This document summarizes a discussion by Dr. Larry Smarr on his research into the dynamics of the interaction between the human gut microbiome and immune system. The discussion details Smarr's personal 'omics profiling over several years, which revealed that he had an autoimmune disease, Crohn's disease. His profiling included analysis of blood and stool samples over time, whole genome sequencing, metabolomics, metagenomics of his gut microbiome, and medical imaging. This integrated analysis helped diagnose his condition and better understand the complex interplay between his genetics, immune system, and microbiome.
A Systems Approachto Personalized MedicineLarry Smarr
A Systems Approach to Personalized Medicine
This talk discusses how one man used various omics technologies like genomics, metagenomics, metabolomics, and imaging to gain insights into his own health. Over a decade, he tracked over a billion data points about himself including his microbiome, genome, blood variables, and medical images. This led to the discovery that he had an inflammatory bowel disease. He then used multi-omics analyses and computing resources to study his condition and microbiome in detail over time. This is an example of a systems approach to personalized medicine.
Integrating Healthcare Informatics, Imaging, and Systems Biology-A Personal E...Larry Smarr
12.09.27
Plenary Lecture
2nd IEEE Conference on Healthcare Informatics, Imaging, & Systems Biology
Title: Integrating Healthcare Informatics, Imaging, and Systems Biology-A Personal Example
Calit2@UCSD
Leveraging Biomedical Big Data:Quantified Self & BeyondLarry Smarr
Larry Smarr discussed how quantifying biomedical data through devices like FitBit and analyzing one's genome, microbiome, blood tests, and medical images over time can provide insights into health and disease. Smarr quantified these data for himself and discovered the source of his chronic inflammation was likely inflammatory bowel disease (Crohn's disease) in his colon, which he was able to detect by analyzing his microbial species, immune biomarkers, and an MRI image. Analyzing these multidimensional data streams longitudinally revealed interactions between one's genetics, microbes, immune system, and symptoms that can enable more predictive, preventative, and personalized approaches to medicine.
This document discusses the role of somatic mutagenesis in the development of autoimmunity, specifically in systemic lupus erythematosus (SLE). It argues that:
1) Antinuclear antibodies (ANA) that arise in SLE predominantly originate from non-autoreactive B cells that undergo somatic hypermutation (SHM) and are transformed into autoreactive cells, rather than arising from autoreactive B cells escaping central tolerance.
2) SHM may create antigenic peptides in the B cell receptor that provide a route for unregulated T cell help to autoreactive B cells.
3) Spontaneous somatic mutagenesis of genes regulating B cell survival and activation may be a stochastic rate-
Adipose derived osteoblasts cells from fat tissuesvijisenbiotech
This study characterized and compared surface proteins of primary osteoblasts isolated from iliac crest bone and osteoblast-like cells differentiated from adipose-derived mesenchymal stem cells. Gene and protein expression analysis using RT-PCR and western blotting showed that both cell types expressed osteoblast markers like osteocalcin, alkaline phosphatase, and collagen type 1, though osteocalcin expression was lower in adipose-derived cells. The study also found expression of stem cell markers and nucleostemin in both osteoblasts and adipose-derived osteoblast-like cells.
Clinical grade ex vivo expanded human natural killer (NK) cellslifextechnologies
This document summarizes a study that evaluated a method for expanding clinical-grade natural killer (NK) cells for adoptive transfer immunotherapy. The study found that:
1) NK cells expanded over 4,000-fold when co-cultured with irradiated lymphoblastoid cells over 21 days.
2) The expanded NK cells had increased expression of activating receptors like TRAIL, FasL, and NKG2D compared to resting NK cells.
3) The expanded NK cells showed significantly higher cytotoxicity against tumor cells treated with bortezomib compared to resting NK cells.
4) The expanded NK cells secreted higher levels of cytokines like IFN-γ when co-c
This document discusses research into using stem cells to recreate and study Type 1 diabetes. It describes two ways to generate pancreatic beta cells from stem cells: direct differentiation of stem cells into beta cells, and direct reprogramming of other cells into beta cells. The goal is to produce beta cells for transplantation as well as to model Type 1 diabetes using patient-specific induced pluripotent stem cells to better understand the disease and identify treatments. Key components mentioned include beta cells, thymic epithelial cells, blood cells, and studying disease onset and progression in a humanized mouse model.
A Systems Approachto Personalized MedicineLarry Smarr
A Systems Approach to Personalized Medicine
This talk discusses how one man used various omics technologies like genomics, metagenomics, metabolomics, and imaging to gain insights into his own health. Over a decade, he tracked over a billion data points about himself including his microbiome, genome, blood variables, and medical images. This led to the discovery that he had an inflammatory bowel disease. He then used multi-omics analyses and computing resources to study his condition and microbiome in detail over time. This is an example of a systems approach to personalized medicine.
Integrating Healthcare Informatics, Imaging, and Systems Biology-A Personal E...Larry Smarr
12.09.27
Plenary Lecture
2nd IEEE Conference on Healthcare Informatics, Imaging, & Systems Biology
Title: Integrating Healthcare Informatics, Imaging, and Systems Biology-A Personal Example
Calit2@UCSD
Leveraging Biomedical Big Data:Quantified Self & BeyondLarry Smarr
Larry Smarr discussed how quantifying biomedical data through devices like FitBit and analyzing one's genome, microbiome, blood tests, and medical images over time can provide insights into health and disease. Smarr quantified these data for himself and discovered the source of his chronic inflammation was likely inflammatory bowel disease (Crohn's disease) in his colon, which he was able to detect by analyzing his microbial species, immune biomarkers, and an MRI image. Analyzing these multidimensional data streams longitudinally revealed interactions between one's genetics, microbes, immune system, and symptoms that can enable more predictive, preventative, and personalized approaches to medicine.
This document discusses the role of somatic mutagenesis in the development of autoimmunity, specifically in systemic lupus erythematosus (SLE). It argues that:
1) Antinuclear antibodies (ANA) that arise in SLE predominantly originate from non-autoreactive B cells that undergo somatic hypermutation (SHM) and are transformed into autoreactive cells, rather than arising from autoreactive B cells escaping central tolerance.
2) SHM may create antigenic peptides in the B cell receptor that provide a route for unregulated T cell help to autoreactive B cells.
