This document summarizes Jonathan Eisen's presentation on seagrass as a model system for plant microbiome studies. It describes how Eisen initially knew little about seagrasses but connected with colleague Jay Stachowicz, a seagrass expert, to learn more. They collaborated on a proposal to study the microbiomes of seagrasses. Initial studies found the microbial communities varied by tissue type, with more variation below ground. A global study by Eisen's group using the Zostera Experimental Network sampled seagrass microbiomes from sites around the world. The study found seagrass leaf microbiomes resembled local water, while roots had microbial communities enriched in sulfur metabolism.
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
The document contains slides from a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2016. The slides discuss various topics relating to metagenomics including the environmental genome shotgun sequencing of the Sargasso Sea, methods for binning sequences from metagenomic data like aligning to reference genomes or assembly, and examples of projects that used shotgun sequencing like the Wolbachia and glassy-winged sharpshooter projects. It also discusses challenges with assembly for metagenomic data due to variations in coverage and the DeLong lab's early work characterizing uncultured marine microbes.
Self-Powered Biosensor for Ascorbic Acid with a Prussian Blue Electrochromic ...DrMJN
We have prepared electrodes modified with either carbon nanoparticles or vertically aligned carbon nanotubes for AA oxidation. We show that by connecting the CNP anode to a Prussian blue electrochromic display we can create a truly self-powered sensor that does not require any external power source for determining the concentration of AA in a sample.
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
EveMicrobial Phylogenomics (EVE161) Class 9Jonathan Eisen
Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 9:
Era II: rRNA Case Study: Built Environment Metaanalysis
This document summarizes Jonathan Eisen's presentation on seagrass as a model system for plant microbiome studies. It describes how Eisen initially knew little about seagrasses but connected with colleague Jay Stachowicz, a seagrass expert, to learn more. They collaborated on a proposal to study the microbiomes of seagrasses. Initial studies found the microbial communities varied by tissue type, with more variation below ground. A global study by Eisen's group using the Zostera Experimental Network sampled seagrass microbiomes from sites around the world. The study found seagrass leaf microbiomes resembled local water, while roots had microbial communities enriched in sulfur metabolism.
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
The document contains slides from a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2016. The slides discuss various topics relating to metagenomics including the environmental genome shotgun sequencing of the Sargasso Sea, methods for binning sequences from metagenomic data like aligning to reference genomes or assembly, and examples of projects that used shotgun sequencing like the Wolbachia and glassy-winged sharpshooter projects. It also discusses challenges with assembly for metagenomic data due to variations in coverage and the DeLong lab's early work characterizing uncultured marine microbes.
Self-Powered Biosensor for Ascorbic Acid with a Prussian Blue Electrochromic ...DrMJN
We have prepared electrodes modified with either carbon nanoparticles or vertically aligned carbon nanotubes for AA oxidation. We show that by connecting the CNP anode to a Prussian blue electrochromic display we can create a truly self-powered sensor that does not require any external power source for determining the concentration of AA in a sample.
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
EveMicrobial Phylogenomics (EVE161) Class 9Jonathan Eisen
Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 9:
Era II: rRNA Case Study: Built Environment Metaanalysis
This document summarizes a study that reconstructed 7,903 bacterial and archaeal genomes from over 1,500 public metagenomes. Key findings include:
- The genomes increase phylogenetic diversity of bacterial and archaeal trees by over 30% and provide first representatives for 17 bacterial and 3 archaeal candidate phyla.
- 245 genomes were recovered from the Patescibacteria superphylum.
- The genomes vary substantially in quality, with 43.5% considered near-complete, 43.8% medium quality, and 12.7% partial.
- The genomes expand representation of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaera
Yaacov Davidov has extensive experience in microbiology. He received his Ph.D in Microbiology from the Hebrew University of Jerusalem and has held several post-doctoral and research positions. Currently, he is the Head of the Campylobacter and Vibrio national reference center at the Central laboratories of the Ministry of Health in Jerusalem. He has published numerous papers on predatory bacteria and their diversity and evolution. Davidov also has experience developing and implementing clinical laboratory tests and managing a national reference laboratory.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
PCR is a method for amplifying a specific DNA sequence using DNA polymerase. It involves repeated cycles of heating and cooling of the DNA sample to separate and copy the DNA strands. Dr. Kary Mullis discovered PCR in 1983 and was awarded the Nobel Prize for it. PCR is now used in a variety of applications including forensics, disease diagnosis, genetic testing, and evolutionary studies. It allows scientists to generate millions of copies of a specific DNA segment.
This study aimed to isolate antibiotic-producing soil bacteria to discover new antibiotics. Researchers collected a soil sample from Connecticut and isolated the bacterium Lysobacter antibioticus based on its zones of inhibition against pathogens. Sequence analysis identified the isolate as L. antibioticus. An ethyl acetate extract of L. antibioticus inhibited the growth of Bacillus subtilis but not the fungus Candida albicans, indicating antibiotic activity. L. antibioticus is known to produce beta-lactams and other antibiotics active against both gram-positive and gram-negative bacteria.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
Wurzbacher, Grimmett, Bärlocher, 2016. Metabarcoding fungal diversity Ivan Grimmett
This document summarizes a study that characterized fungal communities on coarse particulate organic matter (CPOM) like leaves and fine particulate organic matter (FPOM) in a stream in Nova Scotia, Canada using metabarcoding. Maple leaves were exposed in the stream for 4 weeks and 4 FPOM size fractions were collected over the same period by filtration. Pyrosequencing of the samples identified a total of 821 fungal operational taxonomic units, with 726 exclusive to particle samples and 47 to leaf samples. The study aimed to shed light on fungal processing of organic matter in streams and broaden understanding of freshwater fungal diversity.
