...What Shotgun Sequencing has uncovered about the Human Microbiome Institutional affiliation Name Date Introduction The human microbiota consists of microorganisms that live inside as well as on humans and they outnumber the human germ cells and somatic cells ten times (Turnbaugh et al. 2007). The collection of genes of these microbial organisms (the microbiome) provides the characteristics that human beings lack (Zimmer 2010). There are two major techniques that are currently used to characterize the microbiome, namely; the (rRNA) small-subunit ribosomal RNA, and the metagenomic study, wherein shotgun sequencing is used to characterize community DNA of these microorganisms. Shotgun sequencing of the human microbiome Shotgun sequencing, also called shotgun cloning in genetics, is a process used for sequencing long strands of DNA. Shotgun sequencing was referred so by resemblance with the quasi-random shotgun firing pattern. The shotgun sequencing method was developed by Fredrick Sanger in the 1970s. The chain termination sequencing process is only be used to sequence relatively short DNA strands. Longer sequences of DNA must be sub-divided into shorter fragments, and then subsequently reassembled to give the entire sequence (Venter et al. 2004). Shotgun sequencing process, which uses random fragments, is used to sequence shorter fragments of longer DNA strands. The process is faster but more complex process. The DNA strand is randomly broken...
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...The idea that humans have power over our health has a long history in American popular culture. We tend to believe we are the masters of our own destiny and can solve the problems of our internal workings according to our will, power of positive thinking, upbeat attitude or a fighting spirit however we cannot ignore our living environment and the organisms that co-exist among us. As it turns out, we share our bodies with an unimaginably vast array of organisms that seem to play a substantial role in our well-being. Both in and on our body, there are 10 bacterial cells for every single human cell. This collection of organisms that inhabit the human body is referred to as the microbiome and accounts for nearly 2% of our total body weight. Trillions of bacteria and other microorganisms are thriving on our skin, genital areas, mouth, and especially intestines. (Ackerman, 2012) It is estimated that there are more than one thousand species that make up this community living in the digestive system alone. When we think of microbes in the body, we tend to think of bacteria that causes disease or germs that make us sick. Biologist, Sarkis K. Mazmanian believes we focused on the harmful bugs because they are foreign enemies that invade our bodies throughout our life and indifferent to seeing them as part of us and allying to learn more about them. Newborns may begin life as sterile creatures however the moment we passed through our mother’s birth canal, we inherited mom’s commensal...
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...NINTH EDITION Burton’s MICROBIOLOGY FOR THE HEALTH SCIENCES Paul G. Engelkirk, PhD, MT(ASCP), SM(AAM) Biomedical Educational Services (Biomed Ed) Belton, Texas Adjunct Faculty, Biology Department Temple College, Temple, TX Janet Duben-Engelkirk, EdD, MT(ASCP) Biomedical Educational Services (Biomed Ed) Belton, Texas Adjunct Faculty, Biotechnology Department Temple College, Temple, TX Acquisitions Editor: David B. Troy Product Manager: John Larkin Managing Editor: Laura S. Horowitz, Hearthside Publishing Services Marketing Manager: Allison Powell Designer: Steve Druding Compositor: Maryland Composition/Absolute Service Inc. Ninth Edition Copyright © 2011 Lippincott Williams & Wilkins, a Wolters Kluwer business © 2007 Lippincott Williams & Wilkins, © 2004 Lippincott Williams & Wilkins, © 2000 Lippincott Williams & Wilkins, © 1996 Lippincott-Raven, © 1992, 1988, 1983, 1979 JB Lippincott Co. 351 West Camden Street Baltimore, MD 21201 Printed in the People’s Republic of China All rights reserved. This book is protected by copyright. No part of this book may be reproduced or transmitted in any form or by any means, including as photocopies or scanned-in or other electronic copies, or utilized by any information storage and retrieval system without written permission from the copyright owner, except for brief quotations embodied in critical articles and reviews. Materials appearing in this book prepared by individuals as part of their official duties as U.S. government employees...
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...—John F. Kennedy (1917–63) The President of America The bacterium Escherichia coli INTRODUCTION AND SCOPE MICROBIOLOGY is a specialized area of biology (Gr. bios-life+ logos-to study) that concerns with the study of microbes ordinarily too small to be seen without magnification. Microorganisms are microscopic (Gr. mikros-small+ scopein-to see) and independently living cells that, like humans, live in communities. Microorganisms include a large and diverse group of microscopic organisms that exist as single cell or cell clusters (e.g., bacteria, archaea, fungi, algae, protozoa and helminths) and the viruses, which are microscopic but not cellular. While bacteria and archaea are classed as prokaryotes (Gr. pro-before+ karyon-nucleus) the fungi, algae, protozoa and helminths are eukaryotes (Gr. eu-true or good+ karyon-nucleus). Microorganisms are present everywhere on earth, which includes humans, animals, plants and other living creatures, soil,water and atmosphere. Microorganisms are relevant to all of our lives in a multitude of ways. Sometimes, the influence of microorganisms on human life is beneficial, whereas at other times, it is detrimental. For example, microorganisms are required for the production of bread, cheese, yogurt, alcohol, wine, beer, antibiotics (e.g., penicillin, streptomycin, chloramphenicol), vaccines, vitamins, enzymes and many more important products as shown in the Tables 1.1, 1.2, and 1.3. Many products of microbes contribute to public health as...