3) Spontaneous somatic mutagenesis of genes regulating B cell survival and activation may be a stochastic rate-
Adipose derived osteoblasts cells from fat tissuesvijisenbiotech
This study characterized and compared surface proteins of primary osteoblasts isolated from iliac crest bone and osteoblast-like cells differentiated from adipose-derived mesenchymal stem cells. Gene and protein expression analysis using RT-PCR and western blotting showed that both cell types expressed osteoblast markers like osteocalcin, alkaline phosphatase, and collagen type 1, though osteocalcin expression was lower in adipose-derived cells. The study also found expression of stem cell markers and nucleostemin in both osteoblasts and adipose-derived osteoblast-like cells.
Clinical grade ex vivo expanded human natural killer (NK) cellslifextechnologies
This document summarizes a study that evaluated a method for expanding clinical-grade natural killer (NK) cells for adoptive transfer immunotherapy. The study found that:
1) NK cells expanded over 4,000-fold when co-cultured with irradiated lymphoblastoid cells over 21 days.
2) The expanded NK cells had increased expression of activating receptors like TRAIL, FasL, and NKG2D compared to resting NK cells.
3) The expanded NK cells showed significantly higher cytotoxicity against tumor cells treated with bortezomib compared to resting NK cells.
4) The expanded NK cells secreted higher levels of cytokines like IFN-γ when co-c
This document discusses research into using stem cells to recreate and study Type 1 diabetes. It describes two ways to generate pancreatic beta cells from stem cells: direct differentiation of stem cells into beta cells, and direct reprogramming of other cells into beta cells. The goal is to produce beta cells for transplantation as well as to model Type 1 diabetes using patient-specific induced pluripotent stem cells to better understand the disease and identify treatments. Key components mentioned include beta cells, thymic epithelial cells, blood cells, and studying disease onset and progression in a humanized mouse model.
This document summarizes a study examining the effects of cyclocreatine (CCr), a new anticancer agent, on tumor cell proliferation, viability, and cell cycle progression. The study found that CCr completely inhibited proliferation of cervical carcinoma cells within 5 hours by inhibiting progression out of all phases of the cell cycle. Increased cytotoxicity was observed after several days of exposure, most specific to cells in S phase. The authors propose that CCr's inhibition of cell cycle progression reflects its effect on tumor cell energy availability through the creatine kinase system, and that impaired energy homeostasis over several days leads to tumor cell death.
The document discusses apoptosis, or programmed cell death. It defines apoptosis as a tightly regulated suicidal program in cells that activates enzymes to degrade the cell's own DNA and proteins. Apoptosis is important for normal development and tissue homeostasis by removing unwanted cells. The mechanisms of apoptosis involve both intrinsic pathways related to mitochondrial damage and extrinsic pathways activated by death receptors. Key regulators and effectors of apoptosis like caspases, Bcl-2 family proteins, and cytochrome c are discussed. Disorders related to too much or too little apoptosis can lead to conditions like neurodegeneration or cancer.
The document provides an overview of the process for manufacturing biopharmaceuticals. It begins with copying the gene for the desired protein, inserting it into cells, and selecting the highest producing cell clone. This clone is used to create a master cell bank and working cell bank. Each manufacturing batch starts with cells from the working cell bank. The process involves fermenting or culturing the cells to produce the protein, then recovering and purifying the protein through steps like centrifugation, filtration, chromatography. The purified protein is formulated into the drug substance, which is then formulated and filled into final drug product containers ready for distribution.
The document summarizes the key scientific discoveries that established DNA as the genetic material:
1) Experiments in the early 1900s by Morgan, Griffith, and Avery et al. provided early evidence that DNA carries hereditary information and can alter phenotypes.
2) Further experiments in the 1940s-1950s by Chargaff, Hershey and Chase, and Watson and Crick revealed that DNA has a consistent base ratio, is the transforming principle, and forms a double helix structure.
3) The 1958 experiment by Meselson and Stahl, considered "the most beautiful experiment in biology," verified that DNA replication is semi-conservative through labeling DNA with different nitrogen isotopes.
WEBINAR Characterisation of human pluripotent stem cells (ESCs and IPSC) and ...Quality Assistance s.a.
Valérie DEFFONTAINE, R&D Scientist, Quality Assistance
Webinar held on 8th June 2017.
The discovery of human pluripotent stem cells 10 years ago turned the spotlight on the potential of pluripotent stem cells for personalised cell therapy. The scientific interest then quickly shifted towards the use of these cells for safety pharmacology, drug discovery and disease modelling. For all these purposes, in the mid to long term, properly characterised cell banks will be necessary.
The characterisation of embryonic (ESC) and induced pluripotent stem cells (IPSC) used for manufacturing requires the development and validation of analytical methods (e.g. flow cytometry, microscopy, QPCR and bioassays). Cell characterisation includes the testing of cell product identity, determination of impurities, and assessment of biological activity and viability. Among the techniques available, flow cytometry is widely used to assess the expression of cell markers. Our laboratory has developed flow cytometry panels dedicated to the characterisation of extracellular and intracellular markers of ESC and IPSC, and to the detection of cell-related impurities. We proposed a method for the validation of flow cytometry panels according to the recommendations of international guidelines on the validation of analytical methods.
IPSC differentiated into cardiomyocytes and MSC-like cells were also used to test the performance of our flow cytometry panels to accurately monitor the manufacturing process of cell products.
In addition to the technical tips, this webinar aims at presenting a critical view on the use of flow cytometry platform for cell characterisation.
For more information, visit http://www.quality-assistance.com/analytical-services/CBMPs
Monoclonal antibodies are identical antibodies produced by identical immune cells that are clones of a single parent cell. They are produced by fusing antibody-producing cells with tumor cells to create a hybridoma cell line that continuously produces the same antibody. Monoclonal antibodies have important medical uses such as diagnosing pregnancy or HIV infection through detection of specific antigens, and treating cancer by targeting tumor-associated antigens on cancer cells. However, monoclonal antibodies produced in mice can trigger an immune response in humans, so genetically engineered antibodies are being developed to avoid this.
- Astrocytes secrete various neurotrophic and apoptotic factors that can affect neurons. This study investigated the effects of astrocyte-conditioned media (ACM) on SH-SY5Y human neuroblastoma cells.
- Initial experiments found that ACM containing fetal bovine serum (FBS) increased cell viability compared to serum-free ACM, suggesting FBS contains neuroprotective factors. However, astrocytes may also secrete neuroprotective factors.
