This document discusses a motion graphic exploration project created by Kim Chambers. It contains images and a final video from the motion graphic exploration project. The project involved creating motion graphics and compiling them into a final video presentation.
REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA Shruti Gupta
This document discusses archaea, one of the three domains of life. It provides background information on archaea and describes some key findings, including that archaea were originally classified as bacteria but are now recognized as their own domain. The document focuses on specific types of archaea called the Archaea domain. It describes their environments, characteristics, main types, importance in studies, genome sequencing projects and analyses, and concludes by emphasizing the importance of cultivating new archaeal species and using cultivation-independent techniques to understand archaeal diversity.
The document outlines the AP Biology plans and lessons for January 30th through February 10th. It includes lessons on genetics of viruses and bacteria, a transcription and translation quiz, a paper plasmid lab, genetic engineering research, and preparation for and completion of a biotechnology lab. Time is also allotted for completing lab reports during ski week. Key concepts covered in the genetics lessons include viral structure and reproduction, the lytic and lysogenic cycles of bacteriophages, retroviruses like HIV, and hypotheses for the origin of viruses from mobile genetic elements in cells.
1. Hepatitis A virus (HAV) is a non-enveloped icosahedral virus in the Picornaviridae family that infects liver cells and is transmitted through the fecal-oral route.
2. HAV is resistant to detergents, acids, heat up to 60°C, and can survive for many months in water.
3. The hepatitis A vaccine provides lifelong immune protection against re-infection and is routinely recommended for children and high-risk adults.
This document provides an overview of recombinant DNA technology. It discusses the key discoveries that led to the development of this technology, such as Watson and Crick's discovery of DNA structure. It describes the goals and basic procedure of recombinant DNA technology, including isolating DNA, cutting DNA with restriction enzymes, joining DNA together, and amplifying the recombinant DNA in bacteria. It also discusses the enzymes, vectors like plasmids and phage, and techniques used in this technology, as well as its applications in fields like agriculture, medicine, and pharmacology.
Genetic engineering involves artificially manipulating genes through processes like removing a gene from one organism and inserting it into another. This allows combining DNA from different species. Key tools used are restriction enzymes to cut DNA at specific points and DNA ligase to join foreign DNA. Genetic engineering has applications like creating plants resistant to herbicides, producing human proteins in transgenic animals like sheep, and using bacteria to manufacture insulin. However, ethical issues surround releasing genetically modified organisms into the environment, their use as a food source, impact on animal welfare, and genetic engineering of humans.
This document discusses diabetes and how recombinant DNA technology can be used to produce insulin. It begins by outlining what diabetes is and how insulin regulates blood glucose levels. It then explains that recombinant DNA involves combining DNA from different species and inserting it into a host organism, like E. coli bacteria, to produce useful genetic combinations. The key steps are isolating the human insulin gene, inserting it into a bacterial plasmid using DNA-modifying enzymes and ligase, and transforming the bacteria so it can reproduce and produce large quantities of insulin.
This document discusses a motion graphic exploration project created by Kim Chambers. It contains images and a final video from the motion graphic exploration project. The project involved creating motion graphics and compiling them into a final video presentation.
REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA Shruti Gupta
This document discusses archaea, one of the three domains of life. It provides background information on archaea and describes some key findings, including that archaea were originally classified as bacteria but are now recognized as their own domain. The document focuses on specific types of archaea called the Archaea domain. It describes their environments, characteristics, main types, importance in studies, genome sequencing projects and analyses, and concludes by emphasizing the importance of cultivating new archaeal species and using cultivation-independent techniques to understand archaeal diversity.
The document outlines the AP Biology plans and lessons for January 30th through February 10th. It includes lessons on genetics of viruses and bacteria, a transcription and translation quiz, a paper plasmid lab, genetic engineering research, and preparation for and completion of a biotechnology lab. Time is also allotted for completing lab reports during ski week. Key concepts covered in the genetics lessons include viral structure and reproduction, the lytic and lysogenic cycles of bacteriophages, retroviruses like HIV, and hypotheses for the origin of viruses from mobile genetic elements in cells.
1. Hepatitis A virus (HAV) is a non-enveloped icosahedral virus in the Picornaviridae family that infects liver cells and is transmitted through the fecal-oral route.
2. HAV is resistant to detergents, acids, heat up to 60°C, and can survive for many months in water.
3. The hepatitis A vaccine provides lifelong immune protection against re-infection and is routinely recommended for children and high-risk adults.
This document provides an overview of recombinant DNA technology. It discusses the key discoveries that led to the development of this technology, such as Watson and Crick's discovery of DNA structure. It describes the goals and basic procedure of recombinant DNA technology, including isolating DNA, cutting DNA with restriction enzymes, joining DNA together, and amplifying the recombinant DNA in bacteria. It also discusses the enzymes, vectors like plasmids and phage, and techniques used in this technology, as well as its applications in fields like agriculture, medicine, and pharmacology.
Genetic engineering involves artificially manipulating genes through processes like removing a gene from one organism and inserting it into another. This allows combining DNA from different species. Key tools used are restriction enzymes to cut DNA at specific points and DNA ligase to join foreign DNA. Genetic engineering has applications like creating plants resistant to herbicides, producing human proteins in transgenic animals like sheep, and using bacteria to manufacture insulin. However, ethical issues surround releasing genetically modified organisms into the environment, their use as a food source, impact on animal welfare, and genetic engineering of humans.
This document discusses diabetes and how recombinant DNA technology can be used to produce insulin. It begins by outlining what diabetes is and how insulin regulates blood glucose levels. It then explains that recombinant DNA involves combining DNA from different species and inserting it into a host organism, like E. coli bacteria, to produce useful genetic combinations. The key steps are isolating the human insulin gene, inserting it into a bacterial plasmid using DNA-modifying enzymes and ligase, and transforming the bacteria so it can reproduce and produce large quantities of insulin.
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phyl...Jonathan Eisen
The document summarizes a presentation given by Jonathan Eisen from UC Davis on genomic evolvability and the origin of novelty. The presentation discussed how novelty originates in genomes, constraints on evolvability, and how genome dynamics and species evolution can help interpret the past and understand the present. It provided examples of using phylogenetic analysis to predict protein functions and discussed recently evolved new functions, uncharacterized genes, horizontal gene transfer, and gaps in knowledge.