This document summarizes a study that found Bacillus subtilis switches to a multicellular biofilm state in response to impaired respiration. The study found that low oxygen levels increased production of the extracellular matrix that holds biofilm cells together, while high oxygen suppressed matrix production. Two histidine kinases, KinA and KinB, were found to sense impaired respiration and signal through Spo0A to increase matrix gene expression. KinB was found to form a complex with respiratory chain components and likely senses impaired electron transport. KinA may sense a decrease in the NAD+/NADH ratio and directly interacts with NAD+. The study suggests B. subtilis uses impaired respiration as an environmental signal to increase biofilm formation and access to
This study isolated and characterized an extremely arsenic-resistant bacterium, Brevibacterium linens strain AE038-8, from contaminated well water in Tucumán, Argentina. Genome sequencing revealed genes that allow the bacterium to resist and metabolize high concentrations of arsenic, including an ars operon. The genome was sequenced and analyzed to better understand the bacterium's arsenic resistance mechanisms, which could help remediate arsenic contamination.
This document provides a summary of Malavika Sinha's qualifications and experience. Her PhD research at Washington State University involved successfully engineering a fungus to express bacterial genes for hydrocarbon production, representing an important step towards producing biofuels from fungi. She has strong skills in molecular biology, microbiology, and bioinformatics and is looking for postdoctoral research opportunities to continue contributing to advanced biofuel research.
Artist Jo Berry spent nearly six months as an undergraduate student at the University of Nottingham's biological medical college to learn how to utilize living human cells in her artwork. She takes microscope images of living cells back to her studio where she processes them using Zeiss software into remarkable multi-layer images and sculptures. Berry's art project "Hijacking Natural Systems" is funded jointly by the British Wellcome Trust and the Arts Council of England.
A renewed need for a genomic field guide to microbesJonathan Eisen
This document discusses the need for a genomic field guide to microbes. It outlines several challenges to creating such a guide, including the small size and diversity of microbes, as well as difficulties observing and collecting data on them in natural environments. Potential solutions proposed include advances in DNA sequencing technologies that have enabled large-scale cataloging and identification of microbes. Components suggested for inclusion in a field guide are phylogenetic catalogs, functional profiles, biogeography data, identification methods, and information on applications like pathogen detection. Citizen science initiatives are also presented as a way to engage the public in microbiology. The talk concludes by advocating the creation of a comprehensive genomic field guide to microbes.
This document contains lecture slides for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss the use of rRNA PCR and sequencing to study major microbial groups based on 16S rRNA gene sequences. They provide phylogenetic trees comparing sequences from cultivated vs uncultivated microbes in various bacterial divisions. The slides also address issues with phylogenetic analysis like unseen changes over evolutionary time and limitations in representing diversity due to a lack of cultivated microbes. Overall, the slides aim to provide students with an understanding of how rRNA gene sequencing has expanded knowledge of microbial diversity beyond what was known from culture and the challenges that remain in fully resolving deep phylogenetic relationships.
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
Jonathan Eisen talk for 2019 ADVANCE Scholar Award SymposiumJonathan Eisen
Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
Presentation summarising the 2013 ICSB conference in Copenhagen, a requirement of James Hutton Institute Visits Abroad funding. Presented at the Cellular and Molecular Sciences seminar series.
(Complete) Screening Phenotypic Mutations in Citobacter RodentiumKonyin Oluwole
This document is a research proposal submitted by Olukonyinsola Oluwole to the Office of Undergraduate Research at UMass Dartmouth. The proposal summarizes a research project that aims to screen phenotypic mutations in Citobacter Rodentium bacteria through experimental simulations. The goal is to test the hypothesis that pathogenic bacteria adapt in natural environments by losing traits needed for host colonization and toxicity. The anticipated outcome is that the mutated Citobacter Rodentium will lose its pathogenic qualities, allowing for the development of probiotics to treat degenerative intestinal diseases like IBS.
UC Davis EVE161 Lecture 18 by @phylogenomicsJonathan Eisen
This document contains slides for a lecture on metagenomics. It discusses student presentation guidelines, summarizes a published article on characterizing genes from the human gut microbiome, provides details on the methods used in that study to extract and sequence DNA from fecal samples of 124 individuals, and includes some results tables. The study generated over 500 GB of sequence data and identified over 3 million non-redundant microbial genes from the gut microbiome.
A brief description on the phenomenon of Bio-luminescence and it's applications in various industries like to detect good food gone bad in food industries,drug testing in pharmaceuticals industry and as reporter genes in genetic engineering.
This document summarizes a study that reconstructed 7,903 bacterial and archaeal genomes from over 1,500 public metagenomes. Key findings include:
- The genomes increase phylogenetic diversity of bacterial and archaeal trees by over 30% and provide first representatives for 17 bacterial and 3 archaeal candidate phyla.
- 245 genomes were recovered from the Patescibacteria superphylum.
- The genomes vary substantially in quality, with 43.5% considered near-complete, 43.8% medium quality, and 12.7% partial.
- The genomes expand representation of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaera
Yaacov Davidov has extensive experience in microbiology. He received his Ph.D in Microbiology from the Hebrew University of Jerusalem and has held several post-doctoral and research positions. Currently, he is the Head of the Campylobacter and Vibrio national reference center at the Central laboratories of the Ministry of Health in Jerusalem. He has published numerous papers on predatory bacteria and their diversity and evolution. Davidov also has experience developing and implementing clinical laboratory tests and managing a national reference laboratory.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
PCR is a method for amplifying a specific DNA sequence using DNA polymerase. It involves repeated cycles of heating and cooling of the DNA sample to separate and copy the DNA strands. Dr. Kary Mullis discovered PCR in 1983 and was awarded the Nobel Prize for it. PCR is now used in a variety of applications including forensics, disease diagnosis, genetic testing, and evolutionary studies. It allows scientists to generate millions of copies of a specific DNA segment.