- Further experiments fractionated serum-free ACM into sizes below and above 50kDa and 100kDa. Results indicate the presence of two astrocyte-secreted neurotrophic factors below 50kDa and between
Hybridoma technology allows scientists to produce monoclonal antibodies at scale. It involves fusing antibody-producing plasma cells from immunized mice with myeloma cancer cells, creating a hybridoma cell line that is immortal and continuously produces identical monoclonal antibodies. This overcomes the short lifespan of plasma cells. The hybridoma cells are selected and isolated using HAT media, which only the hybridomas can survive in due to possessing a key enzyme. This technique has generated monoclonal antibodies useful for diagnosing and treating various diseases.
Genetic engineering involves direct manipulation of an organism's DNA. It has applications in medicine, agriculture, pollution control and more. Key techniques include isolating genes, manipulating DNA through cloning and PCR, and reintroducing DNA into organisms. This allows transferring genes between species to produce transgenic plants and animals with desired traits. While it promises medical benefits, ethical issues around patenting life and unintended consequences require consideration.
Recombinant DNA technology involves combining DNA segments to form new DNA molecules. In 1973, scientists Boyer and Cohen developed the technique by inserting DNA into a vector molecule that can then be introduced into host cells to replicate. This allows for large-scale production of human proteins in bacteria, such as insulin, growth hormones, and blood clotting factors. Safety measures like physical and biological containment are used to prevent accidental release of recombinant bacteria. While offering medical benefits, recombinant DNA technology does pose risks that must be carefully managed.
This document discusses genetic engineering and biotechnology. It begins by defining genetic engineering as the manipulation of genes, usually outside an organism's natural reproductive process. It then discusses chromosomes and mutations, including examples of chromosome numbers in different species. Techniques for genetic engineering are explained, such as restriction enzymes and bacterial transformation. Applications include creating transgenic bacteria, plants, and animals. Ethical issues related to genetic engineering are also reviewed.
Polymerase chain reaction (PCR) is used to copy and amplify minute quantities of DNA without bacteria. In gel electrophoresis, DNA fragments move in an electric field and are separated by size, and this technique is used in DNA profiling to determine paternity or for forensic investigations. Genetic engineering techniques like PCR, gel electrophoresis, and DNA profiling have various applications and social implications.
This document discusses various applications of stem cell research and therapy. It summarizes that stem cells can differentiate into specialized cell types, cell therapy uses healthy live or freeze-dried cells to treat diseases, and stem cells have been used in animal models to treat conditions like arthritis and Parkinson's disease. Stem cell research also aims to produce tissues for transplantation through cloning cells and growing them on scaffolds.
Monoclonal antibodies are antibodies that are directed against a specific antigen. They are produced by a single clone of cells and can be obtained from immortalized B-lymphocytes or recombinant cell lines. The production of monoclonal antibodies involves immunizing an animal, fusing its spleen cells with myeloma cells to form hybridomas, selecting hybridomas that secrete the desired antibody, and propagating these cells to produce large amounts of monoclonal antibodies. Monoclonal antibodies have various applications in cancer therapy, organ transplantation, disease diagnosis, and protein purification. Recent developments include FDA approvals of monoclonal antibodies for treating cancer and blood disorders.
Recombinant DNA technology involves combining DNA sequences from different species that would not normally occur together to create artificial DNA and alter the genetics of living cells. There are three main methods to create recombinant DNA - transformation, phage introduction, and non-bacterial transformation. Transformation involves selecting a DNA fragment, inserting it into a vector, and introducing the vector into a host cell like E. coli. Recombinant DNA technology has many applications, including producing proteins and hormones, disease diagnosis and treatment, genetically engineering plants, and forensic analysis.
Cord blood is a naturally discarded tissue that contains a high proportion of circulating hematopoietic stem cells. It allows HLA mismatch transplantation, providing cure to hematological malignancies with an attenuated risk of severe graft-versus-host disease through a graft-versus-leukemia effect. Cord blood transplantation is unique in its immunogenetics profile, preserving the immune cells carried in the cord blood graft, including T-regulatory cells and natural killer cells. Early reconstitution of lymphocytes from cord blood grafts predicts better outcomes. Advances in cord blood transplantation aim to take advantage of its immunological properties through donor selection accounting for HLA matching, maternal antigens, and cell dose to maximize graft-versus-leuke
genetic engineering: Genetic engineering, also called genetic modification, is the direct manipulation of an organism's genome using biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. Many organism are manipulated with the help genetic engineering useful for mankind.
Recombinant DNA technology involves combining DNA molecules from different sources and introducing them into host organisms. Some key points:
- Recombinant DNA is produced by joining DNA fragments from different sources using restriction enzymes and DNA ligase.
- Plasmids and bacterial cells are commonly used as vectors to replicate and express recombinant DNA. Foreign DNA is inserted into plasmids which are then introduced into bacterial cells.
- Restriction enzymes from bacteria are used to cut DNA at specific sequences. This allows insertion of foreign DNA. DNA ligase joins the DNA fragments back together.
- Applications include production of therapeutic proteins, genetic testing, gene therapy, and genetically modified crops. Recombinant DNA technology
This document provides an overview of EarthStream, a global recruiting firm focused on the energy, resources, and environment sectors. It describes EarthStream's capabilities in providing talent across technical disciplines to industries facing challenges from increasing global demand for energy and the need for environmental protection. The summary highlights EarthStream's global network and ability to source candidates with skills in areas like engineering, project management, and environmental sciences to help clients meet workforce needs.
This document summarizes a study examining the effects of cyclocreatine (CCr), a new anticancer agent, on tumor cell proliferation, viability, and cell cycle progression. The study found that CCr completely inhibited proliferation of cervical carcinoma cells within 5 hours by inhibiting progression out of all phases of the cell cycle. Increased cytotoxicity was observed after several days of exposure, most specific to cells in S phase. The authors propose that CCr's inhibition of cell cycle progression reflects its effect on tumor cell energy availability through the creatine kinase system, and that impaired energy homeostasis over several days leads to tumor cell death.
The document discusses apoptosis, or programmed cell death. It defines apoptosis as a tightly regulated suicidal program in cells that activates enzymes to degrade the cell's own DNA and proteins. Apoptosis is important for normal development and tissue homeostasis by removing unwanted cells. The mechanisms of apoptosis involve both intrinsic pathways related to mitochondrial damage and extrinsic pathways activated by death receptors. Key regulators and effectors of apoptosis like caspases, Bcl-2 family proteins, and cytochrome c are discussed. Disorders related to too much or too little apoptosis can lead to conditions like neurodegeneration or cancer.
