Li Yingrui Talk at the Beyond the Genome Meeting 2011. "Heading for a Full Solution to Now-Generation Bioinformatics" Covers BGI's missions using "tree" view of genome analysis for discovery.
Bio380 lecture on cancer as an evolutionary process, showing descent with modification, branching evolution and natural selection; focus on genome evolution
Synonymous mutations as drivers in human cancer genomes.Fran Supek
1) The document discusses how synonymous mutations, which do not change the protein sequence, are frequently found to act as drivers in carcinogenesis.
2) Using data from thousands of human cancer genomes, the author finds that oncogenes are enriched for synonymous mutations, showing synonymous mutations can be selected for during cancer development.
3) Further analysis suggests some synonymous mutations may impact mRNA folding, splicing, or microRNA binding sites and thus influence gene expression, providing a means for them to act as drivers.
Genomic variation refers to slight differences in genetic material between organisms. It includes mutations, which are mistakes in DNA copying, and polymorphisms, where multiple alleles exist for a gene. Variations are found throughout genomes and are not evenly distributed. Studying genomic variation helps with genome mapping and screening for genetic diseases. Phylogeny determines evolutionary relationships between species based on physical/genetic similarities from fossils, molecules, and genes. A phylogenetic tree shows inferred relationships in a branching diagram. Synteny refers to homologous genes occurring in the same order on chromosomes, showing closely related species have similar gene order and large syntenic regions. The document compares gene order and syntenic regions among rice, sorghum, maize, and
Genetic variation and evolution and their importance to medicineDavid Enoma
Genetic variation is the driving force of evolution and is important in medicine. Single nucleotide polymorphisms are the most common genetic variation and can influence disease risk and drug responses between individuals and populations. Understanding genetic variation through studies of populations and single genes can provide insights into human evolutionary history, disease susceptibility, and treatment effectiveness.
Puja Das conducted a biology investigatory project on gene therapy in the treatment of cancer under the supervision of her teacher Bilkis Barbhuiyan. The project report discusses gene therapy and how it relates to cancer, explaining that gene mutations can cause cancer and gene therapy aims to cure cancer by inserting normal genes or modifying genes. It also outlines several current approaches to gene therapy for cancer such as using recombinant DNA to boost the immune system's response to cancer, introducing drug-sensitivity genes to activate prodrugs selectively in tumor cells, and protecting bone marrow from chemotherapy using drug-resistance genes.
Genetic variation and its role in health pharmacologyDeepak Kumar
Genetic variation exists at different scales, from single nucleotide polymorphisms within individuals of a species to larger structural differences between species. Genetic variation arises through mutations, recombination, gene flow, genetic drift, and the interaction of these processes over time. The effective population size of a species influences how genetic variation is shaped by these evolutionary forces.
1. The presentation discusses various types of mutations including substitutions, insertions, deletions, and frameshifts.
2. It explains the molecular basis of mutations including that DNA contains genetic instructions encoded by sequences of bases and that mutations occur when the DNA sequence changes.
3. The causes of mutations are discussed as DNA replication errors, external influences like chemicals or radiation, and during processes like genetic recombination.
The document describes experiments conducted to induce apoptosis in non-invasive retinoblastoma cell lines using tissue-specific promoter guided suicide gene transfection. Key objectives included propagating the suicide gene plasmid, transfecting it into a non-invasive retinoblastoma cell line, validating transfection efficiency through various assays, and studying the apoptotic effects induced. Transfection was confirmed at the mRNA and protein level. Assays showed over 60% of transfected cells undergoing early apoptosis and 35% undergoing late apoptosis, demonstrating the suicide gene successfully induced apoptosis in the targeted retinoblastoma cells.
Bio380 lecture on cancer as an evolutionary process, showing descent with modification, branching evolution and natural selection; focus on genome evolution
Synonymous mutations as drivers in human cancer genomes.Fran Supek
1) The document discusses how synonymous mutations, which do not change the protein sequence, are frequently found to act as drivers in carcinogenesis.
2) Using data from thousands of human cancer genomes, the author finds that oncogenes are enriched for synonymous mutations, showing synonymous mutations can be selected for during cancer development.
3) Further analysis suggests some synonymous mutations may impact mRNA folding, splicing, or microRNA binding sites and thus influence gene expression, providing a means for them to act as drivers.
Genomic variation refers to slight differences in genetic material between organisms. It includes mutations, which are mistakes in DNA copying, and polymorphisms, where multiple alleles exist for a gene. Variations are found throughout genomes and are not evenly distributed. Studying genomic variation helps with genome mapping and screening for genetic diseases. Phylogeny determines evolutionary relationships between species based on physical/genetic similarities from fossils, molecules, and genes. A phylogenetic tree shows inferred relationships in a branching diagram. Synteny refers to homologous genes occurring in the same order on chromosomes, showing closely related species have similar gene order and large syntenic regions. The document compares gene order and syntenic regions among rice, sorghum, maize, and
Genetic variation and evolution and their importance to medicineDavid Enoma
Genetic variation is the driving force of evolution and is important in medicine. Single nucleotide polymorphisms are the most common genetic variation and can influence disease risk and drug responses between individuals and populations. Understanding genetic variation through studies of populations and single genes can provide insights into human evolutionary history, disease susceptibility, and treatment effectiveness.