This study aimed to isolate antibiotic-producing soil bacteria to discover new antibiotics. Researchers collected a soil sample from Connecticut and isolated the bacterium Lysobacter antibioticus based on its zones of inhibition against pathogens. Sequence analysis identified the isolate as L. antibioticus. An ethyl acetate extract of L. antibioticus inhibited the growth of Bacillus subtilis but not the fungus Candida albicans, indicating antibiotic activity. L. antibioticus is known to produce beta-lactams and other antibiotics active against both gram-positive and gram-negative bacteria.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
Wurzbacher, Grimmett, Bärlocher, 2016. Metabarcoding fungal diversity Ivan Grimmett
This document summarizes a study that characterized fungal communities on coarse particulate organic matter (CPOM) like leaves and fine particulate organic matter (FPOM) in a stream in Nova Scotia, Canada using metabarcoding. Maple leaves were exposed in the stream for 4 weeks and 4 FPOM size fractions were collected over the same period by filtration. Pyrosequencing of the samples identified a total of 821 fungal operational taxonomic units, with 726 exclusive to particle samples and 47 to leaf samples. The study aimed to shed light on fungal processing of organic matter in streams and broaden understanding of freshwater fungal diversity.
This document summarizes a study that found Bacillus subtilis switches to a multicellular biofilm state in response to impaired respiration. The study found that low oxygen levels increased production of the extracellular matrix that holds biofilm cells together, while high oxygen suppressed matrix production. Two histidine kinases, KinA and KinB, were found to sense impaired respiration and signal through Spo0A to increase matrix gene expression. KinB was found to form a complex with respiratory chain components and likely senses impaired electron transport. KinA may sense a decrease in the NAD+/NADH ratio and directly interacts with NAD+. The study suggests B. subtilis uses impaired respiration as an environmental signal to increase biofilm formation and access to
This study isolated and characterized an extremely arsenic-resistant bacterium, Brevibacterium linens strain AE038-8, from contaminated well water in Tucumán, Argentina. Genome sequencing revealed genes that allow the bacterium to resist and metabolize high concentrations of arsenic, including an ars operon. The genome was sequenced and analyzed to better understand the bacterium's arsenic resistance mechanisms, which could help remediate arsenic contamination.
This document provides a summary of Malavika Sinha's qualifications and experience. Her PhD research at Washington State University involved successfully engineering a fungus to express bacterial genes for hydrocarbon production, representing an important step towards producing biofuels from fungi. She has strong skills in molecular biology, microbiology, and bioinformatics and is looking for postdoctoral research opportunities to continue contributing to advanced biofuel research.
Artist Jo Berry spent nearly six months as an undergraduate student at the University of Nottingham's biological medical college to learn how to utilize living human cells in her artwork. She takes microscope images of living cells back to her studio where she processes them using Zeiss software into remarkable multi-layer images and sculptures. Berry's art project "Hijacking Natural Systems" is funded jointly by the British Wellcome Trust and the Arts Council of England.
A renewed need for a genomic field guide to microbesJonathan Eisen
This document discusses the need for a genomic field guide to microbes. It outlines several challenges to creating such a guide, including the small size and diversity of microbes, as well as difficulties observing and collecting data on them in natural environments. Potential solutions proposed include advances in DNA sequencing technologies that have enabled large-scale cataloging and identification of microbes. Components suggested for inclusion in a field guide are phylogenetic catalogs, functional profiles, biogeography data, identification methods, and information on applications like pathogen detection. Citizen science initiatives are also presented as a way to engage the public in microbiology. The talk concludes by advocating the creation of a comprehensive genomic field guide to microbes.
This document contains lecture slides for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss the use of rRNA PCR and sequencing to study major microbial groups based on 16S rRNA gene sequences. They provide phylogenetic trees comparing sequences from cultivated vs uncultivated microbes in various bacterial divisions. The slides also address issues with phylogenetic analysis like unseen changes over evolutionary time and limitations in representing diversity due to a lack of cultivated microbes. Overall, the slides aim to provide students with an understanding of how rRNA gene sequencing has expanded knowledge of microbial diversity beyond what was known from culture and the challenges that remain in fully resolving deep phylogenetic relationships.
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
Jonathan Eisen talk for 2019 ADVANCE Scholar Award SymposiumJonathan Eisen
Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
Presentation summarising the 2013 ICSB conference in Copenhagen, a requirement of James Hutton Institute Visits Abroad funding. Presented at the Cellular and Molecular Sciences seminar series.
(Complete) Screening Phenotypic Mutations in Citobacter RodentiumKonyin Oluwole
This document is a research proposal submitted by Olukonyinsola Oluwole to the Office of Undergraduate Research at UMass Dartmouth. The proposal summarizes a research project that aims to screen phenotypic mutations in Citobacter Rodentium bacteria through experimental simulations. The goal is to test the hypothesis that pathogenic bacteria adapt in natural environments by losing traits needed for host colonization and toxicity. The anticipated outcome is that the mutated Citobacter Rodentium will lose its pathogenic qualities, allowing for the development of probiotics to treat degenerative intestinal diseases like IBS.
UC Davis EVE161 Lecture 18 by @phylogenomicsJonathan Eisen
This document contains slides for a lecture on metagenomics. It discusses student presentation guidelines, summarizes a published article on characterizing genes from the human gut microbiome, provides details on the methods used in that study to extract and sequence DNA from fecal samples of 124 individuals, and includes some results tables. The study generated over 500 GB of sequence data and identified over 3 million non-redundant microbial genes from the gut microbiome.
A brief description on the phenomenon of Bio-luminescence and it's applications in various industries like to detect good food gone bad in food industries,drug testing in pharmaceuticals industry and as reporter genes in genetic engineering.
This document provides an overview of bioluminescence, including why it occurs in nature, how the process works, and opportunities for applications. It discusses current research in using bioluminescence for lighting, biomedical imaging, and the food industry. For lighting, concepts are exploring using bioluminescent bacteria or genetically modified plants as a sustainable light source. In biomedical imaging, bioluminescence could provide a lower-cost alternative to technologies like MRI. And in food, bioluminescence offers a rapid method to detect contamination compared to traditional culture-based techniques. The document outlines several entrepreneurial opportunities and factors for commercializing bioluminescence technologies.