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...have essential roles in our ecosystem or can be used to accomplish beneficial tasks. Human history is full of examples of major devastations caused by bacteria and viruses. Some of these historically important diseases still occur, such tuberculosis and yellow fever. Microorganisms are evolving to cause new infectious disease problems such as Lyme disease and AIDS, which capture public attention. Control and eradication of infectious diseases remain important goals of many microbiologists. The recognition that microorganisms were responsible for what was earlier thought to be "spontaneous generation" opened the door to industrial (pharmaceutical, chemical, energy) and food microbiology, technologies which contribute substantially to today's way of life. Microorganisms in soil and water are essential in the transformation of carbon, nitrogen, oxygen, sulfur and iron to products needed by plants and animals. In various ways, microbes participate in environmental cycling and degradation and global change. In the last few decades, microorganisms have been recognized as ideal model systems for the study of basic biological processes. More recently, microbiologists have brought an exciting dimension to the study of biology through the use of genetic engineering techniques and highly specific protein (antibody) molecules. Accomplishments in these areas already have led to enormous benefits for the human race, but there are many more challenges to be conquered through these kinds of studies...
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...Take Home Test #1 1) What bacteria can be found associated with human breast milk in the typical, normal situation? Bacteria that can be found in human breast milk are very diverse. The typical bacteria that are found in human breast milk have the genus of: Bifidobacterium, Enterococcus, Kocuria, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Propionibacterium, Rothia, Staphylococcus, Streptococcus, and Weissella (Leónides). According to Dr. Leónides and his expertise colleagues, the most popular of the bacteria that are found within human breast milk are: Staphylococcus, Streptococcus, Bifidobacterium, Enterococcus and Lactobacillus. The specific types of Staphylococcus found are: aureus, capitis, epidermidis, hominis. The specific types of Streptococcus found are: mitis, oris, parasanguis, salivarius. The specific types of Bifidobacterium are: adolescentis, bifidum, breve, breve, and longum. Next, the specific types of Enterococcus are: faecalis and faecium, Lastly, the specific types of Lactobacillus are: plantarum and fermentum. (Leónides) According to Dr. Fernandez Leónides and his collegues, studies have shown that certain bacteria in breast milk benefits infants. For example, Lactobacillus, Staphylococcus, Enterococcus, and Bifidobacterium, can sometimes benefit newborns through breastfeeding. The exposure to these bacteria can protect against diarrhea, respiratory diseases, and even reduce the risk of developing other diseases ...
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...CHAPTER THREE 3.1 SPOILAGE MICRORGANISM IN FRESH WHOLE FRUITS 3.2 UNUSUAL CHARACTERISTICS OF SPOILAGE MICRORGANISMS 3.3 SOURCES OF MICROBIAL CONTAMINATION OF CITRUS FRUITS CHAPTER FOUR 4.1 MICROBIAL SPOILAGE OF FRESH CUT FRUITS 4.2 MICROBIOLOGICAL SPOILAGE DEFECTS OF FRESH-CUT CITRUSFRUITS 4.3 IMPACT OF MICROBIOLOGICAL SPOILAGE 4.4 INTRINSIC AND EXTRINSIC FACTORS OF SPOILAGE MICRORGANISM CHAPTER FIVE 5.1 PREVENTION AND CONTROL OF MICROBIAL SPOILAGE IN CITRUS FRUITS 5.2 SUMMARY AND CONCLUTION REFERENCES CHAPTER ONE 1.1 INTRODUCTION Consumption of citrus fruits and fruit juices has substantially risen over the last few years, mostly due to the increasing demand for low-caloric food products with fresh-like characteristics. In addition, there is scientific evidence that consumption of Citrus fruits and vegetables helps prevent many degenerative diseases such as cardiovascular problems and several cancers (Rico et al., 2007). Fresh fruits have a natural protective barrier that acts effectively against most plant spoilage and pathogenic microorganisms. However, as a consequence of inappropriate manipulation during the handling, cutting, shredding, and maintenance of the fruit at ambient temperature and storage conditions, both pathogenic and deteriorative microorganisms may contaminate a product, thus increasing the risk of microbial diseases and spoilage (Beuchat, 1996; Díaz-Cinco et al., 2005). In fact, the number of outbreaks and cases of illness caused by...