Puja Das conducted a biology investigatory project on gene therapy in the treatment of cancer under the supervision of her teacher Bilkis Barbhuiyan. The project report discusses gene therapy and how it relates to cancer, explaining that gene mutations can cause cancer and gene therapy aims to cure cancer by inserting normal genes or modifying genes. It also outlines several current approaches to gene therapy for cancer such as using recombinant DNA to boost the immune system's response to cancer, introducing drug-sensitivity genes to activate prodrugs selectively in tumor cells, and protecting bone marrow from chemotherapy using drug-resistance genes.
Genetic variation and its role in health pharmacologyDeepak Kumar
Genetic variation exists at different scales, from single nucleotide polymorphisms within individuals of a species to larger structural differences between species. Genetic variation arises through mutations, recombination, gene flow, genetic drift, and the interaction of these processes over time. The effective population size of a species influences how genetic variation is shaped by these evolutionary forces.
1. The presentation discusses various types of mutations including substitutions, insertions, deletions, and frameshifts.
2. It explains the molecular basis of mutations including that DNA contains genetic instructions encoded by sequences of bases and that mutations occur when the DNA sequence changes.
3. The causes of mutations are discussed as DNA replication errors, external influences like chemicals or radiation, and during processes like genetic recombination.
The document describes experiments conducted to induce apoptosis in non-invasive retinoblastoma cell lines using tissue-specific promoter guided suicide gene transfection. Key objectives included propagating the suicide gene plasmid, transfecting it into a non-invasive retinoblastoma cell line, validating transfection efficiency through various assays, and studying the apoptotic effects induced. Transfection was confirmed at the mRNA and protein level. Assays showed over 60% of transfected cells undergoing early apoptosis and 35% undergoing late apoptosis, demonstrating the suicide gene successfully induced apoptosis in the targeted retinoblastoma cells.
2000 weinberg. hallsmarcks of cancer new generationNatalia Muñoz Roa
This document summarizes the key hallmarks of cancer that were identified after decades of cancer research. The six essential alterations in cell physiology that were found to collectively dictate malignant growth are: 1) self-sufficiency in growth signals, 2) insensitivity to growth-inhibitory signals, 3) evasion of programmed cell death, 4) limitless replicative potential, 5) sustained angiogenesis, and 6) tissue invasion and metastasis. These six capabilities are thought to be shared by most or all human tumors and represent the successful breaching of anticancer defense mechanisms in cells and tissues. The document provides examples to illustrate each capability and strategies by which cancers acquire them.
This document discusses comparative genomics and the evolution of genes using Drosophila species as a model. It summarizes that 12 Drosophila genomes were compared phylogenetically and this comparison revealed patterns of gene family expansion and contraction over time as well as structural changes and rearrangements like in the Hox cluster. The multi-species comparisons provided strong evidence for gene models and functions are conserved despite sequence divergence across the Drosophila phylogeny.
Genetic and environmental factors are the two keys that make human phenotype variations. When the genomic DNA sequences on equivalent chromosomes of any two individuals are compared, there is substantial variation in the sequence at many points throughout the genome. The term polymorphism was originally used to describe variations in shape and form that distinguish normal individuals within a species from each other. These days, geneticists use the term genetic polymorphisms to describe the inter-individual, functionally silent differences in DNA sequence that make each human genome unique. In order to better understand the phenomenon of genetic polymorphism, an emphasis has been laid on the structures and functions of nucleotides, genes and nucleic acids, including their relationship with polymorphism.
Polymorphism can be caused by factors such as mutation, which is defined as a permanent transmissible change in DNA sequence. Mutations are classified based on where they occur somatic and germ line mutations) and the length of the nucleotide sequences they affect (gene-level and chromosomal mutations). The various types of polymorphisms include; single nucleotide polymorphisms (SNPs), small-scale insertions/deletions, polymorphic repetitive elements, microsatellite variation and haplotypes.
Variations in DNA sequences may have a major impact on how human beings respond to disease, bacteria, viruses, toxins, chemicals, drugs, and other therapies. Many clinical phenotypes observed in diseases seem to have considerable genetic components.
Determining genetic polymorphism can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity. Some of the techniques used in studying polymorphisms include; PCR based techniques and techniques involving DNA based markers.
Key words: Genetic polymorphism, effects in a population,
This document discusses key concepts in comparative genomics including orthologs, paralogs, speciation, and clusters of orthologous genes (COGs). It defines orthologs as genes evolved from a common ancestor through speciation that retain the same function, while paralogs are related through duplication and may evolve new functions. COGs are groups of orthologous genes from different species that are more similar to each other than to other genes within individual genomes. The document notes that COGs can be used to predict gene function and track evolutionary divergence. It provides an example of the NCBI COG database containing over 136,000 proteins from 50 bacteria, 13 archaea and 3 eukaryotes classified into CO
This document summarizes the challenges and progress of human gene therapy. It discusses three categories of gene therapy delivery (ex vivo, in situ, in vivo) and focuses on challenges of using retroviral vectors, including inefficient delivery, inability to transduce non-dividing cells, lack of long-term gene expression, and difficulties with large-scale manufacturing. While over 300 clinical trials have been approved, gene therapy efficiency remains low and no protocols have conclusively treated human disease. The document evaluates efforts to address these challenges through envelope protein engineering, hybrid vectors, and improved regulatory sequences.
The document discusses genetic polymorphisms in Plasmodium falciparum, the parasite that causes malaria. It defines key terms like locus, allele, and genome. It then describes different types of genetic polymorphisms like single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), and short tandem repeats (STRs). The document focuses on polymorphisms related to drug resistance in P. falciparum, discussing genes associated with resistance to chloroquine (pfcrt) and other antimalarial drugs, along with specific mutations in those genes linked to resistance.
