary works. Austin Publishing Group also brings universally peer reviewed journals under one roof thereby promoting knowledge sharing, mutual promotion of multidisciplinary science.
Gene editing application for cancer therapeuticsNur Farrah Dini
The application of TALENs as one of the gene editing tools in order to modify a specific targeted sites on a genome. This method shows a tremendous benefits especially in cancer research.
This document describes a new bioinformatic procedure for identifying the genetic basis of physiological processes in non-model species. The procedure is illustrated by identifying genes involved in cold-induced angiogenesis in carp, a non-model species. The strategy uses ortholog prediction between carp, zebrafish and human to link carp DNA sequences to known angiogenic genes. Conditioned stepped reciprocal best hit BLAST analysis was found to be the most effective ortholog assignment method. Applying this strategy to carp gene expression data identified 135 candidate genes involved in cold-induced angiogenesis, 12 of which were examined in more detail.
This document summarizes a study that analyzed genomic CpG islands (CGIs) across 34 animal genomes to understand their evolutionary context and relationships to other genomic features. The study found that genome size had the strongest correlation with CGI number and density across species, rather than the hypothesized relationships to unique transcription factors or protein-coding sequences. Additionally, average CpG/expected ratio of CGIs and background genomic GC content displayed phylogenetic signal, suggesting these features have been maintained in animal phylogeny. The ratio of unique transcription factors to protein-coding sequences also showed phylogenetic signal.
Lack of association between CD45 C77G polymorphism and multiple sclerosis in ...ijtsrd
Multiple sclerosis (MS) is a severe disabling and demyelinating disease of the nervous system. Its etiology involves profound genetic component. The latest contender known to have been correlated with MS is protein tyrosine phosphatase receptor-type C (PTPRC or CD45); however, to date its role remains contentious. The aim of the current study was to examine the association of functionally significant exon 4 C77G polymorphism of CD45 with MS in Kashmiri population from Indian subcontinent. The preliminary findings of our study revealed absence of C77G in majority of the cases as well as controls. These findings strongly suggest that the alterations in CD45 are sporadically associated with the genesis of MS. In conclusion, results from our study are in accordance with some of the international studies; however, more studies with large datasets from Kashmir as well as other ethnic populations are warranted to validate the above preliminary findings and demonstrate the role of CD45 C77G polymorphism in MS pathogenesis. Insha Zahoor | Amrina Shafi | Mudasir A Mir"Lack of association between CD45 C77G polymorphism and multiple sclerosis in Kashmir" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-1 | Issue-6 , October 2017, URL: http://www.ijtsrd.com/papers/ijtsrd5813.pdf http://www.ijtsrd.com/biological-science/biotechnology/5813/lack-of-association-between-cd45-c77g-polymorphism-and--multiple-sclerosis-in-kashmir/insha-zahoor
Slides from my talk describing CE-Symm and my research on internal symmetry. It was given for jLBR, the weekly seminar series for our department at PSI.
This document discusses the global regulation of cholesterol homeostasis. There are two sources of cellular cholesterol: de novo synthesis and uptake from LDL. Endogenous cholesterol synthesis occurs via the mevalonate pathway, where HMG CoA reductase (HMGR) catalyzes the rate-limiting step. HMGR levels and activity are tightly regulated through transcriptional and post-transcriptional feedback mechanisms mediated by sterols and sterol regulatory elements. When cellular sterol levels increase, HMGR levels and activity decrease via regulated intracellular degradation and transcription factor inhibition. This complex regulatory system maintains appropriate cholesterol levels and prevents toxicity.
Teresita Carvajal has over 30 years of accounting experience including positions as Controller for various companies. She has expertise in financial statement preparation, accounts receivable, accounts payable, payroll, budgeting, and human resources. Her experience includes setting up accounting systems, automating processes, and ensuring compliance with internal controls and tax regulations. She is proficient in QuickBooks, ADP, and other accounting software.