Electron microscopes have higher magnification and resolution than light microscopes, allowing visualization at the nanometer level, but they are more expensive to purchase and operate. Light microscopes are cheaper but have lower magnification and resolution, only allowing visualization at the micron level. Both microscope types have advantages and disadvantages depending on the application and what is being viewed.
Barbituates like phenobarbital are central nervous system depressants that slow brain activity, while stimulants like amphetamines increase brain activity by increasing levels of neurotransmitters like dopamine and norepinephrine. Both classes of drugs work by altering brain chemistry but have opposite effects on mental state and behavior.
IOC 2008 - Lewis and Clark: Early Explorers in Virtual SchoolingMichael Barbour
Barbour, M. K. & Kinsella, J. (2008, February). Lewis and Clark: Early explorers in virtual schooling. Presentation at the Illinois Online Conference for Teaching and Learning, http://www.ilonlineconf.org/
The document summarizes the cultures of India's neighbors. It discusses that each neighboring country has a unique culture. It provides details on the Sherpa people from Nepal who often work as guides in the Himalayas. Bhutan's largest ethnic group originated from Tibet. Most people in Pakistan and Bangladesh practice Islam, while Hinduism is dominant in Nepal and Buddhism is the main religion in Bhutan and Sri Lanka. The document used images and websites as sources to discuss the religions and people of India's surrounding countries.
This document provides information for attendees of a music festival event. It includes details about transportation, meeting times and locations before the event starts, what to wear, what to bring, food and drink options, rules and guidelines during the event, and things to do after the event ends for the night. Attendees are encouraged to help promote the event and bring people to different areas. The document provides tips and reminders to ensure a safe and enjoyable experience for all.
This document discusses the history of music videos. It notes that while their origins date back further, music videos came into prominence in the 1980s when MTV's format was based around them. It describes some early examples like the Beatles' 1964 film A Hard Day's Night and Queen's "Bohemian Rhapsody" video. It also discusses how British TV show Top of the Pops began playing music videos in the late 1970s to boost song sales.
The document discusses portraits and obscuring portraits. Traditionally, portraits aimed to capture the likeness and personality of the subject. However, these portraits have been obscured, making the subjects unclear or vague. Several obscured portrait photos are then included.
The document provides instructions for students to learn classroom expressions. It lists expressions like "repeat after me", "listen", "open your book", "speak", "close your book", and "write the expressions on your paper". The teacher uses the expressions to guide student participation and engagement in the classroom.
This document provides information about greetings, introductions, and saying goodbye in Spanish. It includes the following:
- Common Spanish greetings like "Hola", "Buenos días", "Buenas tardes", and "Buenas noches"
- Ways to say goodbye such as "Adiós", "Hasta luego", and "Hasta la vista"
- How to ask and introduce someone's name
- Phrases for introducing a friend like "Este es mi amigo" and responses like "¡Mucho gusto!"
- An explanation of the traditional Spanish greeting of two kisses on the cheeks.
1) Light travels in straight lines and is a form of energy that moves much faster than sound.
2) Mirrors come in different shapes - plane, convex, and concave - and each type produces distinct image types, whether virtual or real.
3) Reflection occurs when light bounces off a surface, while refraction is when light changes speed as it passes from one medium to another, such as from water to air, causing the bending of light rays.
Greek myths were oral stories that helped explain the world to ancient Greeks. They featured gods and goddesses who lived on Mount Olympus and interacted with human mortals. The myths explained natural phenomena and human experiences through stories of creation, love, war, and the afterlife. Common myths featured Zeus and his family of gods, heroes like Heracles and Odysseus, and dangerous monsters. References to Greek myths are still found today to help understand the ancient world.
Piri Thomas was a Puerto Rican-American writer who grew up in New York City. He became involved with drugs and crime and was imprisoned. While in prison, he discovered his talent for writing. His works celebrate the strength and determination of Puerto Rican and African-American communities in NYC as he grew up facing new responsibilities.
This document discusses using Creative Commons licenses for design projects. It provides examples of design projects that have used various Creative Commons licenses, including projects related to photography, illustrations, software programs, and more. The document encourages readers to remix and reuse works licensed under Creative Commons to build their own designs and projects. It concludes by providing contact information for Creative Commons and links to additional resources.
The document appears to be a biography or retrospective of an individual named Daron Bruce. It includes photos from his childhood, school years, performances in musical theater productions, and time as a teacher. The photos are not viewable as the document notes QuickTime and an uncompressed TIFF decompressor are needed. It highlights places he lived, schools he attended, shows he performed in, and colleagues from his career.
The document appears to be a photo biography of Daron Bruce. It shows pictures from his childhood in Centralia, Illinois through various school and community theater productions. The pictures document his time at Centralia schools, Southern Illinois University, and roles in musicals at different theaters across Tennessee and Illinois from the 1980s to 2011.
The document provides instructions for auditioning for the Real World TV show. It outlines the age requirements, information needed in the application, and suggests filming an audition tape showing daily activities and partying to demonstrate being a versatile person. A storyboard outlines filming oneself describing basic info, then showing footage and pictures of various daily activities and partying to "sell oneself" for the reality TV show role.
The document provides instructions for auditioning for The Real World TV show. It outlines the age requirements, contact information needed for the application, and suggests including a brief bio and footage showing one's versatility and love of partying in the audition tape. Storyboards included depict filming introductory information and showing daily activities to "sell oneself" for the reality TV show role.
The target audience for the film is teenagers aged 16-21. While the film will attract both male and female viewers, the storyline focuses on a teenager seeking fame and popularity, making it predominantly appealing to female viewers. Examples of other films popular with this target audience include American Pie and Superbad. Extensive research was done on these types of "coming of age" comedy films and the target demographic to ensure this film directly substitutes and appeals to 16-21 year old viewers.
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phyl...Jonathan Eisen
The document summarizes a presentation given by Jonathan Eisen from UC Davis on genomic evolvability and the origin of novelty. The presentation discussed how novelty originates in genomes, constraints on evolvability, and how genome dynamics and species evolution can help interpret the past and understand the present. It provided examples of using phylogenetic analysis to predict protein functions and discussed recently evolved new functions, uncharacterized genes, horizontal gene transfer, and gaps in knowledge.
Electron microscopes have higher magnification and resolution than light microscopes, allowing visualization at the nanometer level, but they are more expensive to purchase and operate. Light microscopes are cheaper but have lower magnification and resolution, only allowing visualization at the micron level. Both microscope types have advantages and disadvantages depending on the application and what is being viewed.