Genetic variation occurs both within and among populations and is brought about by mutation, recombination, migration, and genetic drift. There are four main types of genetic variation: mutation, genetic recombination, migration, and genetic drift. Genetic variation is important as it allows individuals and populations to adapt to their environments. It plays a key role in health and pharmacology, for example in gene therapy which aims to treat diseases by replacing, inactivating, or introducing new genes.
Cancer arises from normal cells whose nature is permanently changed, causing them to multiply rapidly and not be subject to normal control. Oncogenes are genes capable of transforming normal cells into cancerous cells and result from mutations of normal proto-oncogenes. Both DNA and RNA tumor viruses can transform cells through integration into the host cell DNA, which results in loss of growth control and tumor formation. Retroviruses contain oncogenes (v-onc) that are homologous to cellular proto-oncogenes (c-onc) and can induce transformation after mutation or other changes to the cell's genome.
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
This document provides an overview of comparative genomics. It defines comparative genomics as combining genomic data and evolutionary biology to study genome structure, evolution and function. It discusses three levels of genome comparison: bulk properties like chromosome size and number, whole genome sequence similarity and organization, and functional genome features. The history of experimental comparative genomics is reviewed, noting that practical comparisons predated widespread genome sequencing.
This document summarizes 3 presentations from the Autumn Immunology Conference 2010:
1) Icelandic ash from a volcanic eruption alters alveolar macrophage phenotype, causing phagocytosis of ash particles and signaling changes.
2) A highly organized mucosal dendritic cell network interacts with effector and regulatory T cells in the intestinal mucosa.
3) Preliminary results show different levels of expression of pro-inflammatory cytokines, VEGFs, and VEGF receptors in filarial and cancer patients, influencing lymphangiogenesis.
The document summarizes genomic comparisons across different organisms. It discusses:
1) The first sequencing of bacterial genomes including Haemophilus influenzae, which has 1.8 million base pairs and 1,749 genes.
2) The sequencing of eukaryotic genomes including Saccharomyces cerevisiae, which has 16 chromosomes and approximately 5,885 protein-coding genes.
3) Key animal and plant genomes sequenced including Arabidopsis thaliana, Drosophila melanogaster, Mus musculus, and Homo sapiens. The human genome is approximately 3 billion base pairs long and contains around 30,000 genes.
“The data presented here and in the literature are consistent with the hypothesis that at least one cancer, retinoblastoma, can be caused by two mutations…. One of these mutations may be inherited as a result of a previous germinal mutation…. Those patients that inherit one mutation develop tumors earlier than do those who develop the nonhereditary form of the disease; in a majority of cases those who inherit a mutation develop more than one tumor.
Alfred Knudson developed the two-hit hypothesis for cancer causation in 1971 to explain hereditary and non-hereditary retinoblastoma. The hypothesis proposed that cancer results from two mutations, with hereditary cancer requiring one mutation inherited in all cells and non-hereditary cancer requiring two spontaneous mutations. This anticipated the discovery of tumor suppressor genes. Later work extended the two-hit model to other childhood cancers and carcinomas. Currently, Knudson's research focuses on using knowledge of hereditary cancers to develop chemoprevention strategies by targeting early somatic events in high-risk individuals.
Tumorigenesis is a multi-step process beginning with an initial genetic change in a normal cell, such as loss of function of the pRb tumor suppressor or overexpression of the c-myc oncogene. This decreases apoptotic cell death and increases cell proliferation. Subsequent genetic changes, like dysfunction of p53 or overexpression of bcl-2, lead to further alterations in phenotype and the emergence of tumor cell heterogeneity. The progression of tumors is influenced by anatomical factors, the organ microenvironment, angiogenic factors, and the host immune response.
This study aimed to induce apoptosis in a non-invasive retinoblastoma cell line through transfection of a suicide gene plasmid driven by a tissue-specific promoter. The researchers transfected the plasmid into the cell line and detected over 10-fold increased expression of the suicide gene. Protein expression was also confirmed through immunofluorescence. Apoptosis assays showed that the suicide gene induced apoptosis in over 60% of the transfected non-invasive retinoblastoma cells. The researchers concluded that the tissue-specific promoter-driven suicide gene in a non-viral vector could be used as a potential treatment for retinoblastoma.
This is the first presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on different levels.
Thanks to Klaas Vandepoele of the PSB department.
Malaria due to Plasmodium falciparum is a major public health concern in Cameroon and Africa, responsible for high rates of morbidity and mortality. While control measures have been effective, an effective vaccine is needed to achieve global malaria elimination goals. This study analyzed genetic diversity in the merozoite surface protein 1 (msp1) gene of P. falciparum isolates from Mount Cameroon. It found 45 distinct DNA fragments in samples from 81 of 173 infected individuals, indicating significant intragenic recombination contributing to parasite diversity. Understanding this diversity is important for vaccine development against P. falciparum.
This document discusses a teaching and learning material (TLM) that helps teach children about the five daily prayers in Islam. The TLM is a slate that displays the name of each prayer, the prayer times, and number of units (Raka'ats) for each prayer. It is meant to be used as a classroom decoration to attractively present this information to students. The document outlines the materials needed to create the TLM, how teachers can use it to support learning, and concludes that it will help children learn the key details about each of the five daily prayers in Islam.