Treatment of Effluent from Granite Cutting Plant by Using Natural Adsorbents ...IJERD Editor
Granite cutting plant is one such industry that releases polluting and turbid effluent. The residue from all these processes is discharged with water as an effluent. The effluent mainly contains many solids that harm the environment. Hence it requires treatment techniques before disposal. Several conventional methods are available for removal of contaminants like coagulation, adsorption, polyelectrolyte methods and biological methods. Most of them are cost prohibitive. The reduction of solids concentration in the effluent before disposal by using the techniques, coagulation followed by adsorption using natural adsorbents, like rice husk carbon and saw dust carbon, in contrast to the usage of activated carbon as it is costly. From a local Granite cutting plant near Anantapur, the effluent is collected and its physico-chemical characteristics are estimated and found to be pH(7.5), TS(4240mg/l), TSS(21560mg/l), TDS(12373mg/l).Effluent obtained is subjected to coagulation by potash alum followed by adsorption using saw dust carbon and rice husk carbon.
- Choudhury Pritam Das is seeking a career opportunity and provides his contact information and career objective.
- He has a B.Tech degree from Ajay Binay Institute of Technology with over 6 years of experience in industrial automation.
- He has expertise in programming PLCs, SCADAs, HMIs, and other automation tools and has experience interfacing these systems with devices like sensors, valves and drives.
- He also provides details on his academic qualifications, projects, training, software skills, strengths and personal information to support his job application.
IoT implementation with InduSoft Web Studio and TagWell from SoftPLC: InduSof...AVEVA
Pairing InduSoft Web Studio with SoftPLC Corporation's TagWell cloud platform is an effective way to bring systems into the new frontier of the Internet of Things and Machine to Machine communication. With SoftPLC’s TagWell, InduSoft Web Studio users can take advantage of native driver communications to effortlessly connect systems that range from wireless interfaces, to a cellular/satellite connected office-based SCADA, or distributed remote units to cloud-based SCADA systems.
The document discusses various machine learning techniques for improving performance when training data is limited, including ensembles, active learning, transfer learning, and semi-supervised learning. It provides examples of how ensemble methods like DECORATE that generate alternative hypotheses can improve accuracy over bagging or boosting on small datasets. Active learning techniques like Active-DECORATE that select the most informative examples for labeling can reduce labeling requirements. Transfer learning approaches exploit related labeled data to improve learning on a new task.
When parents strive to give their children the best of everything at an early age, they are sowing seeds for materially insatiable monsters that are prone to sloth, apathy, avarice and fear.
Don’t stand in self- defense as yet. I have proof. As I sit in my counselor’s chair day after day I encounter an altogether a new disorder that I have come to label as- Parent Induced Wastefulness (PIW).
Austin Larson worked at Dickeys Barbecue Pit from February 2015 to the present. His manager, Rylie Robison, says that Austin is a fast learner, hard worker who is dependable and willing to take on any task. Austin trains new employees thoroughly and provides excellent customer service, regularly receiving positive feedback from guests. Rylie highly recommends Austin and is willing to provide more details about his work.
1) The C-terminal carboxylate group of integrin β1 is necessary for its association with the kindlin-2 adapter protein. Affinity measurements indicate this interaction is coordinated by a putative carboxylate-binding motif in the FERM subdomain F3 of kindlin-2.
2) Injection of mRNA encoding mutant integrin β1 cytoplasmic tails that lack the C-terminal carboxylate group perturbed laterality organ development in zebrafish, indicating the carboxylate group is required for physiological functions.
3) The unusual interaction between integrin β1 and kindlin-2 identified here represents a novel protein-protein interaction mode governed mainly by the integrin
1) The study examined the role of Rho kinase in T cell activation and immune responses.
2) Inhibition of Rho kinase attenuated T cell proliferation, cytokine gene expression, actin polymerization, and aggregation of T cell receptors.
3) Treatment with a Rho kinase inhibitor prolonged survival of allogeneic heart transplants in mice and diminished cytokine mRNA expression in the transplants.
4) Rho kinase promotes structural rearrangements in T cells that are critical for T cell signaling and activation during cellular immune responses.