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...Euphorbia Hirta or "tawa-tawa" Tawa Tawa or Gatas Gatas (Euphorbia Hirt) The Mindoro Post, within its article entitled "Dengue Fever Cure using Tawa tawa" (released The month of January 2010, utilized July 2010), creates, "many individuals understand and also have attested in order to the truth that these people and many more happen to be healed associated with dengue using a simple grass. This particular grass is known as Gatas Gatas within the land associated with Leyte. However in Butuan and Cagayan de Oro these people call this “Tawa Tawa” · At the same time, a wesite upon Filipino therapeutic grass offers the organic category associated with Tawa Tawa grass as well as explains which, "its blossoms tend to be several, each about 5 to 8 cm across. Sepals as well as petals tend to be obovate-oblong, yellowish-green, as well as protected along with big, reddish-brown smears” The effectiveness of Tawa Tawa Plant · One of the studies proving Tawa Tawa's efficacy is an investigatory project entitled "The Effectivity of Euphorbia hirta L. (Tawa-tawa), Prepared in Teabag Form, on Increasing Platelet Levels in Mus musculus (White Mice)." The said science project won the Student Research Presentation sponsored by the College of Agriculture atXavier University - Ateneo de Cagayan in thePhilippines. · The said project, as the title suggests, probes on increasing blood platelet levels using Tawa Tawa plant. For the...
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...Chapter 1 INTRODUCTION Background Euphorbia hirta, belongs to the family of Euphorbiaceae which is a large family of dicotyledons, with about 300 genera and over 5,000 species. Here in the Philippines, the Euphorbia hirta, is commonly referred to as Tawa-tawa or Gatas-gatas in some provinces. It is also known as Asthma weed or Snake weed in the United States. The plants of 3 different species share Phoretic variations, these plants are: (1) Mutha (Cyperus rotundus), (2) Gatas-gatas (Euphorbia hirta) and (3) Botoncillo (Gomphena globosa). Tawa-tawa is usually very abundant in tropical regions such as the Philippines. A simple weed scattered in sunny lawns, waste places and open grasslands. It is pantropic in distribution. The plant is an annual, hairy herb, usually branched from the base, spreading up to 40 cm long. The stem is slender and often reddish and purplish in color, covered with yellowish bristly hairs especially in younger parts. The leaves are oppositely arranged, elliptical-oblong to oblong-lanceolate, 1 to 2.5 cm long, toothed at the edge, and blotched with purple in the middle. In the axils appear numerous involucres, purplish or greenish, dense, axillary, short stalk clusters or crowded cymes, about 1 mm long. The capsules are broadly ovoid, hairy, three-angled, about 1.5 cm. The small green flowers constitute the inflourescence characteristics of the euphorbias. The stem and the leaves produce white or milky juice when cut (Lind and Tallantire...
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...Aacknowledgement First of all I like to thank God almighty who authorise me to research on this topic. I submit my sincere thanks to my supervisor Medhat Khattar for his valuable presence, time, effort, guidance and help to complete this dissertation. My dissertation would not have been completed without the help of lab technicians Nick and Suzy, I am extremely grateful for their help, suggestions and encouragement. I might want to thank my family for impacting in me a comprehension for the significance of education and an appreciation for diligent work. I extraordinarily value the majority of the penances that were made so as to realize the open doors that I have gotten, and it is my trusts that this proposition embodies what I have realized. Much obliged to you for your dedication, bolster, and affection. I might likewise want to thank my grandparents for the numerous hours of math mentoring as a youngster. In spite of the fact that it may have appeared to be inconsequential, it was the premise for my prosperity and the establishment of my hobbies in Designing. I might want to devote this proposition to my family, without whom I would not be seeking after a profession with an instruction from my university undergraduate days. I also thank my supervisor’s effort and good work channelled towards making me a better microbiologist in the world. I sincerely extend my thanks all concerned people who together with me in this regard. Table of Contents I Declaration......
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...Sala, Amy J. Symstad, and David Tilman Critical processes at the ecosystem level influence plant productivity, soil fertility, water quality, atmospheric chemistry, and many other local and global environmental conditions that ultimately affect human welfare. These ecosystem processes are controlled by both the diversity and identity of the plant, animal, and microbial species living within a community. Human modifications to the living community in an ecosystem as well as to the collective biodiversity of the earth can therefore alter ecological functions and life support services that are vital to the well-being of human societies. Substantial changes have already occurred, especially local and global losses of biodiversity. The primary cause has been widespread human transformation of once highly diverse natural ecosystems into relatively species-poor managed ecosystems. Recent studies suggest that such reductions in biodiversity can alter both the magnitude and the stability of ecosystem processes, especially when biodiversity is reduced to the low levels typical of many managed systems. Our review of the available evidence has identified the following certainties concerning biodiversity and ecosystem functioning: • • • • Human impacts on global biodiversity have been dramatic, resulting in unprecedented losses in global biodiversity at all levels, from genes and species to entire...