Blogs, podcasts, social networking sites, and virtual worlds were discussed as popular social media platforms currently and may evolve in the future. Blogs like Huffington Post and TMZ had millions of monthly visitors. Podcast Alley contained 90,000 podcasts across genres. Facebook had 700 million monthly visitors, focusing on photo sharing, while Myspace had 80 million focusing on music. World of Warcraft had over 11 million subscribers interacting in a virtual world. Twitter may become a new blogging platform, while sites may aggregate content and merge features through personalization.
2000 weinberg. hallsmarcks of cancer new generationNatalia Muñoz Roa
This document summarizes the key hallmarks of cancer that were identified after decades of cancer research. The six essential alterations in cell physiology that were found to collectively dictate malignant growth are: 1) self-sufficiency in growth signals, 2) insensitivity to growth-inhibitory signals, 3) evasion of programmed cell death, 4) limitless replicative potential, 5) sustained angiogenesis, and 6) tissue invasion and metastasis. These six capabilities are thought to be shared by most or all human tumors and represent the successful breaching of anticancer defense mechanisms in cells and tissues. The document provides examples to illustrate each capability and strategies by which cancers acquire them.
This document discusses comparative genomics and the evolution of genes using Drosophila species as a model. It summarizes that 12 Drosophila genomes were compared phylogenetically and this comparison revealed patterns of gene family expansion and contraction over time as well as structural changes and rearrangements like in the Hox cluster. The multi-species comparisons provided strong evidence for gene models and functions are conserved despite sequence divergence across the Drosophila phylogeny.
Genetic and environmental factors are the two keys that make human phenotype variations. When the genomic DNA sequences on equivalent chromosomes of any two individuals are compared, there is substantial variation in the sequence at many points throughout the genome. The term polymorphism was originally used to describe variations in shape and form that distinguish normal individuals within a species from each other. These days, geneticists use the term genetic polymorphisms to describe the inter-individual, functionally silent differences in DNA sequence that make each human genome unique. In order to better understand the phenomenon of genetic polymorphism, an emphasis has been laid on the structures and functions of nucleotides, genes and nucleic acids, including their relationship with polymorphism.
Polymorphism can be caused by factors such as mutation, which is defined as a permanent transmissible change in DNA sequence. Mutations are classified based on where they occur somatic and germ line mutations) and the length of the nucleotide sequences they affect (gene-level and chromosomal mutations). The various types of polymorphisms include; single nucleotide polymorphisms (SNPs), small-scale insertions/deletions, polymorphic repetitive elements, microsatellite variation and haplotypes.
Variations in DNA sequences may have a major impact on how human beings respond to disease, bacteria, viruses, toxins, chemicals, drugs, and other therapies. Many clinical phenotypes observed in diseases seem to have considerable genetic components.
Determining genetic polymorphism can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity. Some of the techniques used in studying polymorphisms include; PCR based techniques and techniques involving DNA based markers.
Key words: Genetic polymorphism, effects in a population,
This document discusses key concepts in comparative genomics including orthologs, paralogs, speciation, and clusters of orthologous genes (COGs). It defines orthologs as genes evolved from a common ancestor through speciation that retain the same function, while paralogs are related through duplication and may evolve new functions. COGs are groups of orthologous genes from different species that are more similar to each other than to other genes within individual genomes. The document notes that COGs can be used to predict gene function and track evolutionary divergence. It provides an example of the NCBI COG database containing over 136,000 proteins from 50 bacteria, 13 archaea and 3 eukaryotes classified into CO
This document summarizes the challenges and progress of human gene therapy. It discusses three categories of gene therapy delivery (ex vivo, in situ, in vivo) and focuses on challenges of using retroviral vectors, including inefficient delivery, inability to transduce non-dividing cells, lack of long-term gene expression, and difficulties with large-scale manufacturing. While over 300 clinical trials have been approved, gene therapy efficiency remains low and no protocols have conclusively treated human disease. The document evaluates efforts to address these challenges through envelope protein engineering, hybrid vectors, and improved regulatory sequences.
The document discusses genetic polymorphisms in Plasmodium falciparum, the parasite that causes malaria. It defines key terms like locus, allele, and genome. It then describes different types of genetic polymorphisms like single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), and short tandem repeats (STRs). The document focuses on polymorphisms related to drug resistance in P. falciparum, discussing genes associated with resistance to chloroquine (pfcrt) and other antimalarial drugs, along with specific mutations in those genes linked to resistance.
Genetic variation occurs both within and among populations and is brought about by mutation, recombination, migration, and genetic drift. There are four main types of genetic variation: mutation, genetic recombination, migration, and genetic drift. Genetic variation is important as it allows individuals and populations to adapt to their environments. It plays a key role in health and pharmacology, for example in gene therapy which aims to treat diseases by replacing, inactivating, or introducing new genes.
Cancer arises from normal cells whose nature is permanently changed, causing them to multiply rapidly and not be subject to normal control. Oncogenes are genes capable of transforming normal cells into cancerous cells and result from mutations of normal proto-oncogenes. Both DNA and RNA tumor viruses can transform cells through integration into the host cell DNA, which results in loss of growth control and tumor formation. Retroviruses contain oncogenes (v-onc) that are homologous to cellular proto-oncogenes (c-onc) and can induce transformation after mutation or other changes to the cell's genome.
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
This document provides an overview of comparative genomics. It defines comparative genomics as combining genomic data and evolutionary biology to study genome structure, evolution and function. It discusses three levels of genome comparison: bulk properties like chromosome size and number, whole genome sequence similarity and organization, and functional genome features. The history of experimental comparative genomics is reviewed, noting that practical comparisons predated widespread genome sequencing.