This study simultaneously used circular dichroism, absorbance, and fluorescence spectroscopy to observe the unfolding of native and mutated horse heart cytochrome c proteins when exposed to increasing concentrations of the denaturant guanidine hydrochloride. By comparing the unfolding processes and thermodynamic properties of the native and mutated proteins, the study aimed to better understand the relative stability between native and mutated protein structures and gain insights into current scientific theories of protein unfolding.
This document summarizes research on the disruption of the cyclin D/CDK/INK4/Rb regulatory pathway in human neuroblastoma cell lines. The researchers found that 17 neuroblastoma cell lines highly expressed the CDK inhibitors p16INK4a and p18INK4c, but CDK6 kinase activity and phosphorylated Rb were still detected. One cell line was found to have a mutation in CDK6 that disrupts p16INK4a binding and prevents its inhibition of CDK6, bypassing the cell cycle block. The mechanisms allowing CDK6 activity in the other 16 cell lines despite high p16INK4a levels is unknown.
Amanda Myers provides her contact information and career statement, indicating her interest in areas like genetics and human health. She then lists her extensive technical expertise in areas such as chemical hazard identification, risk assessment, and laboratory skills. Her employment history includes work at an advanced testing laboratory conducting human risk assessments and toxicological profiles. She earned degrees in biology and chemistry from Ball State University and has research experience in projects involving database design, protein expression, and earthworm densities based on soil composition.
1. The study found that lncRNA PCAT29 was downregulated in renal carcinoma tissues, while the expression of FLOT1 was upregulated.
2. Overexpression of PCAT29 inhibited cell proliferation, invasion, and migration of renal carcinoma cells by downregulating FLOT1.
3. In a mouse model of renal carcinoma, overexpression of PCAT29 inhibited tumor growth, suggesting PCAT29 suppresses renal carcinoma progression by downregulating FLOT1.
The document discusses lysine crotonylation, which is a newly discovered post-translational modification on histones. It is catalyzed by protein crotonyltransferases and can be removed by decrotonylases. Lysine crotonylation is specifically enriched at active gene promoters and enhancers. The modification is regulated by the balance of crotonyltransferases, which add the mark, and decrotonylases, which remove it. Several histone acetyltransferases have also been found to have histone crotonyltransferase activity.
Research Inventy : International Journal of Engineering and Scienceresearchinventy
Research Inventy : International Journal of Engineering and Science is published by the group of young academic and industrial researchers with 12 Issues per year. It is an online as well as print version open access journal that provides rapid publication (monthly) of articles in all areas of the subject such as: civil, mechanical, chemical, electronic and computer engineering as well as production and information technology. The Journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence. Papers will be published by rapid process within 20 days after acceptance and peer review process takes only 7 days. All articles published in Research Inventy will be peer-reviewed.
Waksman Student Scholars Program PosterWesley Kwong
The document describes an experiment to sequence the DNA of the duckweed plant Landoltia punctata and analyze the protein encoded. Researchers used PCR to amplify duckweed DNA inserted into bacteria. Restriction digest isolated the duckweed DNA, which was sequenced. Analysis identified the protein as Mitogen-Activated Protein Kinase (MAPK), which regulates cellular responses to stimuli and contains conserved domains. The 3D structure of this protein is similar to the human MAPK protein, indicating an evolutionary advantage across kingdoms.
This document discusses the role of the guanine nucleotide exchange factor C3G in neuronal differentiation. It finds that C3G protein levels increase when human neuroblastoma cells are induced to differentiate through serum starvation or treatment with forskolin or nerve growth factor. Overexpression of C3G stimulates neurite growth and increases responsiveness to differentiation signals, in a process dependent on C3G's catalytic domain and the functions of Rap1 and Cdc42. Knockdown of C3G inhibits forskolin- and nerve growth factor-induced differentiation and enhances cell death from serum starvation. C3G phosphorylation and localization to the Golgi are increased by forskolin and nerve growth factor treatment, and C3G
GFP For Exploring Protein-Protein Interactions - Nelson Giovanny Rincon Silva Nelson Giovanny Rincon S
This document describes using green fluorescent protein (GFP) to study protein-protein interactions. GFP from jellyfish has properties that make it useful for this, such as fluorescence and stability. The document discusses fusing GFP to proteins of interest to monitor their interactions. Specifically, it examines fusing GFP to the S-peptide and S-protein fragments of the ribonuclease protein. It describes constructing and purifying these GFP fusion proteins, then using gel retardation and fluorescence polarization assays to measure the interactions and determine binding constants. The assays allow quantifying the fraction of proteins bound versus unbound to study protein binding.