Barbituates like phenobarbital are central nervous system depressants that slow brain activity, while stimulants like amphetamines increase brain activity by increasing levels of neurotransmitters like dopamine and norepinephrine. Both classes of drugs work by altering brain chemistry but have opposite effects on mental state and behavior.
IOC 2008 - Lewis and Clark: Early Explorers in Virtual SchoolingMichael Barbour
Barbour, M. K. & Kinsella, J. (2008, February). Lewis and Clark: Early explorers in virtual schooling. Presentation at the Illinois Online Conference for Teaching and Learning, http://www.ilonlineconf.org/
The document summarizes the cultures of India's neighbors. It discusses that each neighboring country has a unique culture. It provides details on the Sherpa people from Nepal who often work as guides in the Himalayas. Bhutan's largest ethnic group originated from Tibet. Most people in Pakistan and Bangladesh practice Islam, while Hinduism is dominant in Nepal and Buddhism is the main religion in Bhutan and Sri Lanka. The document used images and websites as sources to discuss the religions and people of India's surrounding countries.
This document provides information for attendees of a music festival event. It includes details about transportation, meeting times and locations before the event starts, what to wear, what to bring, food and drink options, rules and guidelines during the event, and things to do after the event ends for the night. Attendees are encouraged to help promote the event and bring people to different areas. The document provides tips and reminders to ensure a safe and enjoyable experience for all.
This document discusses the history of music videos. It notes that while their origins date back further, music videos came into prominence in the 1980s when MTV's format was based around them. It describes some early examples like the Beatles' 1964 film A Hard Day's Night and Queen's "Bohemian Rhapsody" video. It also discusses how British TV show Top of the Pops began playing music videos in the late 1970s to boost song sales.
The document discusses portraits and obscuring portraits. Traditionally, portraits aimed to capture the likeness and personality of the subject. However, these portraits have been obscured, making the subjects unclear or vague. Several obscured portrait photos are then included.
The document provides instructions for students to learn classroom expressions. It lists expressions like "repeat after me", "listen", "open your book", "speak", "close your book", and "write the expressions on your paper". The teacher uses the expressions to guide student participation and engagement in the classroom.
This document provides information about greetings, introductions, and saying goodbye in Spanish. It includes the following:
- Common Spanish greetings like "Hola", "Buenos días", "Buenas tardes", and "Buenas noches"
- Ways to say goodbye such as "Adiós", "Hasta luego", and "Hasta la vista"
- How to ask and introduce someone's name
- Phrases for introducing a friend like "Este es mi amigo" and responses like "¡Mucho gusto!"
- An explanation of the traditional Spanish greeting of two kisses on the cheeks.
1) Light travels in straight lines and is a form of energy that moves much faster than sound.
2) Mirrors come in different shapes - plane, convex, and concave - and each type produces distinct image types, whether virtual or real.
3) Reflection occurs when light bounces off a surface, while refraction is when light changes speed as it passes from one medium to another, such as from water to air, causing the bending of light rays.
Greek myths were oral stories that helped explain the world to ancient Greeks. They featured gods and goddesses who lived on Mount Olympus and interacted with human mortals. The myths explained natural phenomena and human experiences through stories of creation, love, war, and the afterlife. Common myths featured Zeus and his family of gods, heroes like Heracles and Odysseus, and dangerous monsters. References to Greek myths are still found today to help understand the ancient world.
Piri Thomas was a Puerto Rican-American writer who grew up in New York City. He became involved with drugs and crime and was imprisoned. While in prison, he discovered his talent for writing. His works celebrate the strength and determination of Puerto Rican and African-American communities in NYC as he grew up facing new responsibilities.
This document discusses using Creative Commons licenses for design projects. It provides examples of design projects that have used various Creative Commons licenses, including projects related to photography, illustrations, software programs, and more. The document encourages readers to remix and reuse works licensed under Creative Commons to build their own designs and projects. It concludes by providing contact information for Creative Commons and links to additional resources.
The document appears to be a biography or retrospective of an individual named Daron Bruce. It includes photos from his childhood, school years, performances in musical theater productions, and time as a teacher. The photos are not viewable as the document notes QuickTime and an uncompressed TIFF decompressor are needed. It highlights places he lived, schools he attended, shows he performed in, and colleagues from his career.
The document appears to be a photo biography of Daron Bruce. It shows pictures from his childhood in Centralia, Illinois through various school and community theater productions. The pictures document his time at Centralia schools, Southern Illinois University, and roles in musicals at different theaters across Tennessee and Illinois from the 1980s to 2011.
The document provides instructions for auditioning for the Real World TV show. It outlines the age requirements, information needed in the application, and suggests filming an audition tape showing daily activities and partying to demonstrate being a versatile person. A storyboard outlines filming oneself describing basic info, then showing footage and pictures of various daily activities and partying to "sell oneself" for the reality TV show role.
The document provides instructions for auditioning for The Real World TV show. It outlines the age requirements, contact information needed for the application, and suggests including a brief bio and footage showing one's versatility and love of partying in the audition tape. Storyboards included depict filming introductory information and showing daily activities to "sell oneself" for the reality TV show role.
The target audience for the film is teenagers aged 16-21. While the film will attract both male and female viewers, the storyline focuses on a teenager seeking fame and popularity, making it predominantly appealing to female viewers. Examples of other films popular with this target audience include American Pie and Superbad. Extensive research was done on these types of "coming of age" comedy films and the target demographic to ensure this film directly substitutes and appeals to 16-21 year old viewers.
Similar to Jonathan Eisen talk on "Genomic Encyclopedia" at Lake Arrowhead Small Genomes Meeting 2008 (20)
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Talk by Jonathan Eisen for LAMG2022 meetingJonathan Eisen
The document discusses the history of the Lake Arrowhead Microbial Genomes (LAMG) conference. It reveals that LAMG2020 was cancelled due to a secret plan by organizers who formed an "anti-karyote society" that hates eukaryotes. The meeting was to be renamed the "Big, Large, Enormous" meeting of the Lake Arrowhead Big Large Enormous Anti-Karyote Society. The document also hints that several past LAMG speakers have made cryptic comments indicating involvement in a conspiracy surrounding the conference.