The document provides an overview of the process for manufacturing biopharmaceuticals. It begins with copying the gene for the desired protein, inserting it into cells, and selecting the highest producing cell clone. This clone is used to create a master cell bank and working cell bank. Each manufacturing batch starts with cells from the working cell bank. The process involves fermenting or culturing the cells to produce the protein, then recovering and purifying the protein through steps like centrifugation, filtration, chromatography. The purified protein is formulated into the drug substance, which is then formulated and filled into final drug product containers ready for distribution.
The document summarizes the key scientific discoveries that established DNA as the genetic material:
1) Experiments in the early 1900s by Morgan, Griffith, and Avery et al. provided early evidence that DNA carries hereditary information and can alter phenotypes.
2) Further experiments in the 1940s-1950s by Chargaff, Hershey and Chase, and Watson and Crick revealed that DNA has a consistent base ratio, is the transforming principle, and forms a double helix structure.
3) The 1958 experiment by Meselson and Stahl, considered "the most beautiful experiment in biology," verified that DNA replication is semi-conservative through labeling DNA with different nitrogen isotopes.
WEBINAR Characterisation of human pluripotent stem cells (ESCs and IPSC) and ...Quality Assistance s.a.
Valérie DEFFONTAINE, R&D Scientist, Quality Assistance
Webinar held on 8th June 2017.
The discovery of human pluripotent stem cells 10 years ago turned the spotlight on the potential of pluripotent stem cells for personalised cell therapy. The scientific interest then quickly shifted towards the use of these cells for safety pharmacology, drug discovery and disease modelling. For all these purposes, in the mid to long term, properly characterised cell banks will be necessary.
The characterisation of embryonic (ESC) and induced pluripotent stem cells (IPSC) used for manufacturing requires the development and validation of analytical methods (e.g. flow cytometry, microscopy, QPCR and bioassays). Cell characterisation includes the testing of cell product identity, determination of impurities, and assessment of biological activity and viability. Among the techniques available, flow cytometry is widely used to assess the expression of cell markers. Our laboratory has developed flow cytometry panels dedicated to the characterisation of extracellular and intracellular markers of ESC and IPSC, and to the detection of cell-related impurities. We proposed a method for the validation of flow cytometry panels according to the recommendations of international guidelines on the validation of analytical methods.
IPSC differentiated into cardiomyocytes and MSC-like cells were also used to test the performance of our flow cytometry panels to accurately monitor the manufacturing process of cell products.
In addition to the technical tips, this webinar aims at presenting a critical view on the use of flow cytometry platform for cell characterisation.
For more information, visit http://www.quality-assistance.com/analytical-services/CBMPs
Monoclonal antibodies are identical antibodies produced by identical immune cells that are clones of a single parent cell. They are produced by fusing antibody-producing cells with tumor cells to create a hybridoma cell line that continuously produces the same antibody. Monoclonal antibodies have important medical uses such as diagnosing pregnancy or HIV infection through detection of specific antigens, and treating cancer by targeting tumor-associated antigens on cancer cells. However, monoclonal antibodies produced in mice can trigger an immune response in humans, so genetically engineered antibodies are being developed to avoid this.
- Astrocytes secrete various neurotrophic and apoptotic factors that can affect neurons. This study investigated the effects of astrocyte-conditioned media (ACM) on SH-SY5Y human neuroblastoma cells.
- Initial experiments found that ACM containing fetal bovine serum (FBS) increased cell viability compared to serum-free ACM, suggesting FBS contains neuroprotective factors. However, astrocytes may also secrete neuroprotective factors.
- Further experiments fractionated serum-free ACM into sizes below and above 50kDa and 100kDa. Results indicate the presence of two astrocyte-secreted neurotrophic factors below 50kDa and between
Hybridoma technology allows scientists to produce monoclonal antibodies at scale. It involves fusing antibody-producing plasma cells from immunized mice with myeloma cancer cells, creating a hybridoma cell line that is immortal and continuously produces identical monoclonal antibodies. This overcomes the short lifespan of plasma cells. The hybridoma cells are selected and isolated using HAT media, which only the hybridomas can survive in due to possessing a key enzyme. This technique has generated monoclonal antibodies useful for diagnosing and treating various diseases.
Genetic engineering involves direct manipulation of an organism's DNA. It has applications in medicine, agriculture, pollution control and more. Key techniques include isolating genes, manipulating DNA through cloning and PCR, and reintroducing DNA into organisms. This allows transferring genes between species to produce transgenic plants and animals with desired traits. While it promises medical benefits, ethical issues around patenting life and unintended consequences require consideration.
Recombinant DNA technology involves combining DNA segments to form new DNA molecules. In 1973, scientists Boyer and Cohen developed the technique by inserting DNA into a vector molecule that can then be introduced into host cells to replicate. This allows for large-scale production of human proteins in bacteria, such as insulin, growth hormones, and blood clotting factors. Safety measures like physical and biological containment are used to prevent accidental release of recombinant bacteria. While offering medical benefits, recombinant DNA technology does pose risks that must be carefully managed.
This document discusses genetic engineering and biotechnology. It begins by defining genetic engineering as the manipulation of genes, usually outside an organism's natural reproductive process. It then discusses chromosomes and mutations, including examples of chromosome numbers in different species. Techniques for genetic engineering are explained, such as restriction enzymes and bacterial transformation. Applications include creating transgenic bacteria, plants, and animals. Ethical issues related to genetic engineering are also reviewed.
Polymerase chain reaction (PCR) is used to copy and amplify minute quantities of DNA without bacteria. In gel electrophoresis, DNA fragments move in an electric field and are separated by size, and this technique is used in DNA profiling to determine paternity or for forensic investigations. Genetic engineering techniques like PCR, gel electrophoresis, and DNA profiling have various applications and social implications.
This document discusses various applications of stem cell research and therapy. It summarizes that stem cells can differentiate into specialized cell types, cell therapy uses healthy live or freeze-dried cells to treat diseases, and stem cells have been used in animal models to treat conditions like arthritis and Parkinson's disease. Stem cell research also aims to produce tissues for transplantation through cloning cells and growing them on scaffolds.