Circumventing Traditional Bottlenecks In Glioblastoma...Melanie Smith
This study investigated whether the nonstructural protein 2B of human rhinovirus 16 (HRV16) induces an endoplasmic reticulum (ER) stress response. A HRV16 2B fusion protein with GFP was expressed in baby hamster kidney (BHK) cells. Results showed HRV16 2B induced high expression of the ER chaperone GRP78 in a time-dependent manner and activated the PERK-eIF2α signaling pathway, leading to increased expression of p-PERK, p-eIF2α, and CHOP. HRV16 2B decreased expression of p-IRE1 and ATF6 p50. This demonstrated for the first time that the PER
This document discusses computational predictions of potential interactions and signaling crosstalk between CDK5 and other proteins involved in central nervous system pathways. Specifically, it predicts interactions between CDK5 and NogoR1 using online tools and molecular modeling software. Ten amino acid interactions between CDK5 and NogoR1 are identified. Pathway analysis with tools like STRING and Pathway Linker also predict potential crosstalk between CDK5, NogoR1, CDK5R1, GSK3β and RTN4. Molecular dynamics simulations of the CDK5-NogoR1 complex are performed and structural changes analyzed over 10,000 femtoseconds.
The document summarizes several studies that contributed to understanding the molecular basis for substrate poly-specificity of P-glycoprotein (P-gp). Crystal structures of P-gp from mouse and C. elegans confirmed it consists of two homologous halves, each with one transmembrane domain and one nucleotide-binding domain. Studies showed ATP-driven dimerization of the nucleotide-binding domains induces structural changes that lower drug binding affinities, releasing substrates. Docking studies helped identify features distinguishing transported substrates from modulators.
1) The study investigated the effects of gasdermin D on pyroptosis in a mouse model of sepsis-induced acute kidney injury.
2) The results showed that gasdermin D expression was increased in mice with sepsis-induced acute kidney injury and promoted inflammation and pyroptosis in kidney cells.
3) Downregulating gasdermin D decreased inflammation and pyroptosis, and the NLRP3 inflammasome was identified as an important target of gasdermin D in mediating inflammation during sepsis-induced acute kidney injury.
This document contains summaries of 4 poster presentations from a conference on Alzheimer's disease and dementia research.
The first poster discusses findings that the ER stress transcription factor XBP1s protects against amyloid-beta neurotoxicity in a fruit fly model of Alzheimer's and in human neuroblastoma cells. XBP1s prevents the accumulation of free calcium in the cytosol, explaining its neuroprotective effects.
The second poster reports that amyloid-beta oligomers impair neuronal function and morphology in rat and mouse neuronal cultures and hippocampal slices through a mechanism linked to NMDA receptor signaling and activation of the protein Jacob.
The third poster examines the role of O-GlcNAc glycosylation in hippocampal synaptic
This document summarizes research examining the effects of elevated cyclic AMP (cAMP) levels on expression of the chemokine receptor CXCR4 in human hematopoietic progenitor cells. The study finds that increased cAMP, through activation of protein kinase C ζ (PKCζ), leads to higher CXCR4 expression on the cell surface. This enhanced CXCR4 expression results in greater migration, adhesion, survival and homing of progenitor cells. The cAMP/PKCζ pathway interacts with TNFα signaling and converges on CXCR4 expression and secretion of matrix metalloproteinases.
This study aimed to identify proteins that interact with PlzC, a c-di-GMP receptor important for controlling motility, biofilm formation, and virulence in Vibrio cholerae. The researchers used transposon mutagenesis to introduce random mutations in a ΔplzC genetic background. They then screened for secondary mutations that restored wild-type motility on soft agar plates. Several motility-suppressing mutants were selected, sequenced, and further analyzed to identify interacting proteins and understand how they regulate motility through PlzC and c-di-GMP signaling.