This document summarizes 3 presentations from the Autumn Immunology Conference 2010:
1) Icelandic ash from a volcanic eruption alters alveolar macrophage phenotype, causing phagocytosis of ash particles and signaling changes.
2) A highly organized mucosal dendritic cell network interacts with effector and regulatory T cells in the intestinal mucosa.
3) Preliminary results show different levels of expression of pro-inflammatory cytokines, VEGFs, and VEGF receptors in filarial and cancer patients, influencing lymphangiogenesis.
The document summarizes genomic comparisons across different organisms. It discusses:
1) The first sequencing of bacterial genomes including Haemophilus influenzae, which has 1.8 million base pairs and 1,749 genes.
2) The sequencing of eukaryotic genomes including Saccharomyces cerevisiae, which has 16 chromosomes and approximately 5,885 protein-coding genes.
3) Key animal and plant genomes sequenced including Arabidopsis thaliana, Drosophila melanogaster, Mus musculus, and Homo sapiens. The human genome is approximately 3 billion base pairs long and contains around 30,000 genes.
“The data presented here and in the literature are consistent with the hypothesis that at least one cancer, retinoblastoma, can be caused by two mutations…. One of these mutations may be inherited as a result of a previous germinal mutation…. Those patients that inherit one mutation develop tumors earlier than do those who develop the nonhereditary form of the disease; in a majority of cases those who inherit a mutation develop more than one tumor.
Alfred Knudson developed the two-hit hypothesis for cancer causation in 1971 to explain hereditary and non-hereditary retinoblastoma. The hypothesis proposed that cancer results from two mutations, with hereditary cancer requiring one mutation inherited in all cells and non-hereditary cancer requiring two spontaneous mutations. This anticipated the discovery of tumor suppressor genes. Later work extended the two-hit model to other childhood cancers and carcinomas. Currently, Knudson's research focuses on using knowledge of hereditary cancers to develop chemoprevention strategies by targeting early somatic events in high-risk individuals.
Tumorigenesis is a multi-step process beginning with an initial genetic change in a normal cell, such as loss of function of the pRb tumor suppressor or overexpression of the c-myc oncogene. This decreases apoptotic cell death and increases cell proliferation. Subsequent genetic changes, like dysfunction of p53 or overexpression of bcl-2, lead to further alterations in phenotype and the emergence of tumor cell heterogeneity. The progression of tumors is influenced by anatomical factors, the organ microenvironment, angiogenic factors, and the host immune response.
This study aimed to induce apoptosis in a non-invasive retinoblastoma cell line through transfection of a suicide gene plasmid driven by a tissue-specific promoter. The researchers transfected the plasmid into the cell line and detected over 10-fold increased expression of the suicide gene. Protein expression was also confirmed through immunofluorescence. Apoptosis assays showed that the suicide gene induced apoptosis in over 60% of the transfected non-invasive retinoblastoma cells. The researchers concluded that the tissue-specific promoter-driven suicide gene in a non-viral vector could be used as a potential treatment for retinoblastoma.
This is the first presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on different levels.
Thanks to Klaas Vandepoele of the PSB department.
Malaria due to Plasmodium falciparum is a major public health concern in Cameroon and Africa, responsible for high rates of morbidity and mortality. While control measures have been effective, an effective vaccine is needed to achieve global malaria elimination goals. This study analyzed genetic diversity in the merozoite surface protein 1 (msp1) gene of P. falciparum isolates from Mount Cameroon. It found 45 distinct DNA fragments in samples from 81 of 173 infected individuals, indicating significant intragenic recombination contributing to parasite diversity. Understanding this diversity is important for vaccine development against P. falciparum.
This document discusses a teaching and learning material (TLM) that helps teach children about the five daily prayers in Islam. The TLM is a slate that displays the name of each prayer, the prayer times, and number of units (Raka'ats) for each prayer. It is meant to be used as a classroom decoration to attractively present this information to students. The document outlines the materials needed to create the TLM, how teachers can use it to support learning, and concludes that it will help children learn the key details about each of the five daily prayers in Islam.
Blogs, podcasts, social networking sites, and virtual worlds were discussed as popular social media platforms currently and may evolve in the future. Blogs like Huffington Post and TMZ had millions of monthly visitors. Podcast Alley contained 90,000 podcasts across genres. Facebook had 700 million monthly visitors, focusing on photo sharing, while Myspace had 80 million focusing on music. World of Warcraft had over 11 million subscribers interacting in a virtual world. Twitter may become a new blogging platform, while sites may aggregate content and merge features through personalization.
TruConnect offers a simple and cheap mobile internet plan for $4.99 per month plus 3.9 cents per megabyte with no expiration dates, activation fees or contracts. The plan can save customers over $600 compared to major carriers based on actual usage.
The Cortland Main Street Music Series provides free summer concerts in downtown Cortland featuring local, regional, and national musical artists across a variety of genres. The goal is to bring the community together to stimulate cultural and economic activity downtown. Over the past 10 years, attendance at the concerts has grown from small gatherings to thousands of people showing up to enjoy the music and family-friendly carnival atmosphere.
This document discusses 7 species of sea turtles and the threats they face from human activity. It provides details on the appearance and characteristics of each species. The main threats are over-harvesting of eggs and meat, hunting for luxury items, and accidental killing from fishing nets and plastic debris. Conservation efforts include using Turtle Excluder Devices in shrimp nets, establishing protected nesting areas, promoting sustainable tourism, and advocacy work by organizations like the World Wildlife Foundation and Sea Turtle Conservancy.
