Microbiology World Issue 1

Microbiology World

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Sept – Oct, 2013

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Microbiology World

COUNCIL President Mobeen Syed, M.D. King Endward Medical University Lahore MSc. from ASD, BSc. from Punjab University D-Lab from MIT MA USA

Vice-President Sudheer Kumar Aluru, Ph.D Human Genetics, Sri Venkateswara University, India HOD of Biology Department (Narayana Institutions)

Managing Director Dr. D K Acharya, Ph, D Asst Prof., Biotech Dept.

A. M. Collage of Science, Management and Computer Technology, India

Chief Editor Mr. Sagar Aryal Medical Microbiology (M.Sc), Nepal

Reviewers Mr. Samir Aga Department of Immunological Diseases Medical Technologist, Iraq Mr. Saumyadip Sarkar, Ph.D ELSEVIER Student Ambassador South Asia, Reed Elsevier (UK) M.Sc., Research Scholar (Human Genetics), India

Editors Dr. Sao Bang Hanoi Medical University Dean of Microbiology Department (Provincial Hospital) Microbiology Specialist, Vietnam Mr. Tankeshwar Acharya Lecturer: Patan Academy of Health Sciences (PAHS) Medical Microbiology, Nepal Mr. Avishekh Gautam Lecturer: St. Xavier’s College Medical Microbiology, Nepal Mr. Manish Thapaliya Lecturer: St. Xavier’s College Food Microbiology, Nepal

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Table of Content What is Microbiology?

4-7

New Place for Microbial Research

8-10

Who is father of what?

11

Bacterial endocarditis: Serious and Fatal Disease

12-15

Botox.. For beauty and pain relief

16-17

Forensic Science Career

18-20

Monoclonal Antibodies

21-22

Mechanism discovered by which body's cells encourage tuberculosis infection

23-25

How Simple Can Life Get? It’s Complicated

26-28

Safe Clearance of Salmonella

29-30

Funny Microbiology Pictures

31

How many viruses on Earth?

32-33

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What is Microbiology?

The world around us is full of organisms that are too small to be seen with naked eye-bacteria, virus, fungi, algae and protozoa. These microbes live in a wide range of habitats from hot springs to the human body and depth of ocean.

They affect each and every aspects of life on earth.

We can all think of a few microbes that make us ill – the viruses that cause cold and flu, or food poisoning bacteria. However, there are many more microbes living harmlessly alongside us playing a vital role in the planet‘s nutrients cycles, from fixing nitrogen and carbon dioxide at the beginning of the food chain right through to decomposing and recycling essentials nutrients at the end of it.

Microbes are also essential to the production of many foods and medicines – imagine our diet without cheese, bread, yoghurt or a world where the slightest bacterial infection or wound could prove fatal because there were no antibiotics or vaccines.

Microbes have always affected our health, food and environment and they will play an important role in the big issues that face us in the future: climate change, renewable energy resources; healthier lifestyles and controlling diseases.

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What do Microbiologist do?

Because microbes have such an effect on our lives, they are a major source of interest and employment to thousands of people. Microbiologists study microbes: where they occur, their survival strategies, how they can affect us and how we can explain them.

All around our planet there are microbiologists making a difference to our lives – maybe ensuring the safety of our food or treating and preventing diseases or developing green technologies or tracking the role of microbes in climate change.

Basic Reseach Before Microbiologist can solve the problems caused by microbes, or exploits their amazing powers, they have to find out about the detailed workings of microbial cells. The basic knowledge of genetics, cell structure and function can then be used in applied microbiology as well as in other areas of biology.

Healthcare Microbiologists are essential in the fight against infectious diseases. Many work as biomedical scientists in hospitals and Health Protection Agency labs, investigating the samples of body tissues and fluids to diagnose infections, monitor treatments or track disease outbreaks. Some microbiologist work as clinical scientists in hospital and medical school laboratories where they carry out research and give scientific advice to medical staff who treat patients. Other microbiologists work on pathogens that cause diseases, such as ‗flu‘ or TB, and the information they find is used by their colleagues to develop vaccines and better treatments.

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Environment Some microbiologists study how microbes live alongside other creatures in different habitats such as the oceans, salt lakes and Antarctica. They develop early warning sensors to detect pollution and use microbes to treat industrial waste. Other contributes to the worldwide research on climate change, investigating the effect of microbial processes on the composition of atmosphere and climate. Microbiologists also work with technologists and engineers to develop greener sources of energy produced from urban and industrial waste.