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
Phylogenetic and Phylogenomic Approaches to the Study of Microbes and Microbi...Jonathan Eisen
The document discusses Jonathan Eisen's work as a microbiology professor at UC Davis. It provides an overview of his research topics, which include microbial phylogenomics and evolvability, phylogenetic methods and tools, and using phylogenomics to study microbial communities and interactions between microbes and hosts under stress. The document also acknowledges collaborators and funding sources for Eisen's research over the years.
This document summarizes a class on detecting, quantifying, and tracking variations of SARS-CoV-2 RNA from COVID-19 samples. It discusses using quantitative RT-PCR (qRT-PCR) to detect and measure viral RNA levels in samples. Sequencing is used to identify variations in the viral genome over time, and online tools like Nextstrain allow viewing the evolution and global transmission of variants. Genotyping assays are also described that can rapidly screen samples for known single nucleotide variations during PCR.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 8 - COVID RNA DetectionJonathan Eisen
This document summarizes a class on SARS-CoV-2 RNA detection, quantification, and variation. It discusses how qRT-PCR is used to detect and quantify the virus by amplifying and detecting viral RNA. It also covers sequencing to identify variants, how variants evolve over time, and genotyping assays that can screen samples for known single nucleotide variations. Nextstrain and other online tools are presented that use sequencing data to analyze viral phylogenies, track variant distributions globally, and visualize genetic variations across the SARS-CoV-2 genome.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms for those who already suffer from conditions like depression and anxiety.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 5 - COVID VaccinesJonathan Eisen
The document discusses a class on COVID-19 vaccines. It covers topics like vaccine development, current candidates, delivery challenges, and comparisons between vaccines. Moderna and Pfizer mRNA vaccines are highlighted as being similar but having some differences in mRNA region, nanoparticle structure/synthesis, dosage amount, and storage temperature requirements. Other vaccines discussed include Novavax using spike protein nanoparticles, and AstraZeneca and Johnson & Johnson using DNA for spike protein delivered by a modified virus.
EVE198 Winter2020 Class 9 - COVID TransmissionJonathan Eisen
This document discusses modes of SARS-CoV-2 transmission including droplets, aerosols, and surfaces. It emphasizes that surfaces are not as big a risk as initially thought. It provides guidance on limiting transmission from different modes such as distancing, masks, washing hands, cleaning surfaces, and improving ventilation. The focus in 2021 is on droplets and aerosols rather than surfaces.
EVE198 Fall2020 "Covid Mass Testing" Class 8 VaccinesJonathan Eisen
This document discusses a class on vaccines for COVID-19. It covers topics like vaccine development, current candidate vaccines, challenges with vaccine distribution, and how vaccines are being assessed for safety, effectiveness, costs and production feasibility. Over 100 vaccine candidates are in development using platforms like DNA, RNA, viral vectors and inactivated viruses. Efforts like Operation Warp Speed are coordinating development of nucleic acid, viral vector and protein subunit vaccines. Distribution challenges include vaccine production, storage and logistics, number of doses required, and overcoming vaccine nationalism and hesitancy.
EVE198 Fall2020 "Covid Mass Testing" Class 2: Viruses, COIVD and TestingJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Fall2020 "Covid Mass Testing" Class 1 IntroductionJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
5-hydroxytryptamine or 5-HT or Serotonin is a neurotransmitter that serves a range of roles in the human body. It is sometimes referred to as the happy chemical since it promotes overall well-being and happiness.
It is mostly found in the brain, intestines, and blood platelets.
5-HT is utilised to transport messages between nerve cells, is known to be involved in smooth muscle contraction, and adds to overall well-being and pleasure, among other benefits. 5-HT regulates the body's sleep-wake cycles and internal clock by acting as a precursor to melatonin.
It is hypothesised to regulate hunger, emotions, motor, cognitive, and autonomic processes.
“Psychiatry and the Humanities”: An Innovative Course at the University of Mo...Université de Montréal
“Psychiatry and the Humanities”: An Innovative Course at the University of Montreal Expanding the medical model to embrace the humanities. Link: https://www.psychiatrictimes.com/view/-psychiatry-and-the-humanities-an-innovative-course-at-the-university-of-montreal
Computer in pharmaceutical research and development-Mpharm(Pharmaceutics)MuskanShingari
Statistics- Statistics is the science of collecting, organizing, presenting, analyzing and interpreting numerical data to assist in making more effective decisions.
A statistics is a measure which is used to estimate the population parameter
Parameters-It is used to describe the properties of an entire population.
Examples-Measures of central tendency Dispersion, Variance, Standard Deviation (SD), Absolute Error, Mean Absolute Error (MAE), Eigen Value
Summer is a time for fun in the sun, but the heat and humidity can also wreak havoc on your skin. From itchy rashes to unwanted pigmentation, several skin conditions become more prevalent during these warmer months.
- Video recording of this lecture in English language: https://youtu.be/Pt1nA32sdHQ
- Video recording of this lecture in Arabic language: https://youtu.be/uFdc9F0rlP0
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
Osvaldo Bernardo Muchanga-GASTROINTESTINAL INFECTIONS AND GASTRITIS-2024.pdfOsvaldo Bernardo Muchanga
GASTROINTESTINAL INFECTIONS AND GASTRITIS
Osvaldo Bernardo Muchanga
Gastrointestinal Infections
GASTROINTESTINAL INFECTIONS result from the ingestion of pathogens that cause infections at the level of this tract, generally being transmitted by food, water and hands contaminated by microorganisms such as E. coli, Salmonella, Shigella, Vibrio cholerae, Campylobacter, Staphylococcus, Rotavirus among others that are generally contained in feces, thus configuring a FECAL-ORAL type of transmission.
Among the factors that lead to the occurrence of gastrointestinal infections are the hygienic and sanitary deficiencies that characterize our markets and other places where raw or cooked food is sold, poor environmental sanitation in communities, deficiencies in water treatment (or in the process of its plumbing), risky hygienic-sanitary habits (not washing hands after major and/or minor needs), among others.
These are generally consequences (signs and symptoms) resulting from gastrointestinal infections: diarrhea, vomiting, fever and malaise, among others.
The treatment consists of replacing lost liquids and electrolytes (drinking drinking water and other recommended liquids, including consumption of juicy fruits such as papayas, apples, pears, among others that contain water in their composition).
To prevent this, it is necessary to promote health education, improve the hygienic-sanitary conditions of markets and communities in general as a way of promoting, preserving and prolonging PUBLIC HEALTH.
Gastritis and Gastric Health
Gastric Health is one of the most relevant concerns in human health, with gastrointestinal infections being among the main illnesses that affect humans.