Este documento analiza el modelo de negocio de YouTube. Explica que YouTube y otros sitios de video online representan un nuevo modelo de negocio para contenidos audiovisuales debido al cambio en los hábitos de consumo causado por las nuevas tecnologías. Describe cómo YouTube aprovecha la participación de los usuarios para mejorar continuamente y atraer una audiencia diferente a la de los medios tradicionales.
The defense was successful in portraying Michael Jackson favorably to the jury in several ways:
1) They dressed Jackson in ornate costumes that conveyed images of purity, innocence, and humility.
2) Jackson was shown entering the courtroom as if on a red carpet, emphasizing his celebrity status.
3) Jackson appeared vulnerable, childlike, and in declining health during the trial, eliciting sympathy from jurors.
4) Defense attorney Tom Mesereau effectively presented a coherent narrative of Jackson as a victim and portrayed Neverland as a place of refuge, undermining the prosecution's arguments.
Michael Jackson was born in 1958 in Gary, Indiana and rose to fame in the 1960s as the lead singer of The Jackson 5, topping music charts in the 1970s. As a solo artist in the 1980s, his album Thriller broke music records. In the 1990s and 2000s, Jackson faced several legal issues related to child abuse allegations while continuing to release music. He married Lisa Marie Presley and Debbie Rowe and had two children before his death in 2009.
Popular Reading Last Updated April 1, 2010 Adams, Lorraine The ...butest
This document appears to be a list of popular books from various authors. It includes over 150 book titles across many genres such as fiction, non-fiction, memoirs, and novels. The books cover a wide range of topics from politics to cooking to autobiographies.
The prosecution lost the Michael Jackson trial due to several key mistakes and weaknesses in their case:
1) The lead prosecutor, Thomas Sneddon, was too personally invested in the case against Jackson, having pursued him for over a decade without success.
2) Sneddon's opening statement was disorganized and weak, failing to effectively outline the prosecution's case.
3) The accuser's mother was not credible and damaged the prosecution's case through her erratic testimony, history of lies and con artist behavior.
4) Many prosecution witnesses were not credible due to prior lawsuits against Jackson, debts owed to him, or having been fired by him. Several witnesses even took the Fifth Amendment.
Here are three examples of public relations from around the world:
1. The UK government's "Be Clear on Cancer" campaign which aims to raise awareness of cancer symptoms and encourage early diagnosis.
2. Samsung's global brand marketing and sponsorship activities which aim to increase brand awareness and favorability of Samsung products worldwide.
3. The Brazilian government's efforts to improve its international image and relations with other countries through strategic communication and diplomacy.
The three most important functions of public relations are:
1. Media relations because the media is how most organizations reach their key audiences. Strong media relationships are crucial.
2. Writing, because written communication is at the core of public relations and how most information is
Michael Jackson Please Wait... provides biographical information about Michael Jackson including his birthdate, birthplace, parents, height, interests, idols, favorite foods, films, and more. It discusses his background, career highlights including influential albums like Thriller, and films he appeared in such as The Wiz and Moonwalker. The document contains photos and details about Jackson's life and illustrious music career.
The MYnstrel Free Press Volume 2: Economic Struggles, Meet Jazzbutest
The document discusses the process of manufacturing celebrity and its negative byproducts. It argues that celebrities are rarely the best in their individual pursuits like singing, dancing, etc. but become famous due to being products of a system controlled by wealthy elites. This system stifles opportunities for worthy artists and creates feudalism. The document also asserts that manufactured celebrities should not be viewed as role models due to behaviors like drug abuse and narcissism that result from the celebrity-making process.
Michael Jackson was a child star who rose to fame with the Jackson 5 in the late 1960s and early 1970s. As a solo artist in the 1970s and 1980s, he had immense commercial success with albums like Off the Wall, Thriller, and Bad, which featured hit singles and groundbreaking music videos. However, his career and public image were plagued by controversies related to allegations of child sexual abuse in the 1990s and 2000s. He continued recording and performing but faced ongoing media scrutiny into his private life until his death in 2009.