Agriculture Without agriculture there would be no food for us to eat. Microbiologists investigate the vital role of microbes in soil. Some concentrate on plant pests and diseases, developing ways to control them. Others research the pathogens that cause diseases in farm animals.

Microbiologists also use microbes to control insects‘ pests and weeds, especially in developing countries.

Business Microbiologists work in many bioscience and food companies. They carry out research and develop new products or work in quality control to monitor manufacturing processes and check the microbiological safety of goods such as medicines, cosmetics, toiletries, biochemical and food and drink.

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Where do they work?

In the lab Universities, research institutes and industrial companies employ microbiologists to do basic, environmental, healthcare and agricultural research.

Medical Microbiologists also work in hospitals and Health Protection Agency laboratories.

Industrial microbiologist work in a range of companies – from big pharmaceutical, biochemical, biotechnology and food businesses through to smaller firms that develop biopharmaceuticals or specialist products.

Outside the lab If you still love microbiology but find that lab-based work is not for you, there are still some great options where you can use the scientific knowledge and transferable skill you‘ve acquired while studying.

Microbiologists can use their knowledge and skills in a wide range of careers in industry (marketing, technical support and regulatory affairs) education (teaching, museums and science centers), business (patent attorney or accountant) and communications (public relations, journalism and publishing).

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New Place for Microbial Research For the microbiologist, the next best thing to a trip to Mars might well be an expedition to the McMurdo Dry Valleys of Antarctica. Here, in the Earth's coldest and driest deserts, the conditions approach those on our neighboring planet and are thought to also approach the cold-arid limit for life. Not all of the Dry Valleys are equally dry. Some have perennially frozen, glacier-fed lakes and ephemeral streams, and thus have some soil moisture. Here one finds more of life, even three taxa of multicellular animals—tardigrades, rotifers, and, most numerous, bacterial-feeding nematodes.

Lacking such a source of water, thus being one of the truly dry Dry Valleys, is McKelvey Valley. What little snow falls here or blows in sublimates in the cold, hyper-arid conditions.

How cold? The average air temperature is around –20 °C. Winter brings prolonged periods of −55 °C cold; Fig - Endolithic community layer in fractured sandstone

in summer, air temperature can rise to a balmy 0°C. Humidity is low (<10% RH in winter). And then there are the ceaseless katabatic winds (from the Greek word katabatikos meaning "going downhill"). Cold, dense air falls downhill off the East Antarctic Ice Sheet and races through the valley at speeds commonly exceeding 50 km/h, sometimes reaching 320 km/h (200 mph). These winds evaporate all moisture and carry sand grains that scour the barren landscape. All in all, these conditions bear some resemblance to those used to freeze-dry biological samples.

The valley floor is an unstable, gravelly, desiccated mineral soil with high salinity, little organic material, and the lowest nitrate concentrations known for any terrestrial soil. Surface temperatures fluctuate wildly under the intense www.microbiologyworld.com

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summer sun, seesawing between –15° and +27.5°C in a few hours. UV is intense.

And, of course, the winds scour the land and carry off any hint of moisture.

Nevertheless, life carries on. Some intrepid researchers left the comforts of Hong Kong or New Zealand or even relatively balmy Minnesota to look for organisms living under such extreme conditions. As reported in their recent paper, there are some bacteria living in these dry surface soils, mostly Fig - Chasmoliths: a lichenized microbial community protruding from a granite rock fracture

Acidobacter and Actinobacteria. As you might expect, at the top of the list are desiccation tolerant taxa such as Deinococcus and Rubrobacter. There are also numerous nitrogen fixers. With neither photoautotrophs or chemoautotrophs present, organic carbon is at a premium, and its lack is thought to preclude further community development.

Both qualitatively and quantitatively, most of the life in this valley is associated not with the soil, but with the rocks. Here and there the flat-lying sedimentary bedrock is exposed. The rock surfaces, and even the shallow cracks, are likely sterile due to temperature fluctuations and abrasion from windblown sand. But any life that burrows in even just a few millimeters finds more stable temperatures and shelter from the incessant wind, even in the intense cold.