Ebola is a new and deadly disease in Nigeria that spreads quickly from person to person through direct contact with body fluids like blood, vomit, sweat, or saliva of an infected individual. Symptoms like fever, headache, muscle aches, and stomach pain appear 2 to 21 days after exposure. While there is no vaccine, prevention relies on avoiding contact with bushmeat, practicing good hygiene like handwashing, and isolating infected patients through barrier nursing techniques.
This document discusses 7 species of sea turtles and the threats they face from human activity. It provides details on the appearance and characteristics of each species. The main threats are over-harvesting of eggs and meat, hunting for luxury items, and accidental killing through fishing nets and plastic debris. Conservation efforts include using Turtle Excluder Devices in shrimp nets, establishing protected nesting areas, promoting sustainable tourism, and advocacy work by organizations like the World Wildlife Foundation and Sea Turtle Conservancy.
This document provides tips for creating effective PowerPoint presentations. It recommends keeping themes, fonts, and backgrounds clear and consistent, while limiting graphics and images to avoid copyright issues. Presenters should avoid cluttered slides, face the audience, allow time for sound effects, and ensure the presentation flows nicely. Animations, music, and timings should be subtle and not overpowering. The goal is to engage the audience and get the key messages across in a clear manner.
This document lists Arabic names for various objects. It contains the Arabic alphabet and names for objects like rabbit, cow, apple, snake, camel, horse, ring, cock, fly, leg, flower, fish, umbrella, soap, frog, airplane, butterfly, cat, and banana. Each Arabic letter is paired with an object name beginning with that letter in Arabic.
Genetic terms used in psychiatry include:
- Concordance and heritability which measure the genetic influences on traits and diseases
- Mendelian and complex diseases which can be caused by single genes or interactions between genes and environment
- Alleles, haplotypes, loci, genetic maps, and linkage disequilibrium which describe genetic variations and inheritance patterns
Genome-wide association studies typically assay common genetic variants like single nucleotide polymorphisms to identify associations with traits and diseases.
This document discusses genetics concepts and terms relevant to psychiatry. It begins by defining key genetic terms like heritability, Mendelian disease, complex disease, alleles, loci, linkage, and genome-wide association studies. It then discusses underlying concepts in psychiatric genetics like the biopsychosocial model, gene-environment interactions, Mendelian and non-Mendelian inheritance, genetic models, and linkage disequilibrium. Specific examples of gene-environment interactions and Mendelian disorders in psychiatry are provided.
How to transform genomic big data into valuable clinical informationJoaquin Dopazo
This document discusses how to transform genomic big data into valuable clinical information. It begins by defining genomic big data and explaining how individual genome data contains more information than the original experiment. Next, it discusses lessons learned from genome-wide association studies, including that many loci contribute to traits and there is evidence of pleiotropy. However, individual genes cannot fully explain trait heritability. The document then discusses challenges in detecting disease-related variants from exome/genome sequencing data due to the large number of variants and presence of apparently deleterious variants in healthy individuals. It suggests taking a systems approach considering interactions and multigenicity to better understand variation and disease mechanisms.
The document discusses DNA methylation, repetitive DNA sequences, the C-value paradox, and their relationships. It provides background on DNA methylation, how it regulates gene expression and is involved in diseases. It describes highly repetitive and satellite DNA sequences. It explains that the C-value paradox stemmed from the observation that genome size did not correlate with complexity, but this was later resolved by discovering non-coding DNA. The paradox questioned how genome size related to gene number.
1) Genotyping is the analysis of DNA sequence variation to determine an individual's genetic constitution or genotype. It involves identifying polymorphisms like single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs).
2) High throughput genotyping techniques like microarrays allow for the simultaneous genotyping of hundreds of thousands to over a million loci across many individuals. This has applications in disease association studies, plant and animal breeding, and forensic analysis.
3) Linkage mapping involves analyzing co-inheritance patterns of genetic markers and traits in families to determine if genes are linked (located close together) on the same chromosome. It is used to construct genetic maps of chromosome regions and identify quantitative trait loci (QTLs).
A New Generation Of Mechanism-Based Biomarkers For The ClinicJoaquin Dopazo
The document discusses moving from single gene biomarkers to more functional, modular biomarkers for disease. It argues that most diseases are caused by combinations of variants affecting functional modules rather than single genes. The document proposes analyzing genomic data like SNPs and gene expression in the context of protein interaction networks and gene ontologies to better capture disease mechanisms and identify more informative biomarkers. Examples show how this approach can prioritize genes interacting with known disease genes and find enriched functional groups associated with diseases.
The document discusses using targeted next-generation sequencing (NGS) panels to identify genetic causes of nephrotic diseases in individuals with unknown etiology. The study found rare pathogenic/likely pathogenic mutations in nephrotic disease-related genes in 12% of patients using the ACMG-AMP variant classification standards. NGS can improve diagnosis accuracy for nephrotic diseases by discovering uncommon pathogenic variations compatible with clinical diagnoses in 65% of samples. The document provides background on genetics, genetic variations, inheritance patterns, and NGS techniques for detecting mutations.
The document discusses family history and genetics. It introduces key terminology related to genetics, genomics, and epigenetics. It describes pedigrees and provides examples of pedigree charts. It discusses the value of collecting accurate family health histories, including helping to identify genetic risks and target genetic testing and preventative care.
Conferencia de la Dra. Ana María Roa, Bióloga Molecular, sobre Epigenética, impartida en la Universidad Popular Carmen de Michelena de Tres Cantos el 1 de marzo de 2013.