Scientists revived a giant virus that was buried in Siberian ice for 30,000 years. The virus, called Pithovirus, replicates by copying itself in the host cell's cytoplasm. The Human Genome Project aimed to sequence the three billion DNA bases in the human cell, which was completed in 2003 and provided new insights into diagnosing and treating human diseases. John Craig Venter founded Celera Genomics, the first private group to sequence the human genome using a "shotgun method" that helped complete the project. Biology is the study of life through structures, functions, and relationships of living things and their environment.
Henrietta Lacks was born in 1920 in Virginia and died of cervical cancer in 1951. Doctors at Johns Hopkins Hospital took a sample of her tumor without her consent for research purposes. The cells from her tumor, now known as HeLa cells, were the first human cells to survive and thrive in a lab setting. They could be continuously grown and have become the most important cell line in medical research. However, Henrietta's family was unaware that her cells were still alive in labs until many years later. The book documents how her cells contributed to important medical advances while also exposing the unethical practices and lack of consent at the time.
Microbiology
study of organisms too small to be seen by the naked eye.
Microbes or Microorganisms
commonly referred to as “germs” or “bugs”
include bacteria, viruses, fungi, algae, protozoa and helminths.
Prions (“infectious proteins”) are recent addition.
Jonathan Eisen talk at #UCDavis 10/19/15 on "Microbiomes in Food and Agricult...Jonathan Eisen
Slides for talk on "Microbiomes in Food and Agriculture" by JonathanEisen - note - not all slides were used in talk. These were there to stimulate discussion ...
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The document provides an overview of microbiology, including the structure and morphology of microorganisms such as bacteria, fungi, protozoa, and viruses. It discusses topics like bacterial cell structure, flagella and pili, endospores, capsules, inclusion bodies, and the contributions of Anton van Leeuwenhoek, who is considered the father of microbiology.
Lecture 1 bioscience overview 592010 post with videosmeminie
This document summarizes an online bioscience course for IT professionals. The course covers the basics of life through a molecular biology lens over several video lectures. It discusses that life can be defined by growth, metabolism, reproduction and adaptation. The basic unit of life is the cell, which comes in two types - prokaryotic and eukaryotic. All life on Earth is related through evolution from a common ancestor over 3.5 billion years ago. Life functions according to the central dogma of DNA to RNA to protein, with proteins acting as enzymes and molecular machines.
Biology is the study of life. There are several key characteristics that define living things: (1) Organization - all living things are made of cells that are organized into tissues, organs and organ systems, (2) Response to stimuli - living things respond to environmental stimuli, (3) Homeostasis - living things regulate internal conditions to maintain stability, (4) Growth and development - living things increase in size and develop through cell specialization, (5) Reproduction - living things produce new individuals of their own kind, (6) Evolution - species change over time through genetic variation and natural selection, (7) Metabolism - living things require energy to carry out life processes.
The document discusses programmed cell death (PCD) in algae and its potential role in nutrient cycling in polar ecosystems like Antarctica. It presents evidence that PCD may be occurring in the algae Fragilariopsis cylindra in the Ross Sea: 1) Samples taken at different depths showed living algae cells at the surface but few cells at 500m, suggesting PCD. 2) Cells stained with probes for PCD showed fluorescence indicating PCD was occurring in samples from 20m deep. The document hypothesizes that PCD of algae blooms could play a role in nutrient cycling in polar ecosystems similarly to the microbial loop in closed systems like the Great Salt Lake. Continued analysis of over 300 samples is needed to determine the full extent of
This document provides an overview of a course on plants and the environment taught at Fudan University in Shanghai, China. The course covers topics including plant structure and function, reproduction, diversity, evolution, ecology, and interactions between plants and their environment. It includes a syllabus outlining the schedule and requirements, as well as brief biographies of the instructors.
The Human Microbiome and the Revolution in Digital HealthLarry Smarr
2014.01.22
Calit2 Director Larry Smarr speaks as part of the Pensacola Evening Lecture Series, organized by the Florida Institute for Human and Machine Cognition, in Pensacola, FL.
The document provides an overview of topics covered in a biology course, including scientific method, nature of life, cells, biochemistry, genetics, evolution, ecology, and human impacts. It discusses key concepts such as the structures and functions of plant and animal cells, diffusion and osmosis, DNA replication, genetic disorders, natural selection, ecosystem interactions, and the greenhouse effect. Safety protocols for laboratories are also outlined.
The document provides an overview of various topics in biology including cells, DNA, genetics, evolution, and ecology. It discusses key concepts such as the scientific method, cell structures, mitosis, biochemical reactions, DNA replication, genetic disorders, natural selection, photosynthesis, and human impact on the biosphere. Safety protocols for laboratories are also mentioned.
This document provides information about bioluminescence. It begins with an acknowledgement and introduction defining bioluminescence. The document then discusses the history of bioluminescence research, how it evolved in different organisms, and how the bioluminescence reaction works on a chemical level. It lists several bioluminescent organisms and describes some uses of bioluminescence in nature for camouflage, attraction, defense, warning, and communication. The document also outlines several modern applications of bioluminescence in fields like biology, medicine, the environment, and industry. It distinguishes between bioluminescence and biofluorescence and briefly describes two recent research papers on biol
This document provides information about bioluminescence. It begins with an acknowledgement and definition of bioluminescence. There is then a brief history of bioluminescence research and discussion of its evolution in different organisms. The document explains that bioluminescence results from a chemical reaction between luciferin and luciferase, producing light. Examples of bioluminescent organisms are provided, as well as their uses in nature for camouflage, attraction, defense, and communication. Modern applications of bioluminescence in areas like biology, medicine, and the environment are outlined. The difference between bioluminescence and biofluorescence is defined. Recent research publications on biolumines
Bioproduction of bioactive compounds screening of bioproduction conditions of...ainia centro tecnológico
1. The document describes a study screening bioproduction conditions for microalgae and lichen symbionts to produce bioactive compounds. It examines the adaptation of various microalgae like Chlorella and Asterochloris erici to different culture media and processing methods.
2. The results show that Chlorella vulgaris was able to grow under mixotrophic conditions using various carbon sources and treatments like ultrasounds increased bioactivity. Asterochloris erici was adapted from solid to liquid culture and able to be cultured at large scale under autotrophic conditions.