Given the estimate that -6 ºC or -8 ºC is the lower limit for metabolic processes, some activity would be possible in these rock niches for 1000 hours per year at the most. However, that is enough to sustain microbial communities, both the endoliths, organisms that live within the porous structure of the rock itself and the chasmoliths that live within the cracks and crevices.

Due to their structure and mineralogy, sedimentary rocks such as the local sandstone are particularly well-suited for housing endoliths a few millimeters beneath their surface. Enough light penetrates for photosynthesis (at least during the months when there is sun), while damaging UV is reduced. In contrast to the www.microbiologyworld.com

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soil community, these rock dwellers are mostly photoautotrophs. Two distinct communities of bacteria and eukaryotes are detectable, both visibly and experimentally. The upper 2 mm, called the lichen zone, is dominated by a lichenized fungus, Texosporium sancti-jacobi, associated with the green alga Trebouxia jamesii. Below 2 mm, the photosynthetic cyanobacteria rule, mostly Chroococcidiopsis, a genus noted for having radioresistance comparable to that of Deinococcus radiodurans. Low light levels not withstanding, light may not be the factor limiting these endolithic communities, but rather lack of available CO2. The chasmolith communities in the crevices are made up primarily of various lichens and cyanobacteria, combined with a distinctive sprinkling Fig - A typical quartz hypolith showing no external evidence of the underlying microbial community

of other bacterial groups. There is yet a fourth cryptic community here, the hypoliths that live underneath light-colored, translucent stones. These are almost exclusively cyanobacteria, making do in an environment that receives less than 0.1% of the incident light. There are no fungi here, and only a very few algae.

There is a tendency to think that the more extreme the environment, the less the biological diversity. The communities in the Dry Valleys don't conform to that pattern. The endoliths and chasmoliths combined comprise more than 50 bacterial species (based on 98% identity of their 16S rDNA sequences).

Although eukaryotes represent only 5% of these communities, they include four genera of fungi (both Ascomycota and Basidiomycota) as well as three groups of algae. Add in the hypoliths, and these three lithic communities span 16 phyla in two domains.

What about the missing archaea, those masters of extreme environments? Not a one to be found so far, not even one lurking under a rock. Surely there are yet even more surprises to be found by the cryophilic researchers. www.microbiologyworld.com

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Who is father of what?

Subject

Father

Biology

Aristotle

Evolution

Charles Darwin

Genetics

Gregor Mendel

Microbiology Molecular biology

Antonie van Leeuwenhoek and Louis Pasteur Linus Pauling

Neuroscience

Santiago RamĂłn y Cajal

Protozoology

Antonie van Leeuwenhoek

Taxonomy

Carolus Linnaeus

Toxicology

Paracelsus

Virology

Paracelsus

Medical genetics

Victor McKusick

Physiology

Claude Bernard

Molecular biophysics

Gopalasamudram Narayana Iyer Ramachandran Robert Koch, Ferdinand Cohn, Louis Pasteur, Antonie van Leeuwenhoek Edward Jenner

Bacteriology

Immunology

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Bacterial endocarditis: Serious and Fatal Disease An infection of either the heart valves or of the inner surface, called the endocardium, of the heart is Bacterial endocarditis. Endocarditis, which forms vegetation by organisms, is a potentially serious condition because the inflammation (swelling) that occurs inside the heart can interrupt the normal blood flow through the heart valves. So this can trigger a range of complications such as: heart failure, stroke, multiple organ damage. It is relatively uncommon compared with other heart diseases; it is associated with significant morbidity and mortality.

Endocarditis is more common in older people, with half of all cases occurring in people who are over 50. However, cases of endocarditis have been recorded in children, particularly those who are born with congenital heart disease. Twice as many men are affected by endocarditis as women. Endocarditis is regarded as a medical emergency and usually requires admission to an intensive care unit (ICU). Intravenous antibiotics are usually used to treat the underlying infection.

Just under half of all people with endocarditis will require surgery to repair the damage to their heart.