Social Networks: Twitter Facebook SL - Slide 1butest
The document discusses using social networking tools like Twitter and Facebook in K-12 education. Twitter allows students and teachers to share short updates and can be used to give parents a window into classroom activities. Facebook allows targeted advertising that could be used to promote educational activities. Both tools could help facilitate communication between schools and communities if used properly while managing privacy and security concerns.
Facebook has over 300 million active users who log on daily, and allows brands to create public profile pages to interact with users. Pages are for brands and organizations only, while groups can be made by any user about any topic. Pages do not show admin names and have no limits on fans, while groups display admin names and are limited to 5,000 members. Content on pages should aim to provoke action from subscribers and establish a regular posting schedule using a conversational tone.
Executive Summary Hare Chevrolet is a General Motors dealership ...butest
Hare Chevrolet is a car dealership located in Noblesville, Indiana that has successfully used social media platforms like Twitter, Facebook, and YouTube to create a positive brand image. They invest significant time interacting directly with customers online to foster a sense of community rather than overtly advertising. As a result, Hare Chevrolet has built a large, engaged audience on social media and serves as a model for how brands can use online presences strategically.
Welcome to the Dougherty County Public Library's Facebook and ...butest
This document provides instructions for signing up for Facebook and Twitter accounts. It outlines the sign up process for both platforms, including filling out forms with name, email, password and other details. It describes how the platforms will then search for friends and suggest people to connect with. It also explains how to search for and follow the Dougherty County Public Library page on both Facebook and Twitter once signed up. The document concludes by thanking participants and providing a contact for any additional questions.
Paragon Software announces the release of Paragon NTFS for Mac OS X 8.0, which provides full read and write access to NTFS partitions on Macs. It is the fastest NTFS driver on the market, achieving speeds comparable to native Mac file systems. Paragon NTFS for Mac 8.0 fully supports the latest Mac OS X Snow Leopard operating system in 64-bit mode and allows easy transfer of files between Windows and Mac partitions without additional hardware or software.
This document provides compatibility information for Olympus digital products used with Macintosh OS X. It lists various digital cameras, photo printers, voice recorders, and accessories along with their connection type and any notes on compatibility. Some products require booting into OS 9.1 for software compatibility or do not support devices that need a serial port. Drivers and software are available for download from Olympus and other websites for many products to enable use with OS X.
To use printers managed by the university's Information Technology Services (ITS), students and faculty must install the ITS Remote Printing software on their Mac OS X computer. This allows them to add network printers, log in with their ITS account credentials, and print documents while being charged per page to funds in their pre-paid ITS account. The document provides step-by-step instructions for installing the software, adding a network printer, and printing to that printer from any internet connection on or off campus. It also explains the pay-in-advance printing payment system and how to check printing charges.
The document provides an overview of the Mac OS X user interface for beginners, including descriptions of the desktop, login screen, desktop elements like the dock and hard disk, and how to perform common tasks like opening files and folders. It also addresses frequently asked questions for Windows users switching to Mac OS X, such as where documents are stored, how to save or find documents, and what the equivalent of the C: drive is in Mac OS X. The document concludes with sections on file management tasks like creating and deleting folders, organizing files within applications, using Spotlight search, and an overview of the Dashboard feature.
This document provides a checklist for securing Mac OS X version 10.5, focusing on hardening the operating system, securing user accounts and administrator accounts, enabling file encryption and permissions, implementing intrusion detection, and maintaining password security. It describes the Unix infrastructure and security framework that Mac OS X is built on, leveraging open source software and following the Common Data Security Architecture model. The checklist can be used to audit a system or harden it against security threats.
This document summarizes a course on web design that was piloted in the summer of 2003. The course was a 3 credit course that met 4 times a week for lectures and labs. It covered topics such as XHTML, CSS, JavaScript, Photoshop, and building a basic website. 18 students from various majors enrolled. Student and instructor evaluations found the course to be very successful overall, though some improvements were suggested like ensuring proper software and pairing programming/non-programming students. The document also discusses implications of incorporating web design material into existing computer science curriculums.