Among gastric problems, we have GASTRITIS AND GASTRIC ULCERS as the main public health problems. Gastritis and gastric ulcers normally result from inflammation and corrosion of the walls of the stomach (gastric mucosa) and are generally associated (caused) by the bacterium Helicobacter pylor, which, according to the literature, this bacterium settles on these walls (of the stomach) and starts to release urease that ends up altering the normal pH of the stomach (acid), which leads to inflammation and corrosion of the mucous membranes and consequent gastritis or ulcers, respectively.
In addition to bacterial infections, gastritis and gastric ulcers are associated with several factors, with emphasis on prolonged fasting, chemical substances including drugs, alcohol, foods with strong seasonings including chilli, which ends up causing inflammation of the stomach walls and/or corrosion. of the same, resulting in the appearance of wounds and consequent gastritis or ulcers, respectively.
Among patients with gastritis and/or ulcers, one of the dilemmas is associated with the foods to consume in order to minimize the sensation of pain and discomfort.
Breast cancer: Post menopausal endocrine therapyDr. Sumit KUMAR
Breast cancer in postmenopausal women with hormone receptor-positive (HR+) status is a common and complex condition that necessitates a multifaceted approach to management. HR+ breast cancer means that the cancer cells grow in response to hormones such as estrogen and progesterone. This subtype is prevalent among postmenopausal women and typically exhibits a more indolent course compared to other forms of breast cancer, which allows for a variety of treatment options.
Diagnosis and Staging
The diagnosis of HR+ breast cancer begins with clinical evaluation, imaging, and biopsy. Imaging modalities such as mammography, ultrasound, and MRI help in assessing the extent of the disease. Histopathological examination and immunohistochemical staining of the biopsy sample confirm the diagnosis and hormone receptor status by identifying the presence of estrogen receptors (ER) and progesterone receptors (PR) on the tumor cells.
Staging involves determining the size of the tumor (T), the involvement of regional lymph nodes (N), and the presence of distant metastasis (M). The American Joint Committee on Cancer (AJCC) staging system is commonly used. Accurate staging is critical as it guides treatment decisions.
Treatment Options
Endocrine Therapy
Endocrine therapy is the cornerstone of treatment for HR+ breast cancer in postmenopausal women. The primary goal is to reduce the levels of estrogen or block its effects on cancer cells. Commonly used agents include:
Selective Estrogen Receptor Modulators (SERMs): Tamoxifen is a SERM that binds to estrogen receptors, blocking estrogen from stimulating breast cancer cells. It is effective but may have side effects such as increased risk of endometrial cancer and thromboembolic events.
Aromatase Inhibitors (AIs): These drugs, including anastrozole, letrozole, and exemestane, lower estrogen levels by inhibiting the aromatase enzyme, which converts androgens to estrogen in peripheral tissues. AIs are generally preferred in postmenopausal women due to their efficacy and safety profile compared to tamoxifen.
Selective Estrogen Receptor Downregulators (SERDs): Fulvestrant is a SERD that degrades estrogen receptors and is used in cases where resistance to other endocrine therapies develops.
Combination Therapies
Combining endocrine therapy with other treatments enhances efficacy. Examples include:
Endocrine Therapy with CDK4/6 Inhibitors: Palbociclib, ribociclib, and abemaciclib are CDK4/6 inhibitors that, when combined with endocrine therapy, significantly improve progression-free survival in advanced HR+ breast cancer.
Endocrine Therapy with mTOR Inhibitors: Everolimus, an mTOR inhibitor, can be added to endocrine therapy for patients who have developed resistance to aromatase inhibitors.
Chemotherapy
Chemotherapy is generally reserved for patients with high-risk features, such as large tumor size, high-grade histology, or extensive lymph node involvement. Regimens often include anthracyclines and taxanes.
Giloy in Ayurveda - Classical Categorization and SynonymsPlanet Ayurveda
Giloy, also known as Guduchi or Amrita in classical Ayurvedic texts, is a revered herb renowned for its myriad health benefits. It is categorized as a Rasayana, meaning it has rejuvenating properties that enhance vitality and longevity. Giloy is celebrated for its ability to boost the immune system, detoxify the body, and promote overall wellness. Its anti-inflammatory, antipyretic, and antioxidant properties make it a staple in managing conditions like fever, diabetes, and stress. The versatility and efficacy of Giloy in supporting health naturally highlight its importance in Ayurveda. At Planet Ayurveda, we provide a comprehensive range of health services and 100% herbal supplements that harness the power of natural ingredients like Giloy. Our products are globally available and affordable, ensuring that everyone can benefit from the ancient wisdom of Ayurveda. If you or your loved ones are dealing with health issues, contact Planet Ayurveda at 01725214040 to book an online video consultation with our professional doctors. Let us help you achieve optimal health and wellness naturally.
How to Control Your Asthma Tips by gokuldas hospital.Gokuldas Hospital
Respiratory issues like asthma are the most sensitive issue that is affecting millions worldwide. It hampers the daily activities leaving the body tired and breathless.
The key to a good grip on asthma is proper knowledge and management strategies. Understanding the patient-specific symptoms and carving out an effective treatment likewise is the best way to keep asthma under control.
Nutritional deficiency Disorder are problems in india.
It is very important to learn about Indian child's nutritional parameters as well the Disease related to alteration in their Nutrition.
The Children are very vulnerable to get affected with respiratory disease.
In our country, the respiratory Disease conditions are consider as major cause for mortality and Morbidity in Child.
STUDIES IN SUPPORT OF SPECIAL POPULATIONS: GERIATRICS E7shruti jagirdar
Unit 4: MRA 103T Regulatory affairs
This guideline is directed principally toward new Molecular Entities that are
likely to have significant use in the elderly, either because the disease intended
to be treated is characteristically a disease of aging ( e.g., Alzheimer's disease) or
because the population to be treated is known to include substantial numbers of
geriatric patients (e.g., hypertension).
Nano-gold for Cancer Therapy chemistry investigatory projectSIVAVINAYAKPK
chemistry investigatory project
The development of nanogold-based cancer therapy could revolutionize oncology by providing a more targeted, less invasive treatment option. This project contributes to the growing body of research aimed at harnessing nanotechnology for medical applications, paving the way for future clinical trials and potential commercial applications.