Bacteria in the mouth, intestinal tract or urinary tract travel to the heart via the bloodstream but usually don't cause a problem in normal hearts. However, hearts that have defects, often even if the defects have been repaired are vulnerable to infection. As the Once infection occurs, the bacteria continue to grow and may seriously damage the heart. Bacterial endocarditis is most likely to occur in patients who have: Aortic Valve Lesions, Patent Ductus Arteriosus, tetralogy of Fallot, ventricular septal defect, Mitral Valve Prolapse, transposition of the great Arteries. www.microbiologyworld.com

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It is unlikely to occur in patients who have a completely repaired pulmonary valve stenosis, arterial septal defect, ventricular septal defect or patent ductus arteriosus.

Gram positive cocci have always dominated the scene as major etiologic agents.

Gram negative bacilli (GNB) other than Hemophilus, Actinobacillus, Cardiobacterium, Eikenella and Kingella (HACEK) are regarded as less frequent cause of endocarditis. They are associated with certain percentage of Endocarditis in Intravenous drug abuser (IVDU) and Prosthetic valve endocarditis (PVE).

The usual signs of bacterial endocarditis are prolonged fever for two to three days in a person with congenital heart disease that occurs after a procedure in the mouth, intestinal tract or urinary tract. However, the infection may occur without a previous procedure. Symptoms may include: Poor appetite, Fatigue, Joint pain, Rash, Weight loss.

Bacterial endocarditis is classified as, Sub-acute bacterial endocarditis (SBE) is often due to streptococci of low virulence and mild to moderate illness which progresses slowly over weeks and months and has low propensity to hematogenously seed extracardiac sites.

Acute bacterial endocarditis (ABE) is a fulminant illness over days to weeks, and is more likely due to Staphylococcus aureus which has much greater virulence, or disease-producing capacity and frequently causes metastatic infection

Pathophysiology It occurs when bacteria spread through the bloodstream and land inside the heart and grow there. Usually, if there are bacteria circulating in the bloodstream, they don't stick to the inside of the heart: the blood flows smoothly. If the heart is abnormal due to certain types of surgery or other defects, there may be rough surfaces causing www.microbiologyworld.com

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turbulent blood flow (known as a murmur) to which bacteria can attach and cause infection.

Although uncertain, it is believed that cardiac valves and other endocardial surfaces become infected after exposure to micro emboli from bacteria circulating in the bloodstream. Dextran-producing bacteria, such as Streptococcus mutans, have a virulence factor that promotes adherence to endovascular surfaces.

Coagulase-negative staphylococci may produce a biofilm on prosthetic surfaces, which also promotes adherence. Beta-hemolytic streptococci and enteric gramnegative bacteria lack recognized adherence factors, and appear less likely to cause endocarditis. Endocardial surfaces previously damaged from valvular heart disease, endocarditis, surgery, or pacemaker wires provide a favorable environment for thrombus formation. Over time, microorganisms proliferate in the thrombus, resulting in classic vegetation. Microorganisms are released into the circulation, usually on a continuous basis, which often results in interesting findings.

Lab diagnosis Major criteria for probable endocarditis are persistant bacteremia with a new regurgitant heart murmur or valvular heart disease with vesculitis or negative or intermittent bacteremia with fever. Modern blood culture techniques includes three sets suffice for two days, not necessarily beyond this point. CT scan electrocardiogram, echocardiogram, can be done for the diagnosis of disease. New diagnostic approaches like culture of vegetations and infected cardiac valve tissue has shown better result in blood culture negative endocarditis.

When causative microorganisms are cultured or seen histologically in vegetations and valve tissues. In case of streptococcal infection Anti streptolysin O titer can be determined. Latex particle coated with anti-CRP antibodies were used for CRP test by mixing with 50Îźl of patientsâ&#x20AC;&#x2DC; serum Haematuria and pyuria can be observed by microscopy from urine sample of each patient on same day of blood examination when blood culture is seen negative. www.microbiologyworld.com

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Treatment The penicillin, often in combination with gentamicin, remains the cornerstones of therapy for endocarditis caused by penicillin-susceptible streptococci. For penicillin-allergic patients, vancomycin is substituted. For relatively penicillininsensitive streptococci (minimal inhibitory concentration higher than 0.1 to 0.5 mg/mL), the penicillin dosage is higher and duration of therapy is 2 weeks. Gentamicin is given for the first 2 weeks; treatment for endocarditis caused by enterococci is longer; both penicillin and gentamicin are given for 6 weeks, For vancomycin-resistant enterococci (VRE), streptogramin quinupristin-dalfopristin (Synercid) either alone or in combination with doxycycline and rifampin is administered.