1. Learning to Extract Proteins and their Interactions from Medline Abstracts Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Yuk Wah Wong Edward M. Marcotte, Arun Ramani Department of Computer Sciences Institute for Cellular and Molecular Biology University of Texas at Austin Raymond J. Mooney Department of Computer Sciences
7. Yeast Gene Network ~5,800 genes ~5,800 proteins x 2-10 interactions/protein ~12,000 - 60,000 interactions Yeast ~ 10-20,000 known ==> ~1/3 of the way to a complete map!
8. Human Gene Network ~40,000 genes >>40,000 proteins x 2-10 interactions/protein >>80,000 - 400,000 interactions <5,000 known ==> approx. 1% of the complete map! ==> We’re a long ways from the complete map
9. Relevant Sources of Data Biological literature ~14 million documents DNA sequence data ~10 10 nucleotides Gene expression data ~10 8 measurements, but... DNA polymorphisms ~10 7 known Gene inactivation (knockout) studies ~10 5 Protein structure data ~10 4 structures Protein interaction data ~10 4 interactions, but… Protein expression data ~10 4 measurements, but... Protein location data ~10 4 measurements
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12. TI - Two potentially oncogenic cyclins, cyclin A and cyclin D1, share common properties of subunit configuration, tyrosine phosphorylation and physical association with the Rb protein AB - Originally identified as a ‘mitotic cyclin’, cyclin A exhibits properties of growth factor sensitivity, susceptibility to viral subversion and association with a tumor-suppressor protein, properties which are indicative of an S-phase-promoting factor (SPF) as well as a candidate proto-oncogene. Other recent studies have identified human cyclin D1 (PRAD1) as a putative G1 cyclin and candidate proto-oncogene. However, the specific enzymatic activities and, hence, the precise biochemical mechanisms through which cyclins function to govern cell cycle progression remain unresolved. In the present study we have investigated the coordinate interactions between these two potentially oncogenic cyclins, cyclin-dependent protein kinase subunits (cdks) and the Rb tumor-suppressor protein. The distribution of cyclin D isoforms was modulated by serum factors in primary fetal rat lung epithelial cells. Moreover, cyclin D1 was found to be phosphorylated on tyrosine residues in vivo and, like cyclin A, was readily phosphorylated by pp60c-src in vitro. In synchronized human osteosarcoma cells, cyclin D1 is induced in early G1 and becomes associated with p9Ckshs1, a Cdk-binding subunit. Immunoprecipitation experiments with human osteosarcoma cells and Ewing’s sarcoma cells demonstrated that cyclin D1 is associated with both p34cdc2 and p33cdk2, and that cyclin D1 immune complexes exhibit appreciable histone H1 kinase activity. Immobilized, recombinant cyclins A and D1 were found to associate with cellular proteins in complexes that contain the p105Rb protein. This study identifies several common aspects of cyclin biochemistry, including tyrosine phosphorylation and the potential to interact directly or indirectly with the Rb protein, that may ultimately relate membrane-mediated signaling events to the regulation of gene expression. Sample Medline Abstract
13. TI - Two potentially oncogenic cyclins, cyclin A and cyclin D1 , share common properties of subunit configuration, tyrosine phosphorylation and physical association with the Rb protein AB - Originally identified as a ‘mitotic cyclin’, cyclin A exhibits properties of growth factor sensitivity, susceptibility to viral subversion and association with a tumor-suppressor protein, properties which are indicative of an S-phase-promoting factor ( SPF ) as well as a candidate proto-oncogene. Other recent studies have identified human cyclin D1 ( PRAD1 ) as a putative G1 cyclin and candidate proto-oncogene. However, the specific enzymatic activities and, hence, the precise biochemical mechanisms through which cyclins function to govern cell cycle progression remain unresolved. In the present study we have investigated the coordinate interactions between these two potentially oncogenic cyclins, cyclin-dependent protein kinase subunits (cdks) and the Rb tumor-suppressor protein. The distribution of cyclin D isoforms was modulated by serum factors in primary