3. The study demonstrates that bioproduction technologies can be used to obtain high-value compounds from microalgae and lichen
Similar to TTT conference presentation ENGLISH (20)
This student worksheet contains questions about a pGLO bacteria transformation experiment. It asks the student to define terms related to the experiment such as GFP, transgenic, E. coli, plasmids, ampicillin, and arabinose. It also asks how the student will know if the experiment was successful.
The Spiller Lab at Rutgers University studies transgenic organisms. Their goal is to create a transgenic bacteria that glows in the dark by taking the GFP gene from jellyfish and inserting it into E. coli bacteria. The GFP gene will be inserted into the bacterial DNA using a plasmid called pGLO. This will allow the bacteria to produce green fluorescent protein and glow, while also conferring resistance to ampicillin, allowing the bacteria to grow on nutrient plates containing the antibiotic.
1. The document provides instructions for a PGLO lab practice involving transforming E. coli bacteria with plasmid DNA.
2. The instructions include labeling micro test tubes, spreading bacteria on agar plates, heat shocking bacteria to allow plasmid entry, and incubating plates overnight to allow bacterial growth.
3. Students are asked to cut out descriptions of 12 steps and match them to diagrams showing how to complete the bacterial transformation protocol.
The document is a worksheet that asks a student to determine which of 10 animals are most closely related by matching them in pairs. It provides the names of 10 animals - African elephant, kangaroo, horseshoe crab, dugong, crocodile, mountain gorilla, ring-tailed lemur, nine-banded armadillo, three-toed sloth, brown recluse spider, emperor penguin, and possum. The student is instructed to match the animals in pairs of the most closely related.
Manatees are large, slow-moving aquatic mammals that inhabit coastal waters and rivers. They can grow up to 13 feet long and weigh over 1,300 pounds. Despite their massive size, manatees are graceful swimmers that typically glide at 5 miles per hour but can burst up to 15 miles per hour. Manatees give birth underwater and mothers help their calves reach the surface for their first breath. Manatees are herbivores that consume large amounts of water plants. They are classified as endangered due to hunting and accidental collisions with boats.
The document provides instructions for an activity where students are asked to match animals based on which are most closely related. It lists 12 animals and has students work with a partner to determine relationships between the animals. It then has them write down the correct matches.
Elephants have evolved over millions of years from small forest-dwelling animals to the large land mammals we know today. Early elephant ancestors were about the size of a dog and lived in forests in Africa and Asia as far back as 60 million years ago. Over generations, natural selection led to elephants growing larger in size to survive in more open grassland habitats, developing trunks and tusks, and living in herds for protection and survival.
Dugongs are large marine mammals that graze on seagrasses along coastlines from East Africa to Australia. They can stay underwater for up to six minutes and breathe either by fully surfacing or standing on their tails. Dugongs spend most of their time alone or in small groups but sometimes gather in large herds, and mothers care for calves for around 18 months. Although now protected, dugongs were historically hunted for their meat and other products, and their populations remain vulnerable.
Birds have different types of beaks adapted for eating different kinds of food. The worksheet matches bird beaks to tools that represent their beak functions and has students hypothesize what each bird eats based on its beak. To test their hypotheses, students will need to research each bird species to determine if their predictions about the birds' diets match the actual types of food each bird eats in the wild.
This document describes the beaks, diets, and habitats of various bird species from around the world. It discusses African spoonbills, lesser flamingos, yellow-naped amazon parrots, speckled pigeons, white-faced whistling ducks, griffon vultures, red-billed hornbills, hammerkops, Egyptian geese, chestnut mandibled toucans, blue and yellow macaws, king penguins, and Magellanic penguins. Each entry provides details about the bird's taxonomy, geographical range, habitat, and diet that is adapted to its particular beak type.
Este documento proporciona instrucciones para un taller sobre la transformación de bacterias con el plásmido pGLO y la posterior purificación de la proteína GFP. El taller se llevará a cabo en dos días, comenzando con la transformación bacteriana con pGLO para inducir la resistencia a ampicilina y la expresión de GFP, seguido del cultivo bacteriano y la inducción de GFP con arabinosa.
Are you interested in the pGLO™ experiment? Learn more about this hands-on laboratory activity with a FREE download of BioRad’s pGLO™ experiment power point.
The researchers aimed to bioengineer a new red fluorescent protein tag from cyanobacteriochromes in Thermosynechococcus elongatus. They transfected Jurkat cells with plasmids containing fluorescent protein tags for visualization under advanced microscopes. Electroporation and the plasmid pAcGFP1-Tubulin were found to be most efficient for transfection. Future goals include optimizing expression of their engineered 569 fluorescent tag in mammalian cells.
The document summarizes steps taken to purify a fluorescent protein tag from a cyanobacteriochrome found in Thermosynechococcus elongatus, including:
1) Transforming E. coli with the gene for the cyanobacteriochrome tag and inducing protein expression.
2) Lysing the cells using a microfluidizer and centrifuging to remove cell debris.
3) Purifying the fluorescent tag protein using a chitin bead column.
4) Analyzing purity using SDS-PAGE gel electrophoresis and a spectrophotometer.
The document discusses engineering a red fluorescent protein tag from the cyanobacterium Thermosynechococcuselongatus for use as an easily detectable protein marker. The tag would respond to different light wavelengths and could be used to study protein expression and transformation in T. elongatus cells. Existing green fluorescent protein tags from jellyfish require a different light wavelength to be detected. The engineered red tag would use the GAF domain protein and phycocyanobilin chromophore from T. elongatus to fluorescently label and image proteins when expressed in host cells.
This document summarizes a student research project on bioengineering fluorescent protein tags from cyanobacteriochromes found in Thermosynechococcus elongatus BP-1. The student presented on expressing genes from T. elongatus that produce cyanobacteriochromes, which are light-sensitive blue/green pigments, in E. coli cells. The goal was to engineer red fluorescent cyanobacteriochromes by using a two-plasmid system involving genes for heme oxygenase and reductase in E. coli cells containing the cyanobacteriochrome genes.