Cancer remains one of the leading causes of death worldwide, prompting the need for innovative treatment methods. Nanotechnology offers promising new approaches, including the use of gold nanoparticles (nanogold) for targeted cancer therapy. Nanogold particles possess unique physical and chemical properties that make them suitable for drug delivery, imaging, and photothermal therapy.
Jonathan Eisen talk on "Genomic Encyclopedia" at Lake Arrowhead Small Genomes Meeting 2008
1. A Genomic Encyclopedia of
Bacteria and Archaea
(GEBA)
Jonathan A. Eisen
U. C. Davis and J. G. I.
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2. Outline
• Background
– Why history matters
– Gaps in available genomes
• The GEBA pilot project
• Future needs
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3. The Tree of Life
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4. Famous Arrowhead 2004 Quotes
• Space-time continuum of genes and genomes
• Gene sequences are the wormhole that allows
one to tunnel into the past
• The human mind can conceive of things with
no basis in physical reality
• Thoughts can go faster than the speed of light
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5. Famous Arrowhead Quotes 2006
• Publications, student degrees, etc.
• Not trying to say anything bad about
anyone
• The human guts are a real milieu
• Where’s you evening gown?
• You better kiss everybody
• This is how you do metagenomics on 50
dollars, and that’s Canadian dollars
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6. QuickTime™ and a
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7. QuickTime™ and a
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8. Major Microbial Sequencing Efforts
• Coordinated, top-down efforts
– Fungal Genome Initiative (Broad/Whitehead)
– Gordon and Betty Moore Foundation Marine Microbial Genome
Sequencing Project
– Sanger Center Pathogen Sequencing Unit
– NHGRI Human Gut Microbiome Project
– NIH Human Microbiome Program
• White paper or grant systems
– NIAID Microbial Sequencing Centers
– DOE/JGI Community Sequencing Program
– DOE/JGI BER Sequencing Program
– NSF/USDA Microbial Genome Sequencing
• Covers lots of ground and biological diversity
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9. The Tree of Life
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10. The Tree is not Happy
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11. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides bacteria
Chlorobi
Fibrobacteres
Marine GroupA
WS3
Gemmimonas
Firmicutes
Fusobacteria
Actinobacteria
OP9
Cyanobacteria
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroflexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquificae
Thermudesulfobacteria
Thermotogae
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Hugenholtz, 2002
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12. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA • Genome
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria three phyla
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroflexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquificae
Thermudesulfobacteria
Thermotogae
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Hugenholtz, 2002
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13. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA • Genome
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria three phyla
Synergistes
Deferribacteres
Chrysiogenetes • Some other
NKB19
Verrucomicrobia
Chlamydia phyla are
OP3
Planctomycetes
Spriochaetes
only sparsely
Coprothmermobacter
OP10 sampled
Thermomicrobia
Chloroflexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquificae
Thermudesulfobacteria
Thermotogae
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Hugenholtz, 2002
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14. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA
• Genome
WS3
Gemmimonas sequences are
Firmicutes
Fusobacteria mostly from
Actinobacteria
OP9
Cyanobacteria
three phyla
Synergistes
Deferribacteres
Chrysiogenetes
• Some other
NKB19
Verrucomicrobia
Chlamydia
phyla are
OP3
Planctomycetes only sparsely
Spriochaetes
Coprothmermobacter
OP10
sampled
Thermomicrobia
Chloroflexi
TM7
• Same trend in
Deinococcus-Thermus
Dictyoglomus
Aquificae
Archaea,
Thermudesulfobacteria
Thermotogae Eukaryotes
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15. Need for Tree Guidance Well Established
• Common approach within some eukaryotic groups
– NHGRI animal projects
– FGI at Whitehead
– Plant sequencing at JGI
• Phylogenetic gaps in bacterial and archaeal projects
commonly lamented in literature
• Many small projects funded to fill in some gaps
– DOE/TIGR Sequencing
– Multiple CSP projects
– Multiple NSF/USDA projects
– Private projects (e.g., Integrated Genomics, Diversa)
– TIGR (Eisen, Ward) Bacterial Tree of Life Project
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16. Why Increase Taxonomic Coverage?
• Mechanisms of diversification
• Gene discovery
• Annotation, functional prediction
• Metagenomic analysis
• Species phylogeny and classification
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17. Proteobacteria
• Eisen-Ward TM6 • At least 40
OS-K
NSF Tree of Acidobacteria
Termite Group phyla of
OP8
Life Project Nitrospira
Bacteroides
bacteria
Chlorobi
• A genome Fibrobacteres
Marine GroupA
• Genome
WS3
from each of Gemmimonas sequences are
Firmicutes
eight phyla Fusobacteria mostly from
Actinobacteria
OP9
Cyanobacteria
three phyla
Synergistes
Deferribacteres
Chrysiogenetes
• Some other
NKB19
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Verrucomicrobia
Chlamydia
phyla are only
OP3
Planctomycetes sparsely
Spriochaetes
Coprothmermobacter
OP10
sampled