Monoclonal antibodies are antibodies that are directed against a specific antigen. They are produced by a single clone of cells and can be obtained from immortalized B-lymphocytes or recombinant cell lines. The production of monoclonal antibodies involves immunizing an animal, fusing its spleen cells with myeloma cells to form hybridomas, selecting hybridomas that secrete the desired antibody, and propagating these cells to produce large amounts of monoclonal antibodies. Monoclonal antibodies have various applications in cancer therapy, organ transplantation, disease diagnosis, and protein purification. Recent developments include FDA approvals of monoclonal antibodies for treating cancer and blood disorders.
Recombinant DNA technology involves combining DNA sequences from different species that would not normally occur together to create artificial DNA and alter the genetics of living cells. There are three main methods to create recombinant DNA - transformation, phage introduction, and non-bacterial transformation. Transformation involves selecting a DNA fragment, inserting it into a vector, and introducing the vector into a host cell like E. coli. Recombinant DNA technology has many applications, including producing proteins and hormones, disease diagnosis and treatment, genetically engineering plants, and forensic analysis.
Cord blood is a naturally discarded tissue that contains a high proportion of circulating hematopoietic stem cells. It allows HLA mismatch transplantation, providing cure to hematological malignancies with an attenuated risk of severe graft-versus-host disease through a graft-versus-leukemia effect. Cord blood transplantation is unique in its immunogenetics profile, preserving the immune cells carried in the cord blood graft, including T-regulatory cells and natural killer cells. Early reconstitution of lymphocytes from cord blood grafts predicts better outcomes. Advances in cord blood transplantation aim to take advantage of its immunological properties through donor selection accounting for HLA matching, maternal antigens, and cell dose to maximize graft-versus-leuke
genetic engineering: Genetic engineering, also called genetic modification, is the direct manipulation of an organism's genome using biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. Many organism are manipulated with the help genetic engineering useful for mankind.
Recombinant DNA technology involves combining DNA molecules from different sources and introducing them into host organisms. Some key points:
- Recombinant DNA is produced by joining DNA fragments from different sources using restriction enzymes and DNA ligase.
- Plasmids and bacterial cells are commonly used as vectors to replicate and express recombinant DNA. Foreign DNA is inserted into plasmids which are then introduced into bacterial cells.
- Restriction enzymes from bacteria are used to cut DNA at specific sequences. This allows insertion of foreign DNA. DNA ligase joins the DNA fragments back together.
- Applications include production of therapeutic proteins, genetic testing, gene therapy, and genetically modified crops. Recombinant DNA technology
This document provides an overview of EarthStream, a global recruiting firm focused on the energy, resources, and environment sectors. It describes EarthStream's capabilities in providing talent across technical disciplines to industries facing challenges from increasing global demand for energy and the need for environmental protection. The summary highlights EarthStream's global network and ability to source candidates with skills in areas like engineering, project management, and environmental sciences to help clients meet workforce needs.
The document discusses Portuguese "Hidden Champions", which are companies that are worldwide leaders in their industry segments but are not widely known by the general public. It provides examples of several Portuguese hidden champion companies, including Nelo (kayaks), Vision Box (biometric and border control systems), Yellow Wood Fingerboard (fingerboard products), Petratex (swimwear innovation), WeDo Technologies (revenue assurance software), COBUS (airport buses), Corticeira Amorim (cork derivatives), Fepsa (felt for hats), Sonae Industria (wood panels), and Portucel Soporcel (paper production). It also outlines strategies used by hidden champions, such as differentiation, innovation
El documento describe la organización de una reunión en @sparkbouy y proporciona la dirección web y nombre de Chris Sparshott, creador de @sparkbouy, repetidas veces.
Lotus Domino provides robust email security capabilities including strong password authentication and encryption. As email threats like spam, phishing and malware have increased, comprising up to 90% of email traffic, integrated email security solutions are needed. IBM Lotus Protector extends Domino's security with antispam, antivirus, encryption, data loss prevention and other tools to protect against modern threats while maintaining Domino's access controls and policies. It offers deployment options including virtual appliances, dedicated hardware, and integration with existing Domino infrastructure.
This document discusses signs that an aging parent may need more assistance and options to consider, including having the parent move in, hiring home health care, nursing homes, adult day programs, and assisted living. It provides details on services typically included in assisted living facilities and things to look for such as activities, meals, and specialized care for dementia patients. It encourages touring facilities and understanding included services and costs.
LiveDeal is a marketing company that provides customized online marketing solutions for small businesses, including search engine marketing, website creation and optimization, and directory listings. They work with clients to understand their target customers and create tailored marketing packages within the client's budget. LiveDeal guarantees a minimum number of annual visitors to clients' websites through their performance-based agreements.
The document discusses different approaches to writing, including writing as a product versus as a process. It provides tips for generating ideas such as listing, mapping, and outlining. It also discusses the writing process, including doing an initial "down draft," then revising and organizing in an "up draft," and finally carefully editing in a "dental draft." Reading papers out loud is recommended as part of the revision process.
FISMArts - Improving Retention of FISMA Guidance Details with Mnemosynedanphilpott
FISMA guidance is a large body of complex and technical knowledge. Not recalling the details can have serious impacts. The FISMArts project aims to make memorization of those details easier using spaced repetition based memorization software called Mnemosyne. This presentation introduces how this is done and how others can take advantage of the software.
This document provides an overview of IBM's LotusLive cloud computing and software-as-a-service (SaaS) offerings. It discusses how LotusLive enables smarter collaboration across organizations through secure, flexible cloud services. Specific LotusLive products are introduced, including LotusLive Meetings, Events, Connections, Notes, and iNotes for online meetings, events management, collaboration, and email.
This document discusses research on linkages between academia and industry. It presents survey results from Mexico on the interactions between firms, universities, and public research centers (PRCs) on knowledge flows and benefits. The surveys found that the main reasons for interaction were human resources and training. Knowledge flows from universities included human resources, while PRCs provided training. Benefits included using laboratories and developing techniques. Regression models showed collaboration was associated with product/process innovation and benefits like publications. In conclusion, firms had limited absorptive capacity and saw interactions as developing capabilities and complementing them, while researchers saw knowledge creation as more important.
Belize is located in Central America and bordered by Mexico and Guatemala. It has a diverse landscape that includes mountains, swamps, tropical jungles, and the world's second largest barrier reef off its coast. Most Belizeans are of mixed Maya, Spanish, African, and British ancestry. The main highways are paved but the rest are dirt roads. There are numerous ancient Mayan ruins throughout Belize. Rural villages have thatched huts and limited infrastructure like running water.