The researcher expressed the wrong fluorescent protein from Thermosynechococcus elongatus, with the pelleted proteins being blue instead of the expected yellow. Through DNA sequencing and comparison to published sequences, they determined the expressed protein was gene 0569 instead of the target gene 0911. Contamination of samples or mislabeling likely occurred. The researcher took steps to verify the correct gene, such as sequencing plasmid DNA from older stock and improving lab techniques, to obtain the expected yellow fluorescent protein in future expressions.
Congreso de Biotecnología Arequipa Perú June 2011Mills Cbst
This document summarizes research to bioengineer a new red fluorescent protein tag from a cyanobacteriochrome found in Thermosynechococcus elongatus. The researchers aim to develop a small, photostable red tag as an alternative to commonly used green and yellow fluorescent proteins from jellyfish. They use molecular biology techniques like PCR, site-directed mutagenesis, and transfection of E. coli and mammalian cells to express and purify the mutated protein, which they characterize through spectroscopy and microscopy. The goal is to create a useful new tool for cellular imaging applications.
Stay informed! Mills CBST is funded by the National Science Foundation, Chemical, Bioengineering, Environmental, and Transport Systems (CBET) division. This highlight describes in detail the work of Mills CBST, led by Dr. Susan Spiller.
Main news related to the CCS TSI 2023 (2023/1695)Jakub Marek
An English 🇬🇧 translation of a presentation to the speech I gave about the main changes brought by CCS TSI 2023 at the biggest Czech conference on Communications and signalling systems on Railways, which was held in Clarion Hotel Olomouc from 7th to 9th November 2023 (konferenceszt.cz). Attended by around 500 participants and 200 on-line followers.
The original Czech 🇨🇿 version of the presentation can be found here: https://www.slideshare.net/slideshow/hlavni-novinky-souvisejici-s-ccs-tsi-2023-2023-1695/269688092 .
The videorecording (in Czech) from the presentation is available here: https://youtu.be/WzjJWm4IyPk?si=SImb06tuXGb30BEH .
Skybuffer AI: Advanced Conversational and Generative AI Solution on SAP Busin...Tatiana Kojar
Skybuffer AI, built on the robust SAP Business Technology Platform (SAP BTP), is the latest and most advanced version of our AI development, reaffirming our commitment to delivering top-tier AI solutions. Skybuffer AI harnesses all the innovative capabilities of the SAP BTP in the AI domain, from Conversational AI to cutting-edge Generative AI and Retrieval-Augmented Generation (RAG). It also helps SAP customers safeguard their investments into SAP Conversational AI and ensure a seamless, one-click transition to SAP Business AI.
With Skybuffer AI, various AI models can be integrated into a single communication channel such as Microsoft Teams. This integration empowers business users with insights drawn from SAP backend systems, enterprise documents, and the expansive knowledge of Generative AI. And the best part of it is that it is all managed through our intuitive no-code Action Server interface, requiring no extensive coding knowledge and making the advanced AI accessible to more users.
Fueling AI with Great Data with Airbyte WebinarZilliz
This talk will focus on how to collect data from a variety of sources, leveraging this data for RAG and other GenAI use cases, and finally charting your course to productionalization.
Letter and Document Automation for Bonterra Impact Management (fka Social Sol...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on automated letter generation for Bonterra Impact Management using Google Workspace or Microsoft 365.
Interested in deploying letter generation automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
How to Interpret Trends in the Kalyan Rajdhani Mix Chart.pdfChart Kalyan
A Mix Chart displays historical data of numbers in a graphical or tabular form. The Kalyan Rajdhani Mix Chart specifically shows the results of a sequence of numbers over different periods.
Building Production Ready Search Pipelines with Spark and MilvusZilliz
Spark is the widely used ETL tool for processing, indexing and ingesting data to serving stack for search. Milvus is the production-ready open-source vector database. In this talk we will show how to use Spark to process unstructured data to extract vector representations, and push the vectors to Milvus vector database for search serving.
Taking AI to the Next Level in Manufacturing.pdfssuserfac0301
Read Taking AI to the Next Level in Manufacturing to gain insights on AI adoption in the manufacturing industry, such as:
1. How quickly AI is being implemented in manufacturing.
2. Which barriers stand in the way of AI adoption.
3. How data quality and governance form the backbone of AI.
4. Organizational processes and structures that may inhibit effective AI adoption.
6. Ideas and approaches to help build your organization's AI strategy.
Introduction of Cybersecurity with OSS at Code Europe 2024Hiroshi SHIBATA
I develop the Ruby programming language, RubyGems, and Bundler, which are package managers for Ruby. Today, I will introduce how to enhance the security of your application using open-source software (OSS) examples from Ruby and RubyGems.
The first topic is CVE (Common Vulnerabilities and Exposures). I have published CVEs many times. But what exactly is a CVE? I'll provide a basic understanding of CVEs and explain how to detect and handle vulnerabilities in OSS.
Next, let's discuss package managers. Package managers play a critical role in the OSS ecosystem. I'll explain how to manage library dependencies in your application.
I'll share insights into how the Ruby and RubyGems core team works to keep our ecosystem safe. By the end of this talk, you'll have a better understanding of how to safeguard your code.
Digital Marketing Trends in 2024 | Guide for Staying AheadWask
https://www.wask.co/ebooks/digital-marketing-trends-in-2024
Feeling lost in the digital marketing whirlwind of 2024? Technology is changing, consumer habits are evolving, and staying ahead of the curve feels like a never-ending pursuit. This e-book is your compass. Dive into actionable insights to handle the complexities of modern marketing. From hyper-personalization to the power of user-generated content, learn how to build long-term relationships with your audience and unlock the secrets to success in the ever-shifting digital landscape.
Skybuffer SAM4U tool for SAP license adoptionTatiana Kojar
Manage and optimize your license adoption and consumption with SAM4U, an SAP free customer software asset management tool.