Thermomicrobia
Based on Chloroflexi
TM7
• Solution I:
Hugenholtz, Deinococcus-Thermus
Dictyoglomus sequence more
2002 Aquificae
Thermudesulfobacteria
Thermotogae phyla
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18. The Tree of Life is Still Angry
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19. Within Phyla Diversity Immense
• Each phyla represents billions of years of
evolution
• Some have hundreds of major lineages,
most with no genomes
• Need to sample within phyla too
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20. Major Lineages of Actinobacteria
2.5.1 Acidimicrobidae
2.5.1.1 Unclassified
2.5.1.2 "Microthrixineae
2.5.1.3 Acidimicrobineae
2.5.1.4 BD2-10
2.5.1.5 EB1017
2.5.2 Actinobacteridae
2.5.2.1 Unclassified
2.5.2.10 Ellin306/WR160
2.5.2.11 Ellin5012
2.5.2.12 Ellin5034
2.5.2.13 Frankineae
2.5.2.14 Glycomyces
2.5.2.15 Intrasporangiaceae
2.5.2.16 Kineosporiaceae
2.5.2.17 Microbacteriaceae
2.5.2.18 Micrococcaceae
2.5.2.19 Micromonosporaceae
2.5.2.2 Actinomyces
2.5.2.20 Propionibacterineae
2.5.2.21 Pseudonocardiaceae
2.5.2.22 Streptomycineae
2.5.2.23 Streptosporangineae
2.5.2.3 Actinomycineae
2.5.2.4 Actinosynnemataceae
2.5.2.5 Bifidobacteriaceae
2.5.2.6 Brevibacteriaceae
2.5.2.7 Cellulomonadaceae
2.5.2.8 Corynebacterineae
2.5.2.9 Dermabacteraceae
2.5.3 Coriobacteridae
2.5.3.1 Unclassified
2.5.3.2 Atopobiales
2.5.3.3 Coriobacteriales
2.5.3.4 Eggerthellales
2.5.4 OPB41
2.5.5 PK1
2.5.6 Rubrobacteridae
2.5.6.1 Unclassified
2.5.6.2 "Thermoleiphilaceae QuickTime™ and a
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2.5.6.3 MC47
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2.5.6.4 Rubrobacteraceae
22. Proteobacteria
TM6
OS-K
• At least 100 phyla of
Acidobacteria
Termite Group bacteria
OP8
Nitrospira
Bacteroides • Genome sequences are
Chlorobi
Fibrobacteres
Marine GroupA mostly from three phyla
WS3
Gemmimonas
Firmicutes
• Most phyla with cultured
Fusobacteria
Actinobacteria
species are sparsely
OP9
Cyanobacteria
Synergistes
sampled
Deferribacteres
Chrysiogenetes
NKB19
• Lineages with no cultured
Verrucomicrobia
Chlamydia
OP3
taxa even more poorly
Planctomycetes
Spriochaetes sampled
Coprothmermobacter
OP10
Thermomicrobia • Solution - use tree to really
Chloroflexi
TM7
Deinococcus-Thermus
fill gaps
Dictyoglomus
Aquificae
Well sampled phyla
Thermudesulfobacteria
Thermotogae
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23. QuickTime™ and a
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24. GEBA Pilot Project: Components
• Project management (David Bruce, Lynne Goodwin et al)
• Selection of strains (Phil Hugenholtz, Nikos Kyrpides,
Jonathan Eisen)
• Culture collection and DNA prep (DSMZ, Hans-Peter
Klenk)
• Libraries and DNA (Eileen Dalin et al.)
• Sequencing and closure (Susan Lucas, Alla Lapidus et al.)
• Annotation and database needs (Nikos Kyrpides)
• Analysis (Dongying Wu, Martin Wu, Jenna Morgan,
Victor Kunin, Marcel Huntemann, Neil Rawlings, Ian
Paulsen, Gary Xie, Patrick Chain, Patrik D’Haeseleer,
Sean Hooper, Iain Anderson, Mavrommatis Kostas)
• Adopt a microbe education project (Cheryl Kerfeld)
• Outreach (David Gilbert)
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25. GEBA Pilot I:
Identifying Lineages without
Genomes
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26. QuickTime™ and a
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27. QuickTime™ and a
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28. QuickTime™ and a
TIFFQuickTime™ and a
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are needed to see this picture.
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29. GEBA Pilot II:
Selecting Targets
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30. Key Criteria
• Phylogenetic novelty
– Working from top of tree down
– Also selected one phylum to fill in in more detail -
Actinobacteria
• Culturable
– Type strain preferred is all else equal
• DOE mission relevance
• Ready availability to us and community
– Of strain
– Of DNA
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31. GEBA Pilot III:
Partnership with DSMZ
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32. GEBA Biggest Challenge:
Getting DNA
• Getting quality DNA is biggest bottleneck
• Decided to test as part of the GEBA pilot
the possibility of getting DNA directly from
culture collections
• DSMZ offered to do for free
• ATCC is doing a small number for a fee
• Working with other culture collections
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33. QuickTime™ and a
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34. Quantification gel of the genomic DNA isolated from Microorganisms
Microorganisms
Conexibacter woesei (DSM 14684T)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Lane 1: c(λ-Marker)= 15 ng Lane 9: DSM 18081, Patulibacter minatonensis
Lane 2: c(λ-Marker)= 30 ng Lane 10: DSM 14684, Conexibacter woesei
Lane 3: c(λ-Marker)= 50 ng Lane 11: DSM 11002, Dethiosulfovibrio peptidovorans
Lane 4: DNA Molecular Weight Marker II (Roche Lane 12: DSM 11551, Halogeometricum borinquense
236250) Lane 13: DNA Molecular Weight Marker II (Roche
Lane 5: DSM 13279, Collinsella stercoris 236250)
Lane 6: DSM 43043, Intrasporangium calvum Lane 14: c(λ-Marker)= 125 ng
Lane 7: DSM 18053, Dyadobacter fermentans Lane 15: c(λ-Marker)= 250 ng
Lane 8: DSM 20476, Slackia heliotrinireducens Lane 16: c(λ-Marker)= 500 ng
Conexibacter woesei (DSM 14684T) was taken from the German Collection of Microorganisms
and Cell Cultures (DSMZ). The genomic DNA was isolated using the Qiagen Genomic 500 DNA
Kit (Qiagen 10262). The genomic DNA was 10-250 kb in size as determined by Pulsed Field Gel
Electrophoresis (PFGE). The bulk of DNA had a size of 50-250 kb (see attached PFGE image).