Installation Of Lotus Mashups1.1 On Linux v5 in vmwareChris Sparshott
This document provides step-by-step instructions for installing IBM Lotus Mashups on Linux. It lists system requirements and notes to watch out for errors with SELinux. The steps include disabling SELinux, adding domain names to the hosts file, installing Java and Lotus Mashup Centre, setting the admin password, launching first steps and Lotus Mashups, creating a sample mashup, and installing Infosphere Mashup Hub. Contact information is also provided at the end.
Amazon EC2 is a web service that allows users to launch virtual machine instances that can be used to build and host applications. The document discusses how EC2 provides scalable computing capacity in the cloud and works with Amazon S3 for storage. It provides step-by-step instructions for launching an EC2 instance, installing MySQL, PHP and WordPress to build a simple blog, and using S3 for backups.
Personal Data Tracking and the Digital Transformation of HealthcareLarry Smarr
This document summarizes a talk given by Dr. Larry Smarr on personal data tracking and the digital transformation of healthcare. Some key points:
- Smarr has been tracking over 100 of his own health variables like blood tests, microbiome, sleep, and more for over a decade to study trends.
- Analyzing this personal data revealed he had undiagnosed Crohn's disease, which he was able to confirm and treat using medical imaging.
- Tracking his own immunological biomarkers over time showed major immune system dysfunction that provided insight into his condition.
- Analyzing his gut microbiome identified changes in bacterial phyla that correlated with his Crohn's disease and response to treatment.
- Sm
Tracking Immune Biomarkers and the Human Gut Microbiome: Inflammation, Croh...Larry Smarr
Larry Smarr presented on tracking immune biomarkers and the human gut microbiome in relation to inflammation, Crohn's disease, and colon cancer. He turned his own body into a "genomic observatory" by tracking over 100 of his own blood and stool biomarkers and sequencing his gut microbiome multiple times. His research found high levels of inflammation and an abundance of Fusobacteria in his microbiome when inflammation was highest. Following antibiotic and steroid therapy, inflammation and Fusobacteria were greatly reduced. This integrated personal omics approach provides insights into the links between inflammation, gut microbes, and colon cancer risk.
Using Genetic Sequencing to Unravel the Dynamics of Your Superorganism BodyLarry Smarr
The document summarizes a talk given by Dr. Larry Smarr on his research tracking extensive health data on himself over many years. Some key points:
1) Smarr collected over a billion data points defining his body, including DNA sequencing, medical images, and daily biomarkers, revealing episodic inflammation related to his Crohn's disease.
2) Analysis of his gut microbiome via metagenomic sequencing showed many typically abundant bacterial species were severely depleted compared to healthy individuals.
3) Tracking changes over time demonstrated the coupled dynamics of his immune system and gut microbiome in response to therapies, similar to ecological models of invasive species dominating after natives are disturbed.
12.04.25
Pioneer Session: "N=1: Pioneers of Self-Tracking“
Panel at the Genomes, Environment, and Traits Conference
Harvard Medical School
Title:My N=1 Experience
Cambridge, MA
Quantifying My Body:The Role of the Human and Microbiome DNALarry Smarr
12.04.16
Invited Talk
Systems Biology and the Microbiome
Institute for Systems Biology
Title: Quantifying My Body:The Role of the Human and Microbiome DNA
Seattle, WA
Discovering Yourself with Computational BioinformaticsLarry Smarr
This document summarizes a presentation given by Dr. Larry Smarr on his self-experimentation with quantifying biomarkers and 'omics data to gain insights into his health. Smarr has tracked over 100 blood biomarkers, sequenced his microbiome, and analyzed over 1 million SNPs from his genome. Computational analysis of this data helped diagnose Smarr with Crohn's disease and revealed shifts in his microbiome from healthy to diseased states. Smarr advocates integrating multi-omics data to achieve predictive, preventative and participatory medicine.
Towards Digitally Enabled Genomic Medicine: the Patient of The FutureLarry Smarr
12.02.22
Invited Speaker
Hacking Life
TTI/Vanguard Conference
Title: Towards Digitally Enabled Genomic Medicine: the Patient of The Future
San Jose, CA
Using Supercomputers to Discover the 100 Trillion Bacteria Living Within Each...Larry Smarr
This document summarizes a talk given by Dr. Larry Smarr on using supercomputers to analyze the human microbiome. It discusses how next-generation sequencing and analysis of microbial DNA reveals major differences between healthy and diseased gut microbiomes. Computational analysis of Smarr's own microbiome time series, in addition to data from hundreds of individuals, provides insights into inflammatory bowel disease. Large supercomputers and visualization resources were crucial for processing and comparing petabytes of sequencing data to advance understanding of microbiome dynamics and their links to human health and disease.
The document summarizes a seminar given by Dr. Larry Smarr on supercomputing the human microbiome. Some key points:
- The human microbiome contains 100 trillion microorganisms and their DNA contains 300 times as many genes as human DNA.
- Dr. Smarr has been collecting extensive data from his own body over 7 years to study his personal microbiome and immune system interactions using high performance computing.
- Analyzing microbiome data requires massive computing resources, such as millions of core hours on supercomputers. This reveals details of microbial ecology and genetics in health and disease.
- Computational analysis of microbiome sequencing data from many subjects shows major shifts in microbial populations between healthy and
The document discusses supercomputing analysis of the human microbiome. It describes how the human body hosts 100 trillion microorganisms containing 300 times as many genes as human DNA. Dr. Smarr has been collecting extensive personal health data over 7 years, including microbiome samples, to study the coupled immune-microbial system. Analyzing this data requires elaborate software running on high performance computers. The analysis can compare individuals with diseases to healthy populations and track disease progression over time.
Tracking Large Variations in My Immune Biomarkers and My Gut Microbiome: Infl...Larry Smarr
This document provides a 3-sentence summary of a presentation by Dr. Larry Smarr on tracking changes in his immune biomarkers and gut microbiome in relation to inflammation, Crohn's disease, and colon cancer:
Over the past decade, Dr. Smarr has quantified over a billion data points on his body through measures like blood tests, MRI/CT scans, and analysis of his gut microbiome, discovering through this data that he has episodic chronic inflammation and Crohn's disease affecting his colon. By comparing his biomarkers and symptoms over time and visualizing his microbiome ecology, Dr. Smarr has gained insights into the dynamics and invasiveness of species in his gut microbiome as it relates to his autoimmune
Inflammation, Gut Microbiome, Bacteriophages, and the Initiation of Colorecta...Larry Smarr
This document summarizes a lecture on inflammation, the gut microbiome, bacteriophages, and the initiation of colorectal cancer. The lecturer discusses his personal experience with Crohn's disease and extensive self-monitoring. Analysis of his microbiome data over time revealed shifts correlated with inflammation levels. Certain bacteria like Fusobacterium nucleatum and E. coli were found at highest levels during peak inflammation. The lecturer's genetic analysis revealed SNPs linked to autoimmune disease that may have predisposed him to Crohn's. The lecture explores the role of the microbiome in mediating inflammation and cancer initiation in the gut.