Más información en:
http://www.universidadpopularc3c.es/index.php/actividades/conferencias/event/448-conferencia-una-revision-de-los-conocimientos-fundamentales-de-la-biologia-de-la-celula-la-epigenetica
Bioinformatics is an interdisciplinary field that uses computational tools and techniques to analyze and interpret biological data. It plays a key role in areas like agriculture and healthcare. Some major areas of bioinformatics research include gene finding, protein structure prediction, and drug design. All organisms possess genetic material DNA that controls cell functioning and is the basis for inheritance. Understanding genomes, genes, and how genetic information is expressed presents many challenges. Comparative genomics through genome projects of different organisms can provide insights into evolution and aid in drug development.
Learning Objectives Define inheritance Define allele and trait Describe.docxwrite5
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This document defines key genetics concepts and outlines learning objectives related to inheritance and evolution. It describes how DNA encodes genes, which determine physical traits. Genes are passed from parents to offspring, with dominant alleles usually determining visible traits. In stable populations, allele frequencies remain constant due to random mating and lack of evolutionary pressures. However, mutations, genetic drift, gene flow and natural selection can drive changes in allele frequencies over generations. The document introduces a simulation model where students can observe inheritance and evolution by tracking the rim color of "model bugs" over multiple generations.
Lecture given for the Data Mining course at Uppsala university in October 2013. The presentation talks about data analysis in the context of genomics, next-generation sequencing, metagenomics etc.
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PharmaCon2007 Congress, Dubrovnik, Croatia "New Technologies and Trends in Pharmacy, Pharmaceutical Industry and Education" http://www.pharmacon2007.com
Abstract is available at http://www.pharmaconnectme.com
This document provides an overview of biotechnology and related topics. It defines biotechnology as the integration of science and engineering to life processes to solve problems or manufacture products. It discusses core biotechnologies like monoclonal antibodies, biosensors, cell culture, and recombinant DNA. It explains how these biotechnologies are used in areas like healthcare, pharmaceuticals, and environmental remediation. It also summarizes the science of cells, DNA, genes, and proteins as the foundations of modern biotechnology.
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إضغ بين إيديكم من أقوى الملازم التي صممتها
ملزمة تشريح الجهاز الهيكلي (نظري 3)
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تتميز هذهِ الملزمة بعِدة مُميزات :
1- مُترجمة ترجمة تُناسب جميع المستويات
2- تحتوي على 78 رسم توضيحي لكل كلمة موجودة بالملزمة (لكل كلمة !!!!)
#فهم_ماكو_درخ
3- دقة الكتابة والصور عالية جداً جداً جداً
4- هُنالك بعض المعلومات تم توضيحها بشكل تفصيلي جداً (تُعتبر لدى الطالب أو الطالبة بإنها معلومات مُبهمة ومع ذلك تم توضيح هذهِ المعلومات المُبهمة بشكل تفصيلي جداً
5- الملزمة تشرح نفسها ب نفسها بس تكلك تعال اقراني
6- تحتوي الملزمة في اول سلايد على خارطة تتضمن جميع تفرُعات معلومات الجهاز الهيكلي المذكورة في هذهِ الملزمة
واخيراً هذهِ الملزمة حلالٌ عليكم وإتمنى منكم إن تدعولي بالخير والصحة والعافية فقط
كل التوفيق زملائي وزميلاتي ، زميلكم محمد الذهبي 💊💊
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How Barcodes Can Be Leveraged Within Odoo 17Celine George
In this presentation, we will explore how barcodes can be leveraged within Odoo 17 to streamline our manufacturing processes. We will cover the configuration steps, how to utilize barcodes in different manufacturing scenarios, and the overall benefits of implementing this technology.
Temple of Asclepius in Thrace. Excavation resultsKrassimira Luka
The temple and the sanctuary around were dedicated to Asklepios Zmidrenus. This name has been known since 1875 when an inscription dedicated to him was discovered in Rome. The inscription is dated in 227 AD and was left by soldiers originating from the city of Philippopolis (modern Plovdiv).
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Iván Bornacelly, Policy Analyst at the OECD Centre for Skills, OECD, presents at the webinar 'Tackling job market gaps with a skills-first approach' on 12 June 2024
1. Heading for full solution to Now Generation Informatics BGI-Shenzhen Sep 19, 2011
2. Nothing in biology makes sense except in light of evolutionTheodosius Dobzhansky “Tree” type of thinking of Genomics They are different, they are also related
3. What is the scope of bioinformatics? Bioinformatics is to understand the tree of life. Bioinformatics will: Draw trees (basic information) Map information on trees (association/cause-effect) Show the trees (visualizations, databases, clouds)
4. Mission 1: Tree of Species A set of different genes (sequence) made different forms of life
5. Mission 1: Tree of Species Draw De novo genome assembly Multiple sequence mapping and alignment Phylogenic tree construction Map In-depth Annotation Comparative genomicss Show Genome browsers
6. Dinner “taste good, sequence it!” Peking Duck cucumber Cabbage kung pao chicken Mapotoufu oyster
7. Factory Silk and silkworm Oil and castor bean “Useful, sequence it!” Cloth and cotton
8. Zoo “look cute, sequence it!” Panda Polar bear and Penguin Antelope
9. Misson 2: Tree of Individuals A set of different variations (sequence) made different individuals/cells of Human
12. Approximately 90% of the variability in allele frequencies is of this sort.From Mary-Claire King
13. International project to construct a next generation baseline data set for human genetics Sequence level HapMap, an order of magnitude deeper Consortium with multiple centres, platforms, funders Aims Find >95% accessible SNPs at allele frequencies above 1%, down towards 0.1% in coding regions Genotype them and place on haplotype backgrounds Also discover and characterize indels, structural variants
16. Male mutation rate ~7x higher than female mutation rateFrom 1000G Project From Mary-Claire King Development of agriculture in the past 10,000 years and of urbanization and industrialization in the past 700 years has led to rapid populations growth and therefore to the appearance of vast numbers of new alleles, each individually rare and specific to one population or even to one family.