The DNA concentration is 500 ng/µl as estimated from the gel. Spectrophotometric measurements
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35. GEBA Pilot IV:
Sequencing Progress
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36. QuickTime™ and a
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37. GEBA Pilot Target List
35
30
25
20
15
# of Genomes
10
5
0
B: Aquificae
B: Chloroflexi Deinococci Firmicutes
B: B:
B: Bacteroidetes B: Fusobacteria B: Spirochaetes Halobacteria Thermococci
A: A: Archaeoglobi Thermoprotei
A: A:
B: AminanaerobiaDeferribacteres
B: B: Deferribacteres B: Planctomycetes A: Methanobacteria
B: Haloanaerobiales Thermovenabulae
B: Thermodesulfobia Methanomicrobia
B: A:
B: Gemmatimonadetes
B: Delta Proteobacteria
B: Epsilon B: Gamma Proteobacteria
Proteobacteria B: Thermodesulfobacteria
B: Actinobacteria (High GC)
Phyla
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38. GEBA Pilot Status 5-12-08
35
30
25
Closed
20
Post Draft
Production
15 Library
Awaiting Material
# of Genomes
10
5
0
B: Aquificae B: Firmicutes
B: Chloroflexi
B: Deinococci
B: Bacteroidetes A: HalobacteriaA:
A: Thermococci
B: Fusobacteria B: Spirochaetes A: ArchaeoglobiThermoprotei
B: Aminanaerobia Deferribacteres
B: Deferribacteres
B: B: Planctomycetes
B: Haloanaerobiales A: A: Methanomicrobia
Methanobacteria
B: Thermodesulfobia
B: Thermovenabulae
B: Gemmatimonadetes
B: Delta Proteobacteria
B: Epsilon Proteobacteria B: Thermodesulfobacteria
B: Gamma Proteobacteria
B: Actinobacteria (High GC)
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39. Non Active Projects
16
14
12
10
Abandoned
8 On Hold
# of6Genomes
4
2
0
B: Aquificae
B: ChloroflexiDeinococciFirmicutes
B: B:
B: Bacteroidetes B: Fusobacteria B: Spirochaetes Halobacteria A: Thermoprotei
A: A: Archaeoglobi
A: Thermococci
B: Aminanaerobia Deferribacteres
B: Deferribacteres
B: B: Planctomycetes A: Methanobacteria
B: HaloanaerobialesThermovenabulae
B: ThermodesulfobiaMethanomicrobia
B: A:
B: Gemmatimonadetes
B: Delta Proteobacteria
B: EpsilonB: Gamma Proteobacteria
Proteobacteria B: Thermodesulfobacteria
B: Actinobacteria (High GC)
Phyla
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40. GEBA Pilot Data Release
30
25
20
15
# of Genomes
10
5
0
B: Aquificae
B: Chloroflexi Deinococci Firmicutes
B: B:
B: Bacteroidetes B: Fusobacteria B: Spirochaetes A: Halobacteria A: Thermococci
A: Archaeoglobi A: Thermoprotei
B: Aminanaerobia Deferribacteres
B: B: Deferribacteres B: Planctomycetes A: Methanobacteria
B: HaloanaerobialesB: Thermovenabulae
B: Thermodesulfobia A: Methanomicrobia
B: Delta Proteobacteria Gemmatimonadetes
B:
B: Epsilon Proteobacteria B: Thermodesulfobacteria
B: Gamma Proteobacteria
B: Actinobacteria (High GC)
Phyla
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41. Progress Report
GEBA Status 5-12-08
Closed
3%
Awaiting Material
26%
Post Draft
51%
Library
9%
Production
11%
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42. Progress
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43. Data
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45. GEBA Pilot V:
Benefit?
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46. Why Increase Taxonomic Coverage?
• Mechanisms of diversification
• Gene discovery
• Annotation, functional prediction
• Metagenomic analysis
• Species phylogeny and classification
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47. Value of 100 diverse genomes I:
Gene discovery
• Gene families
– Will compare and contrast gene family
diversity in these genomes versus random
samples of previous genomes
– Will assess rate of gene family discovery and
whether / how much it is diminishing
• Specific examples of novelty
– Focusing on DOE mission areas
– Do we find novel forms of hydrogenases,
cellulases, C-fixation, etc
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48. Value of 100 diverse genomes II:
Annotation
• Ortholog identification
– Filling in gaps will help identify orthologs between species
– Diverse GC content and amino acid composition should also
improve ortholog identification
• Examination of the rate of hypothetical protein conversion
to “known” proteins
• Non-homology functional prediction should improve
greatly
– Phylogenetic profiling
– Rosetta Stone domain sharing
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49. QuickTime™ and a
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Based on Wu et al. 2005
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50. QuickTime™ and a
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51. Value of 100 diverse genomes III:
Metagenomics
• More diverse genomes should improve anchoring
and binning of all metagenomic data sets
• Will test by running phylotyping software
comparing to genome data sets with and without
GEBA genomes
– Megan
– AMPHORA
• Should be a good complement to reference
genome sequencing
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52. dnaG
0.7
frr
infC
0.6 nusA
pgk
pyrG
0.5 rplA
rplB
rplC
0.4 rplD
rplE
rplF
0.3
rplK
rplL
0.2 rplM
rplN
rplP
0.1 rplS
rplT
rpmA
0 rpoB
rpsB
rpsC
Aquificae Chlorobi rpsE
Chlamydiae Firmicutes
Chloroflexi
Acidobacteria
Bacteroidetes Spirochaetes rpsI
Cyanobacteria Actinobacteria
Planctomycetes rpsJ
Betaproteobacteria
Deltaproteobacteria
Alphaproteobacteria rpsK
Epsilonproteobacteria Unclassified Bacteria
Gammaproteobacteria rpsM
Unclassified Proteobacteria rpsS
smpB
tsf
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53. Value of 100 diverse genomes IV:
Mechanisms of Diversification
• Lateral gene transfer
– Lateral gene transfer is fundamentally important in
microbial evolution
– However, when we find “foreign” DNA in genomes we
usually cannot pinpoint the origin of that DNA
– Having more diverse genomes may help better pin
down source groups for each piece of foreign DNA
• Eukaryotic diversification
– Of ~200 eukaryotic specific gene families
– How many now show up in bacteria and archaea
– Any patterns to where there are found?
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54. CRISPR - expanding the possible
34 out of 56 genomes contain CRISPR
1-13 arrays (loci) per genome
Halingium ochraceum SMP-2, DSM 14365
807 repeats in total
a single repeat contains 382 repeats
Verminephrobacter eisenieae: 249 repeats
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55. Value of 100 diverse genomes V:
Phylogeny
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56. 16s Says Hyphomonas is in Rhodobacteriales
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Badger et al.
2005
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57. WGT Says Its Related to Caulobacterales
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Badger et al.
2005
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58. Tree of Life Example II
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60. GEBA - What’s Next
• Repeat and/or scale up
• Need to determine the value of finished
versus unfinished genomes
• Apply this method to other groups
– Microbial eukaryotes
– Viruses
• Really fill in bacterial and archaeal tree
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61. The slopes of the linear regression Lines represent the PD contribution of the genomes
(each window contains 50 genomes)
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62. Slope (50 genome windows)
Window position
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63. Greengenes ssrRNA
Slope (50 genome windows)
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64. GEBA: Long Run
• Need active community input
• Involvement of multiple funding agencies,
labs, genome centers
• Integration/ communication among all large
scale projects
• Follow recommendations of NAS, ASM,
AAM reports
• Adopt a Microbe - Link to educational
initiatives
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Editor's Notes
Gets better with more markers - but we do not have lots of sequences for these markers. We can get them from genomes. The more diverse the genomes, thebeter the marker set will be