Capturing the Interactive Dynamics of the Human Host/Microbiome SystemLarry Smarr
1) Dr. Larry Smarr reported on results from a decade of self-quantification, including longitudinal measurements of his gut microbiome and over 100 biomarkers, to better understand the interactive dynamics of the human-microbiome system in health and disease.
2) Analysis found that Smarr's gut microbiome was unstable with high levels of E. coli, unlike healthy individuals, and computational analysis linked this dysbiosis to chronic inflammation identified in his biomarkers.
3) Smarr underwent robotic colon resection surgery in 2016, and analysis found his gut microbiome changed more dramatically after surgery than from colonoscopy or typical differences between individuals, eventually achieving a healthy post-surgical state.
Using Supercomputers and Gene Sequencers to Discover Your Inner MicrobiomeLarry Smarr
This keynote talk discusses research using supercomputers and gene sequencing to study the human microbiome. The human microbiome contains 100 trillion microorganisms and their genes outnumber human genes 300 to 1. The speaker has been collecting data from his own body over 7 years to study his microbiome and immune system interactions. Collaborating researchers have sequenced his gut microbiome over time as well as samples from autoimmune disease patients. Supercomputers are needed to analyze the massive amount of sequencing data and reveal details of microbial ecology and genetics in health and disease. Studying the human microbiome will revolutionize medicine in the next decade.
Dr. Larry Smarr presented an invited talk at the Personalized Life Extension Conference in San Francisco on March 31, 2012. In 3 sentences: Dr. Smarr discussed how he has transformed from a patient who only reported subjective feelings of health or illness to one who closely monitors over 100 quantitative biomarkers in his blood and stool on a regular basis to gain detailed insights into his physical state, which led to a diagnosis of Crohn's disease. He emphasized the importance of measuring various internal variables, the human microbiome, and genomic data to better understand one's health and find opportunities for improvement.
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human GenomicsLarry Smarr
This presentation on February 27, 2014 to NGS and the Future of Medicine at Illumina Headquarters in La Jolla, CA, was made by Calit2 Director Larry Smarr.
Similar to Janssen immune system_&_microbiome_022213 (1) (20)
Big Data and Superorganism Genomics: Microbial Metagenomics Meets Human Genomics
Janssen immune system_&_microbiome_022213 (1)
1. “Dynamics of the Interaction Between
the Human Gut Microbiome and Immune System”
Discussion
Janssen La Jolla Research and Development
La Jolla, CA
February 22, 2013
Dr. Larry Smarr
Director, California Institute for Telecommunications and Information
Technology
Harry E. Gruber Professor,
Dept. of Computer Science and Engineering
1
Jacobs School of Engineering, UCSD
3. From One to a Billion Data Points Defining Me:
The Exponential Rise in Body Data in Just One Decade!
Billion:Microbial Genome
My Full DNA,
MRI/CT Images
Improving Body
SNPs
Million: My DNA SNPs,
Zeo, FitBit
Discovering Disease
Blood
Variables
One: Hundred: My Blood Variables
Weight Weight
My
4. Visualizing Time Series of
150 LS Blood and Stool Variables, Each Over 5 Years
Calit2 64 megapixel VROOM
5. Complex Reactive Protein
From Blood Sample
27x Upper Limit
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal Range
<1 mg/L
Antibiotics
Antibiotics
Normal
6. Lactoferrin
From Stool Sample
124x Upper Limit
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal Range Antibiotics
<7.3 µg/mL
Antibiotics
7. High Lactoferrin Biomarker Led Me to Hypothesis
I Had Inflammatory Bowel Disease (IBD)
IBD is an Autoimmune Disease Which Comes in Two Subtypes:
Crohn’s and Ulcerative Colitis
Scand J Gastroenterol.
42, 1440-4 (2007)
My Values May 2011
My Values 2009-10
High Level of Calprotectin
Confirmed Hypothesis
9. Confirming the IBD (Crohn’s) Hypothesis:
Finding the “Smoking Gun” with MRI Imaging
Liver I Obtained the MRI Slices
Transverse Colon
From UCSD Medical Services
and Converted to Interactive 3D
Working With
Small Intestine Calit2 Staff & DeskVOX Software
Descending Colon
MRI Jan 2012
Cross Section
Diseased Sigmoid Colon
Major Kink
Sigmoid Colon
Threading Iliac Arteries
11. Interactively Exploring My Body
With Calit2 Virtual Reality Facilities
TourCAVE
StarCAVE
VROOM
www.youtube.com/watch?v=9c4DtJ_L_Ps
zSpace
Photo & CalVR software Courtesy of Jurgen Schulze, Calit2
12. Connecting Colonoscopy “Inside View”
With MRI “Outside View”
LS Colon Images and Colonoscopy Video
On Calit2 Director’s Colony OptIPortable Wall
13. Why Did I Have an Autoimmune Disease like IBD?
Despite decades of research,
the etiology of Crohn's disease
remains unknown.
Its pathogenesis may involve
a complex interplay between
host genetics,
immune dysfunction,
and microbial or environmental factors.
--The Role of Microbes in Crohn's Disease
So I Set Out to Quantify All Three!
Paul B. Eckburg & David A. Relman
Clin Infect Dis. 44:256-262 (2007)
14. I Wondered if Crohn’s is an Autoimmune Disease,
Did I Have a Personal Genomic Polymorphism?