Prevention Bacterial endocarditis is one of the most dreaded complications of structural heart disease. Its mortality rate in the pre-antibiotic era was nearly 100% and remains high even today; approaching 20-30 %. This is mainly due to increasing organism resistance to antibiotics and emergence of fungal infections in response to multiple antibiotic treatments. So the prevention is important.

Prophylaxis for Bacterial endocarditis is effective only if appropriate antibiotic is given in a sufficient amount at the right time. Antibiotics should be administered at time only when there is likelihood of bacteremia so as not to give a bacterial resistance. Better the antibiotic administered at a perioperative period. If a procedure involves affected tissue, it is necessary to provide additional doses of antibiotic for treatment of an established infection. The recommended prophylactic regimen for dental and oral procedures is a single dose of oral amoxicillin. If the patient is unable to take oral medication, parenteral administration of antibiotic is required. If parenteral amoxicillin is not available, ampicillin is the alternative.

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Botox.. For beauty and pain relief The modern era of microbiology also recognize for its application in the different field. The micro organism is not always harmful but it also contributes in making different useful products. One of the products is Botox injections which have highly demand in these days.

The exotoxin produced by Clostridium botulinum is one of the most powerful poisons known. These are spore formers anaerobic solid bacteria mostly found naturally on many foods. They survive usually in cooking materials and inadequate canning procedures. In this conditions toxin can be produced and if ingested it causes botulism. A few milligrams of this exotoxin are sufficient to kill the entire population of a large city. The botulinum toxin blocks transmission of acetyl choline nerve signals to the muscles, resulting in paralysis and often in death. The toxin from type A organism of Clostridium botulinum is known as Botox has become useful in treating various conditions.

Botox is a type of exotoxin produced by Clostridium botulinum, mostly by A type. These are anaerobic soil bacteria and are spore formers found naturally on many foods.

Nowadays it is used as injection for various purposes. Botox injections may be one of the most significant medical advances of the past most useful century. It was first introduced in 1970â&#x20AC;&#x2DC;s. The most usual use of botox is cosmetic treatment to remove facial lines, such as frown lines. Extremely dilute botox is injected directly into the area, inactivating the muscles that are causing the frown or other lines. www.microbiologyworld.com

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Botox injections are also provided for the treatment of various types of headaches and chronic pain. There were minimal side effects and in fact it was felt that Botox has less potential complication than many oral medications commonly used to treat headache pain.

It is also used for the treatment of Fig: Clostridium botulinum spores severe under arm sweating known as primary axillary hyperhydrosis, which affects millions in their every day social and public interactions.

Botox is also used to receive a number of very painful conditions involving muscle contractions, such as dystonia (severe muscle cramping). For example, cervical dystonia is a painful disease in which muscles in the neck and shoulder contact involuntaries causing jerky movements, muscle pain and tremors. Injections of Botox directly into the affected areas give relief for 3 to 4 months, after which the treatment may be repeated. Another example is Parkinsonâ&#x20AC;&#x2DC;s disease, a condition in which certain nerve cells are lost, resulting in tremor, impaired movement, and in some cases, dystonia.

Botox injected into the affected muscles can give dramatic, although temporary relief. It has come a long way in proving to patients that its effects are dramatic, especially in its ability to rejuvenate facial expressions and recapture a youthful presentation.

So inspite of its powerful and dangerous properties, botulinum toxin when used with great care can be a useful therapeutic agent.

- Sanjay Kumar Pathak

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Forensic Science Career What is Forensic Science?

The word forensic comes from the Latin word forensis: public; to the forum or public discussion; argumentative, rhetorical, belonging to debate or discussion.

From there it is a small step to the modern definition of forensic as belonging to, used in or suitable to courts of judicature, or to public discussion or debate.

Forensic science is science used in public, in a court, or in the justice system. Any science used for the purposes of the law is a forensic science. Forensic science can be simply defined as the application of science to the law. In criminal cases forensic scientists are often involved in the search for and examination of physical traces which might be useful for establishing or excluding an association between someone suspected of committing a crime and the scene of the crime or victim. Such traces commonly include blood and other body fluids, hairs, textile fibers from clothing etc, materials used in buildings such as paint and glass, footwear, tool and tyre marks, flammable substances used to start fires and so on. Sometimes the scientist will visit the scene itself to advice about likely sequence of events, any indicators as to who the perpetrator might be, and to join in the initial search for evidence. Other forensic scientistâ&#x20AC;&#x2DC;s analyses suspected drugs of abuse, specimens from people thought to have taken them or to have been driving after drinking too much alcohol, or to have been poisoned.