SAM4U, an SAP complimentary software asset management tool for customers, delivers a detailed and well-structured overview of license inventory and usage with a user-friendly interface. We offer a hosted, cost-effective, and performance-optimized SAM4U setup in the Skybuffer Cloud environment. You retain ownership of the system and data, while we manage the ABAP 7.58 infrastructure, ensuring fixed Total Cost of Ownership (TCO) and exceptional services through the SAP Fiori interface.
Programming Foundation Models with DSPy - Meetup SlidesZilliz
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
leewayhertz.com-AI in predictive maintenance Use cases technologies benefits ...alexjohnson7307
Predictive maintenance is a proactive approach that anticipates equipment failures before they happen. At the forefront of this innovative strategy is Artificial Intelligence (AI), which brings unprecedented precision and efficiency. AI in predictive maintenance is transforming industries by reducing downtime, minimizing costs, and enhancing productivity.
Trusted Execution Environment for Decentralized Process MiningLucaBarbaro3
Presentation of the paper "Trusted Execution Environment for Decentralized Process Mining" given during the CAiSE 2024 Conference in Cyprus on June 7, 2024.
Dive into the realm of operating systems (OS) with Pravash Chandra Das, a seasoned Digital Forensic Analyst, as your guide. 🚀 This comprehensive presentation illuminates the core concepts, types, and evolution of OS, essential for understanding modern computing landscapes.
Beginning with the foundational definition, Das clarifies the pivotal role of OS as system software orchestrating hardware resources, software applications, and user interactions. Through succinct descriptions, he delineates the diverse types of OS, from single-user, single-task environments like early MS-DOS iterations, to multi-user, multi-tasking systems exemplified by modern Linux distributions.
Crucial components like the kernel and shell are dissected, highlighting their indispensable functions in resource management and user interface interaction. Das elucidates how the kernel acts as the central nervous system, orchestrating process scheduling, memory allocation, and device management. Meanwhile, the shell serves as the gateway for user commands, bridging the gap between human input and machine execution. 💻
The narrative then shifts to a captivating exploration of prominent desktop OSs, Windows, macOS, and Linux. Windows, with its globally ubiquitous presence and user-friendly interface, emerges as a cornerstone in personal computing history. macOS, lauded for its sleek design and seamless integration with Apple's ecosystem, stands as a beacon of stability and creativity. Linux, an open-source marvel, offers unparalleled flexibility and security, revolutionizing the computing landscape. 🖥️
Moving to the realm of mobile devices, Das unravels the dominance of Android and iOS. Android's open-source ethos fosters a vibrant ecosystem of customization and innovation, while iOS boasts a seamless user experience and robust security infrastructure. Meanwhile, discontinued platforms like Symbian and Palm OS evoke nostalgia for their pioneering roles in the smartphone revolution.
The journey concludes with a reflection on the ever-evolving landscape of OS, underscored by the emergence of real-time operating systems (RTOS) and the persistent quest for innovation and efficiency. As technology continues to shape our world, understanding the foundations and evolution of operating systems remains paramount. Join Pravash Chandra Das on this illuminating journey through the heart of computing. 🌟
6. Microscopic imagingDefinition: the study of the interaction of light with biological material- where “light” includes all forms of radiant energy whose quantum unit is the photon
7. Exploring the Microbial World Sample microbial environment Control microbes Transform E. coli with Green Fluorescent Protein (GFP)
8. Culture Sample Media Media contain nutrients Liquid and semisolid forms Luria Broth (LB) Agar Petri plate http://www.bestliveshopping.com/toys-165795011-B004MKHNJK-Pre_made_LB_Agar_Plate_10_plates
9. How to make LB agar plates? Materials Erlenmeyer flask Sodium chloride (NaCl) Yeast extract Tryptone Agar powder Deionized (DI) water Sterile Petri plates
10. Tools for Sterilization LB Agar http://www.missingfeatures.com/2007/06/25/building-a-better-microwave/ http://www.sz-wholesale.com/shenzhen_China_products/Pressure-Cooker_1.htm Microwave Pressure cooker http://sites.google.com/site/scienceprofonline/Lab-gradeAutoclave2.JPG Autoclave
11. Agar handling guidelines Label bottom only with name, date and initials (ex/ LB agar 11/4/11 RM) When pouring, store agar plates right side up When solidified, store in refrigerator up side down in container http://www.benchfly.com/video.php?video=164
17. Learning Outcomes! At the end of this session, students will have an appreciation of &/or be able to: Introduction to microbiology and bacteriology Differentiate between fungi and bacteria growth characteristics Importance of antibiotic selection and resistance genes Impact of disinfectants and antiseptics in controlling microbes
18. III. Transform E. coli with Green Fluorescent Protein (GFP) Transformation Introduce foreign DNA pGLO plasmid GFP
19. Green Fluorescent Protein (GFP) Jelly fish Aequoreavictoria Visual marker http://brainwindows.wordpress.com/2008/10/08/2008-nobel-prize-in-chemistry-to-gfp/
21. GFP changes genetic makeup http://askville.amazon.com/genetically-blue-eyed-parents-produce-brown-eyed-child/AnswerViewer.do?requestId=2969837 E. coli glowing colonies E. coli colonies
22. Transform E. coli with Green Fluorescent Protein (GFP) Why teach? Important modern biotechnology technique Central framework of molecular biology DNA RNA Protein trait/physical characteristic
23. Advantages Compatible with 50 min class periods Serves entire class of 32 students Up to 4 students per group Striking results! pGLO Bacterial Transformation Kit
Editor's Notes
Talk about me graduate to mills college
Label molecules so they can see inside the cell … red fluorescent tag that would allow researcher to locate particular molecules using advance microscopes under cells
Definition: the study of the interaction of light with biological material- where “light” includes all forms of radiant energy whose quantum unit is the photon
Today’s session includes three experiments. First, we are going to sample microbes from your environment of interest. Second, we are going to control microbes using antiseptics, antibiotics, and disinfectants. Third, I am going to teach you how we can use microbes for our advantage by transforming them with green fluorescent protein (GFP). Now put some gloves on and spray your benches with ethanol to clean the area that you are going to be working on.