From www.23andme.com Polymorphism in
Interleukin-23 Receptor Gene
— 80% Higher Risk
ATG16L1
of Pro-inflammatory
Immune Response
IRGM
NOD2 SNPs Associated with CD
Now Comparing
163 Known IBD SNPs
with 23andme SNP Chip
15. Crohn’s May be a Related Set of Diseases
Driven by Different SNPs
NOD2 (1)
rs2066844
Female
CD Onset
At 20-Years Old
Il-23R
rs1004819
Me-Male
CD Onset
At 60-Years Old
16. White Blood Cell Count
From Blood Sample
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal Range
4-10,000 cells/µL
Normal
Antibiotics
17. Neutrophils as % of WBCs
From Blood Sample
Normal Range
31-71%
Normal
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
18. Lymphocytes as % of WBCs
From Blood Sample
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal
Antibiotics
Lymphocytes Include B Cells, T cells, and Natural Killer Cells
19. Eosinophils as % of WBCs
From Blood
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal
Normal Range
1-7%
Antibiotics
20. Monocytes as % of WBCs
From Blood
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal
Normal Range
5-12%
21. Calprotectin
From Stool Sample
50x Upper Limit
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal Range
<50 µg/g
Antibiotics
22. Secretory IgA
From Stool Sample
7x Upper Limit
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Antibiotics
Antibiotics Normal Range
54-204 mg/dL
Normal
23. Lysozyme
From Stool Sample
2x Upper Limit
Antibiotics Antibiotics
Peak Sec IgA, Lysozyme 1/30/12
Peak CRP, Calprotectin 12/28/11
Peak Lactoferrin 5/2/11
Normal
Normal Range
<600 ng/mL
24. Putting Multiple Immunological Biomarker Time Series
Together, Reveals Major Immune Dysfunction
Green : Inside Range
Orange: 1-10x Over
Red: 10-100x Over
Purple: >100x Over
Source: Calit2 Future Health Expedition Team
25. Four Immune Biomarkers Over Time
Compared with Four Signs/Symptoms
Here Immune biomarkers are normalized 0 to 1,
with 1 being the highest value in five years
Source: Photo of Calit2 64-megapixel VROOM
26. Microbes are 90% of Your Cells-So I Set Out
to Determine My Gut Microbes & Their Time Variation
Shipped Stool Sample
December 28, 2011
I Received
a Disk Drive April 3, 2012
With 35 GB FASTQ Files
Weizhong Li, UCSD
NGS Pipeline:
230M Reads
Only 0.2% Human
Required 1/2 cpu-yr at SDSC
Per Person Analyzed!
28. LS Viral Species Comprise >97%
Relative Abundance of Virus + Bacteria + Archaea
LS Virus Species Which Are
>1% of Total Abundance
In an Average Healthy Person,
None of LS Viruses Exceed 0.01%
of the Total Relative Abundance of
Viruses + Bacteria
In Average Healthy Person, Viruses
Are <2% of Total Abundance
30. What is a “Healthy” Gut Microbiome?
Considerable Phyla Variation Found in HMP
Note: Euryarchaeota Are So Rare
That They Arent Graphed!
Source: “Structure, function and diversity of the healthy human
microbiome,” HMP Consortium, Nature, 486, 207-212 (2012)
31. Phyla Gut Microbial Abundance Without Viruses:
LS, Crohn’s, UC, and Healthy Subjects
Source: Weizhong Li, UCSD; Calit2 FuturePatient Expedition
LS Crohn’s Ulcerative Healthy
Colitis
Toward Noninvasive
Microbial Ecology Diagnostics
32. LS Time Series Gut Microbiome Classes
vs. Healthy, Crohn’s, Ulcerative Colitis
33. Microbial Metagenomics Can Diagnose Disease States
Using Principal Component Analysis
From www.23andme.com
Mutation in Interleukin-23
Receptor Gene—80% Higher
Risk of Pro-inflammatory
Immune Response
IBD Patients Harbored,
on Average,
25% Fewer
SNPs Associated with CD
Microbial Genes
than the Individuals
Not Suffering from IBD.
2009
35. Healthy, CD, UC and LS
Relative Abundance of Proteobacteria to Actinobacteria
36. Bacteroides fragilis Levels Different For
Healthy and IBD Human Gut-Differentiates CD and UC
Healthy
Ulcerative
Colitis
LS Crohn’s
Disease
Source: Analysis by LS working on Weizhong Li Data
37. Almost All Abundant Species (≥1%) in Healthy Subjects
Are Severely Depleted in LS Gut
38. Top 20 Most Abundant Microbial Species
In LS vs. Average Healthy Subject
152x Number Above
LS Blue Bar is Multiple
of LS Abundance
765x
Compared to Average
148x Healthy Abundance
Per Species
849x
483x
220x
201x169x
522x
Source: Sequencing JCVI; Analysis Weizhong Li, UCSD
LS December 28, 2011 Stool Sample
39. Comparing 3 LS Time Snapshots (Left)
with Healthy, Crohn’s, UC (Right Top to Bottom)
Calit2 VROOM-FuturePatient Expedition
40. LS Gut Microbe Species 12/28/11 (red)
compared to Average of 35 Healthy Subjects (blue)
Derived from metagenomic sequencing of LS stool sample.
Each species is a bar,
height is logarithmic abundance,
species are divided into microbial phyla
Source: Photo of Calit2 64-megapixel VROOM
41. 200 LS Gut Microbe Species at 3 Times
12/28/11, 4/3/12, 8/7/12
Red is at Highest Value of CRP
Blue is the Day After End of Antibiotic/Prednisone Therapy
Green is Four Months Later
Source: Photo of Calit2 64-megapixel VROOM
42. Closeup of Uncommon LS Microbes
12/28/11 Stool Sample
Two separate
45x research teams
Reduced have found
strikingly high
By 8% 90x concentrations
Therapy Increased Reduced of Fusobacterium
in tumor samples
By By collected from
Therapy Therapy colorectal cancer
patients.
October 18, 2011
43. From War
to Gardening
“I would like to lose the language of warfare,”
said Julie Segre, a senior investigator at
the National Human Genome Research Institute.
”It does a disservice to all the bacteria
that have co-evolved with us
and are maintaining the health of our bodies.”
44. DIY Systems Biology -
Toward P4 Healthcare
Over 1000 Downloads So Far
Download pdfs from Journal:
http://onlinelibrary.wiley.com/doi/10.1002/biot.201100495/full
45. Integrative Personal Omics Profiling
Reveals Details of Clinical Onset of Viruses and Diabetes
Cell 148, 1293–1307, March 16, 2012
• Michael Snyder,
Chair of Genomics
Stanford Univ.
• Genome 140x
Coverage
• Blood Tests 20
Times in 14 Months
– tracked nearly
20,000 distinct
transcripts coding
for 12,000 genes
– measured the
relative levels of
more than 6,000
proteins and 1,000
metabolites in
Snyder's blood