Yet others specialize in firearms, explosives, or documents whose authenticity is questioned.

Forensic scientists can appear for either side â&#x20AC;&#x201C; prosecution or defense in criminal matters, and plaintiff or defendant in civil ones. They tend to present their findings and opinions in written form either as formal statements of evidence or reports. Sometimes they are required to attend court to give their evidence in person. www.microbiologyworld.com

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Why Study Forensic Science?

Forensic science is a subject that fascinates most of us. What makes forensic science so exciting to study is the nature of the problems to be solved, and this provides its own intrinsic rewards. Great emphasis is placed not only on developing the skills of forensic examination, but also on their application and on the communication of findings to the lay-person. Forensic science is a rigorous scientific discipline, and as such its graduates are highly employable individuals possessing the knowledge and skills for both subject-related employments, such as in a forensic laboratory, or non-subject-related employment in a wider range of careers.

Where Will I Work?

Forensic scientists work in laboratories, at crime scenes, in offices, and in morgues. They may work for federal, state and local government, forensic laboratories, medical examiners offices, hospitals, universities, toxicology laboratories, police departments, medical examiner/coroner offices, or as independent forensic science consultants.

What Do Forensic Scientists Do? The forensic sciences form a vital part of the entire justice and ¬regulatory system.

Some of the different divisions, or disciplines, of forensic science have become identified primarily with law enforcement — an image enhanced by television and movies. This is misleading because forensic scientists are involved in all aspects of criminal cases, and the results of their work may serve either the defense or the prosecution. The forensic scientist‘s goal is the evenhanded use of all available information to determine the facts and, subsequently, the truth.

The forensic scientist‘s role in the civil justice arena is expanding. Issues range from questions of the validity of a signature on a will, to a claim of product www.microbiologyworld.com

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liability, to questions of whether a corporation is complying with environmental laws, and the protection of ¬constitutionally guaranteed individual rights.

Forensic science is a rewarding career where the love of science can be applied to the good of society, public health, and public safety.

How Do I Become a Forensic Scientist?

You will need: • a bachelor‘s degree — get one in science; some forensic sciences require advanced degrees; take chemistry, biology, math, and English composition • good speaking skills — take public speaking, join the drama club, toastmasters, the debate team • good note-taking skills • the ability to write an understandable scientific report • intellectual curiosity • personal integrity

How Much Money Will I Make?

Income in the forensic sciences varies greatly depending upon your degree, your actual job, where you work, and how many hours you work. You may never ―get rich‖ but you will have a good income. You will be satisfied with your job, knowing you are contributing to justice — keeping the good guys on the street and helping put the bad guys in jail. Forensic scientists work different hours, depending upon what they do. Some work in forensic laboratories and work 40 hours a week, Monday through Friday. Others work out in the field on digs and may work different hours. Still others are ―on call‖ and work after their regular shift and receive overtime or compensatory time. Essentially every branch or forensic science offers opportunity for personal growth, career advancement, and increasing financial compensation. www.microbiologyworld.com

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Monoclonal Antibody An antibody is a Y-shaped protein produced by a type of white blood cell known as a B cell. B cells are made in the bone marrow of the body and then travel to such organs as the spleen and the lymph nodes. Mature B cells respond to foreign substances called antigens. They then differentiate into plasma cells, which secrete antibodies. Antibodies neutralize or mark antigens for destruction with the help of other cells of the immune system- the system of organs, tissues, cells, and cell products, including antibodies, responsible for ridding the body of disease causing organisms or substances.

In 1975, Argentine born British immunologist Cesar Milstein and German immunologist Georges Kohler discovered a technique to generate a quantity of white blood cells that uniformly produce only one type of antibody. These antibodies, known as monoclonal antibodies, target only one specific antigen-for example, one particular virus or toxin.

White blood cells naturally produce many different types of antibodies, each designed to mark one specific antigen. Creating monoclonal antibodies allowed scientist to tag one specific substance. By the mid-1990s monoclonal antibodies were commonly used in biomedical research and in diagnostic devices such as home pregnancy tests.