Before we even get into the actual experiment, I have to teach you how to make the media necessary in preparation for all of the three experiments that we are going to cover today. You as teachers are going to be able to do this in your classroom or lab space. The media that you will making is a rich culture sample media that contains nutrients necessary for the growth of invisible organisms that you are going to sample. So, there are different types of media but I’ll teach you how to make the semisolid form. What you see in the right corner is a Luria Broth agar petri plate. Most commonly known as LB plate.
To make LB Agar plates you can use a beaker, an Erlenmeyer flask, or any glassware resistant to heat of any size or shape as long as it has more then enough space to hold your solution. For instance, if you are making 250 ml LB agar you would have to use a 500 ml flask. Then, you follow the protocol written in your worsheet. Mix all the ingredients, then put foil on top and place it into the pressure cooker. You are going to be pouring the agar into these petri plates that come in packs of sterile sleeves.
You can use these tools for stereilization of the agar. However, I prefer the pressure cooker if you don’t have an autoclave because it does not require constant monitoring.
Once placed into the pressure cooker you can use this time to label plates. In front of you, you have two plates labelled with the name of the media called LB agar, the date that it was made, and my initials. Now, using a sharpie you are going to label the bottom of both plates with the area that you are going to be sampling later on, the date and your initials.Another agar handling guidelines is that when pouring LB agar plates, store them right side up. Once they have been solidified, you can store the plates in a refrigerator up side down. In this picture you can see the difference between a plate that has been solifidied and one that has been recently been poured.
Grab your Experiment I worksheet. As part of your introduction, I have added the terminology used in describing bacterial colonies so you can teach your students the different types of colony shapes, colony margins and colony surface characteristics. Today you are going to be studying an environment of your choice, testing for the presence of bacteria and fungi. Now I want you to think about places that you are interested in sampling. Common places to sample. For instance, bathroom, door handles, a wound or a part of their body.Once you have chosen what to sample, hypothesize about the growth of the specie present in the environment of your choice. Then, make a prediction based on your hypothesis using if/then. Remember that a Hypothesis is a testable statement, an educated guess. A prediction is that if the hypothesis is true you will find lot of microbes on the plate o no microbes at all. For instance, “the janitor has clean the bathroom really well ” is a hypothesis. A prediction, if the janitor has clean the bathroom really well, then I will not find any bacterial colonies growing on my plate.Now let’s get into the procedure. In front of you, you have sterile cotton swabs foiled with aluminium and two LB labelled plates. Hypothesis where students think where microbes can exists … what you think is true “there will be more bacteria on my computer keyboard than on my hands after I wash them” not good too broadTry to get a look into invisible world that was not imagining before microscope take one minute and talk to your neighbor and formulate a hypothesis about what would you expect from the environment that you are sampling from
Since the sample collection is the most important step, before you actually sample you environment of interest you have to remember thatYou are working with unidentified organisms .. They are too small to seeYou have to prevent contamination from carrying you cotton swab all over until you actually swab the plate. Use the foil that has been covering your sterile cotton swab to cover it if neccesary.I want you to sample two plates identically so they can be replicates. It is important that you do this twice in two different plates bc you are going to need a control sample for your next expermiment. Be careful no to break the surface of the agar and poke holes. Gently grab and spread it around the surface of the plate. Then, you can wait at from 1-3 days depending of the temperature where you store the plates to see results. For instance, we are going to analyze these plates that I have here with me. I’m going to let you take the plates so you can analyze them at home. Also, in the worksheet you are going to be able to find questions in the results and discussion section that you can use as homework for your students.
Now grab your experiment II worksheet. You can combine Experiment I and II if you want. However, it is important to remember to formulate your hypothesis and prediction for this experiment as well.
Depending on the size of the LB petri dish, you are going to choose the number of agents of your choice. For instance, in this small plate we are going to be using two agents. You should pick one from a different group.I have brought several antibiotics such as …..
, antiseptics such as … and disinfectants such as ….Remember that an antibiotic will kill certain bacteria, an antiseptics will kill bacteria in your skin, and disinfectant can be use to clean surface or furniture.So, if you choose an antibiotic agent, dispense the disk onto the surface of the agar. If you choose an antiseptic or disinfectant. Pick up a sterile filter disk using sterile tweezers. Then, dip the filter halfway into one of the chemical solutions. Let the solution diffuse into the disk. Make sure the disk is not too wet before placing it onto the surface of the agar. Remember to keep disks away from the edge of the plate and once they are placed onto the agar, they should not be move.So, grab one of your replicate plates and follow the protocol. The other plate will be used as your control. Once they have been incubated for a few days, you can expect a zone of inhibition, which is represented by the clear area around the disk. If the bacteria is resistant to the agent chosen, then no zone of inhibition will be present. If the bacteria is susceptible to the agent chosen, then a zone of inhibition will be present.In the worksheet you are going to be able to find instruction for calculating the zone of inhibtion as well as questions for homework.
There are many microbes that are important to your body (mention that)
Now the third experiment consist on transforming E. coli with Green Fluorescent protein, most commonly known as GFP. When I say transformation that means that we are going to be introducing a foreign DNA into E. coli. This foreign DNA in this case is called plasmid pGLO. This plasmid contains genes such as GFP.
GFP was isolated from a jelly fish called Aequorea victoria. Since it fluoresces bright green when exposed to blue light, it helps to track a trait inside a cell. GFP is an important tool for many scientistist because is works as a visual marker so we basically can label whatever we want.
GFP changes the genetic makeup of the DNA. Since proteins are extremely small and cannot be seen normally, when attaching GFP to them it makes a protein fluoresce. Here you can see a 3D version of the protein after it has been translated from the DNA, that’s how the gene normally will look like. However, if we transform the DNA into this GFP gene before the stop codon or just after the promoter in the beginning of the gene, the protein that is coded by the DNA then is coded green.