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...INTRODUCTION Biotechnology is one of the innovative branches of science. Biotechnology has created new revolutions in this era by contributing industries, medical sciences, food technologies and genetics. "Biotechnology is basically defined as the use of living organisms, their parts and their biochemical processes for the creation of beneficial products." Bio-technology has its roots in the distant past and has a large, highly profitable, modern industrial outlets of great value to society for e.g. the fermentation, bio-pharmaceutical and food industries. The main reasons must be associated with the rapid advances in molecular biology, in particular, recombinant DNA technology, which is now giving bio-scientists a remarkable understanding and control over biological processes. Some Technologies used in Biotechnology: 1. Bioprocessing technology * The use of bacteria, yeast, mammalian cells and/or enzymes to manufacture products * Large scale fermentation and cell cultures, carried out in huge bioreactors, manufacture useful products * Products: Insulin, vaccines, vitamins, antibiotics, amino acids, etc. 2. Monoclonal antibodies (MCAb) * Definition: Producing antibodies for medicine by cloning a single cell * MCAb are used for Home Pregnancy tests * Used to detect cancer (they bind to tumor cells) * Used to detect diseases in plants and animals and environmental pollutants 3. CELL...
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...|INTRODUCTION | Bacteria, one-celled organisms visible only through a microscope. Bacteria live all around us and within us. The air is filled with bacteria, and they have even entered outer space in spacecraft. Bacteria live in the deepest parts of the ocean and deep within Earth. They are in the soil, in our food, and on plants and animals. Even our bodies are home to many different kinds of bacteria. Our lives are closely intertwined with theirs, and the health of our planet depends very much on their activities. Bacterial cells are so small that scientists measure them in units called micrometers (µm). One micrometer equals a millionth of a meter (0.0000001 m or about 0.000039 in), and an average bacterium is about one micrometer long. Hundreds of thousands of bacteria would fit on a rounded dot made by a pencil. Bacteria lack a true nucleus, a feature that distinguishes them from plant and animal cells. In plants and animals the saclike nucleus carries genetic material in the form of deoxyribonucleic acid (DNA). Bacteria also have DNA but it floats within the cell, usually in a loop or coil. A tough but resilient protective shell surrounds the bacterial cell. Biologists classify all life forms as either prokaryotes or eukaryotes. Prokaryotes are simple, single-celled organisms like bacteria. They lack a defined nucleus of the sort found in plant and animal cells. More complex organisms, including all plants and animals, whose cells have a nucleus, belong to the...
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...Engineering in Civil and Environmental Engineering Abstract This purpose of this study was to investigate the effectiveness and the performance of the BioSand filter in Nepal. To achieve this, the author undertook a field trip to Nepal in January, 2001. The trip was made possible with generous support provided by the Department of Civil and Environmental Engineering of MIT. The author spent 3 weeks in Nepal - 4 days in the vicinity of Tansen in the central Palpa region and 9 days in the Nawalparasi district in the Terai collecting water samples. Turbidity measurements were taken and presence/absence tests for total coliform, E.coli and H2S producing bacteria were carried out. At MIT, membrane filtration tests were also carried out. This study found that while filtered water from the BSFs...
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...BRINNINSTOL Characteristics of Cells: true of all living cells * Communicate with environment * Molecules being exchanged—recognized by other cells—causes cell to do something (releasing toxins; move) * Growing—one cell divides and becomes two cells (binary fisson) * Some form appendages—form differently, look dfrnt, function dfrnt—spores, cysts, flagella * Evolve—ancestral cell Microbial Communities Table 1.1 More water than land Most microbes in soil Origin of Earth * 3.8 billion years ago—evidence of microbial cells Agriculture * Bacteria in plant (soybean plant) fixes nitrogen to usable nitrogen for environment * Cows have microbes in digestive tract to digest grass into sugar Energy—biofuels (methane, ethanol—from sugar cane) produced from microbial Disease—Cause & Treatment * More death-causing bacteria in 1900’s than today (in US!) Food—Microbes make food—bread, beer, cheese, 1665—Hooke; first to describe microorganisms through primitive microscope; drew picture of sprouting bodies 1676—Leeuwenhoek; first to describe bacteria; tiny microscope; drew multiple pictures of dfrnt kinds Four Types of Light Microscopy: 1. Brightfield: simplest; stained and illuminated, 10x 100x 1000x 2. Phase Contrast: cast shadow; shows depth 3. Darkfield: black background; light refracted 4. Fluorescent: fluorescent stained; naturally fluorescent; *requires UV light source ...
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