fetal rat lung epithelial cells. Moreover, cyclin D1 was found to be phosphorylated on tyrosine residues in vivo and, like cyclin A , was readily phosphorylated by pp60c-src in vitro. In synchronized human osteosarcoma cells, cyclin D1 is induced in early G1 and becomes associated with p9Ckshs1 , a Cdk-binding subunit. Immunoprecipitation experiments with human osteosarcoma cells and Ewing’s sarcoma cells demonstrated that cyclin D1 is associated with both p34cdc2 and p33cdk2 , and that cyclin D1 immune complexes exhibit appreciable histone H1 kinase activity. Immobilized, recombinant cyclins A and D1 were found to associate with cellular proteins in complexes that contain the p105Rb protein. This study identifies several common aspects of cyclin biochemistry, including tyrosine phosphorylation and the potential to interact directly or indirectly with the Rb protein, that may ultimately relate membrane-mediated signaling events to the regulation of gene expression. Sample Medline Abstract
14. Sample Medline Abstract TI - Two potentially oncogenic cyclins, cyclin A and cyclin D1 , share common properties of subunit configuration, tyrosine phosphorylation and physical association with the Rb protein AB - Originally identified as a ‘mitotic cyclin’, cyclin A exhibits properties of growth factor sensitivity, susceptibility to viral subversion and association with a tumor-suppressor protein, properties which are indicative of an S-phase-promoting factor ( SPF ) as well as a candidate proto-oncogene. Other recent studies have identified human cyclin D1 ( PRAD1 ) as a putative G1 cyclin and candidate proto-oncogene. However, the specific enzymatic activities and, hence, the precise biochemical mechanisms through which cyclins function to govern cell cycle progression remain unresolved. In the present study we have investigated the coordinate interactions between these two potentially oncogenic cyclins, cyclin-dependent protein kinase subunits (cdks) and the Rb tumor-suppressor protein. The distribution of cyclin D isoforms was modulated by serum factors in primary fetal rat lung epithelial cells. Moreover, cyclin D1 was found to be phosphorylated on tyrosine residues in vivo and, like cyclin A , was readily phosphorylated by pp60c-src in vitro. In synchronized human osteosarcoma cells, cyclin D1 is induced in early G1 and becomes associated with p9Ckshs1 , a Cdk-binding subunit. Immunoprecipitation experiments with human osteosarcoma cells and Ewing’s sarcoma cells demonstrated that cyclin D1 is associated with both p34cdc2 and p33cdk2 , and that cyclin D1 immune complexes exhibit appreciable histone H1 kinase activity. Immobilized, recombinant cyclins A and D1 were found to associate with cellular proteins in complexes that contain the p105Rb protein. This study identifies several common aspects of cyclin biochemistry, including tyrosine phosphorylation and the potential to interact directly or indirectly with the Rb protein, that may ultimately relate membrane-mediated signaling events to the regulation of gene expression.
32. Collective Information Extraction The control of human ribosomal protein L22 ( rpL22 ) to enter into the nucleolus and its ability to be assembled into the ribosome is regulated by its sequence . The nuclear import of rpL22 depends on a classical nuclear localization signal of four lysines at positions 13 – 16 … Once it reaches the nucleolus , the question of whether rpL22 is assembled into the ribosome depends upon the presence of the N - domain . e 1 e 2 e 3 e 4 ribosomal protein L22 ( rpL22 ) of rpL22 depends whether rpL22 is acronym repetition repetition repetition overlap e 5 L22
39. Generalizing Rules using Longest Common Subsequence The self - association site appears to be formed by interactions between helices 1 and 2 of beta spectrin repeat 17 of one dimer with helix 3 of alpha spectrin repeat 1 of the other dimer to form two combined alpha - beta triple - helical segments . Title - Physical and functional interactions between the transcriptional inhibitors Id3 and ITF-2b . - (7) interactions (0) between (5) PROT (9) PROT (17) .
48. Integrating Extracted Data with Existing Databases Extracted : 6,580 interactions between 3,737 human proteins Total: 31,609 interactions between 7,748 human proteins.