17. What’s the whole picture of genetic variants ? Billion Genomes Project Personal genomics with phenotype information Allele Frequency 50% 5% 0.5% 0.05% Rarer Alleles Stronger Effects Common Alleles Less Effects Very Rare Alleles Strongest Effects Eg: CFTR delta 508 PCSK9 C679X Eg: MC4R, ABCA1 1q21.1 in SCZ Common/rare Disease Mendelian Disease
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19. domestication event lead to a 90% reduction in effective population size during the initial bottleneckPublished in Science 16 Oct.
20. from Andersson and Georges, Nature Reviews of Genetic5: 202-212 (2004) selective sweep: inheritance of regions around adaptive alleles extent of selective sweep for domestication in MAIZE: tb1 locus (60 to 90-kb) (Clark et al. 2004), Y1 locus (about 600-kb) (Palaisa et al. 2004)
21. Domestication Genome variation during silkworm domestication 354 candidate domesticated genes 159 tissue-specific expressed (silk gland, midgut, testis) Published in Science 16 Oct.
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23. Expression level difference in placentaEPAS1: endothelial Per-Arnt-Sim (PAS) domain protein 1 The signal of selection The gene (EPAS1) showing strongest selection signal (up to 80% frequency change in allele distribution), Han: 9%; Tibetan: 87%
25. PCA analysis for 85 Danish samples (based on gene profiling) BMI data Gene level
26. Misson 2. Tree of Individuals Draw (Complete spectrum of) variation identification Population frequencies and spectrums Map Selection and evolution Phenotypic traits Intermediate phenotypes
27. Misson 3: Tree of Cells Cell lineages are characterized by single biological levels and their inter-correlations.
28. On DNA Differentiate the cancer and normal cells by PCA analysis ET AML + : cancer *: normal *:cells possibly mixed (from tumor, but clustered to normal cells) these cancers are really heterogeneous. BTCC
29. Phylogenetic trees clearly show subpopulations in ET and AML cancers ET AML Essential Thrombocythemia Acute Myeloid Leukemia
30. Inferring key genes in AML (a typical heterozygous cancer) Key Gene? Key Gene for sub-pop? Consensus Tree
31. Key genes for AML MLL ALK G1~G6: different subpopulations from AML cancer MLL: myeloid/lymphoid or mixed-lineage leukemia, recurrent translocations in acute leukemias that may be characterized as acute myeloid leukemia (AML; MIM 601626), acute lymphoblastic leukemia (ALL), or mixed lineage (biphenotypic) leukemia (MLL).
32. LILRA1 G1~G6: different subpopulations from AML cancer LILRA1: leukocyte immunoglobulin-like receptor Inferring key genes in AML (a typical heterozygous cancer)
33. CTNNA1 G1~G6: different subpopulations from AML cancer CTNNA1:Leukocyte transendothelial migration; Pathways in cancer Inferring key genes in AML (a typical heterozygous cancer)
34. CTSS G1~G6: different subpopulations from AML cancer CTSS: cathepsin Inferring key genes in AML (a typical heterozygous cancer)
35. PPP2R1A G1~G6: different subpopulations from AML cancer PPP2R1A: TGF-beta signaling pathway Inferring key genes in AML (a typical heterozygous cancer)
36. DIAPH1 G1~G6: different subpopulations from AML cancer DIAPH1: Focal adhesion; Regulation of actin cytoskeleton Inferring key genes in AML (a typical heterozygous cancer)
37. LILRA1 G1~G6: different subpopulations from AML cancer LILRA1: leukocyte immunoglobulin-like receptor Inferring key genes in AML (a typical heterozygous cancer)
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39. 3. Tree of cells Draw Single-cell information acquisition technologies Map Single-cell metrics measurement technologies
40. Integrating DNA variation, molecular traits, and phenotypes to construct causal gene networks Gene works in a network!
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42. Finally: Where are the papers? On what paper you draw and map and show? It is harder and harder to find a platform efficient enough Sample house High-throughput biology Capable computing system with high I/O performance Interlinked database and standardized formats Bioinformatics workflows to perform in silico analysis on data
43. Making data PUBLIC! Does not mean making data downloadable in theory Does mean the public could make use of data New types of databases with operations to the data are required New academic credit system to motivate high-quality easy-to-access datasets. http://www.gigasciencejournal.com http://climb.genomics.cn
44. Acknowledgements Great International Efforts The Genome 10K Consortium The 1000 Genomes Project Consortium The 1000 Plant Genomes Project Consortium The 5000 insects Project Consortium (pending) BGI Initiatives and collaboration framework The 1000 Plant and Animal Genomes Project The 10K Microbial Genomes Project http://ldl.genomics.org.cn
45. Acknowledgements Prof. Rasmus Nielson’s lab in UC Berkeley and in University of Copenhagen Prof. Richard Durbin’s lab in Wellcome Trust Sanger Insititute Prof. Tak-Wah Lam and Siu-Ming Yiu’s lab in Department of Computer Sciences, Hong Kong University Dr. Heng Li in Broad Insititute …