How monoclonal antibodies work Scientists use MAbs to identify and measure minute quantities of hormones, infectious substances, toxins, and other molecules in tissues and fluids. MAbs can also be used to identify malignant cells (cells with abnormal growth) in tissues. For example, to help diagnose cancers hidden in the body, radioactive substances are attached to MAbs that recognize and target cancer cells. These www.microbiologyworld.com

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MAbs are ten injected into a patient‘s body. The MAbs find cancer cells for which they targeted and blind to them. A special machine that uses film sensitivity to radioactivity is used to take an internal picture of the patient‘s body. This image reveals any cells to which the MAbs attached, indicating the presence of cancer.

Researchers use MAbs created to target a muscle protein called myosin to assess the extent of damage to the heart after a heart attack. Myosin exists in large quantities in healthy muscle tissue. When MAbs for myosin are injected into the heart muscle of a heart-attack patient, the MAbs bind to any remaining myosin, enabling researchers to determine how much of this protein was lost during the heart attack, an indication of the extent of heart damage. MAbs targeted for a blood protein called fibrin, which is produced when blood coagulates, can locate the site of blood clots in a patient. MAbs can also be used to determine whether the tissue of a potential organ donor is compatible with the tissue of a recipient. After a patient receives an organ transplant, different MAbs can then be used to help prevent the patient‘s immune system from rejecting the new organ.

One well-known example of a MAb-based technology is the home pregnancy kit. In one version of this test, a MAb specific for human chorionic gonadotropin (HCG), a hormone elevated in urine only during pregnancy, is purified and bound to plastic test tube. A urine sample is collected and added to the tube, and if HCG is present, the MAb attaches to it. A second MAb also specific for HCG, is then added. This second MAb has an additional molecule linked to it, such as an enzyme that changes the color of the urine in the final step of the test. In the absence of HCG in the urine, the second purified antibody will not be bound and no change in urine color will occur.

MAbs can also be used to diagnose the human immunodeficiency virus (HIV) that causes AIDS. A laboratory test determines whether an individual is producing antibodies against HIV. In this test, a MAb is used to test the blood of a patient for the presence of another type of antibody that binds to the virus.

Only patients who have been exposed to HIV will have the second type of antibody in their blood.

- Bidur Aryal www.microbiologyworld.com

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Mechanism discovered by which body's cells encourage tuberculosis infection Scientists have discovered a signaling pathway that tuberculosis bacteria use to coerce disease-fighting cells to switch allegiance and work on their behalf.

Epithelial cells line the airways and other surfaces to protect and defend the body. Tuberculosis bacteria co-opt these epithelial cells into helping create tubercles: the small, rounded masses characteristic of TB. The tubercles enable the bacteria to expand their numbers and spread to other locations. By inciting parts of the immune system to go into overdrive, this same molecular signaling pathway may play other roles in inflammatory conditions such as arthritis and some forms of heart disease and cancer.

"If we could keep this pathway from inciting the host immune system, we may be well on the way to finding innovative new therapies against TB, as well as other serious disorders," said the senior researcher on the study, Dr. Lalita Ramakrishnan, University of Washington (UW) associate professor of microbiology, medicine, and immunology. The results appear in the Dec. 10, 2009, express edition of Science.

Global health researchers are eager for new treatments for TB because many strains worldwide have become resistant to standard antimicrobials. Blocking a host pathway that the bacteria use would be an entirely different approach, Ramakrishnan explained, because it would keep the body from allowing the infection to take hold and be sustained, rather than a treatment aimed at killing the bacteria themselves. A host pathway blocker, if one becomes available, might also be quicker than current therapies, which take a long time to subdue the TB infection.

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"Most diseases, such as high blood pressure and depression, are already being treated by blockers and inhibitors of host enzymes and pathways," Ramakrishnan noted, "Many of these turn down certain cell signals as part of their therapeutic action. We and some other researchers are now exploring the possibility of blocking or inhibiting molecular mechanisms in the body to prevent or treat infectious diseases as well. " Earlier studies in the zebrafish by the Ramakrishnan lab demonstrated that TB tubercles were not, as previously thought, the way that the body walls off the bacteria to protect itself. Instead, these nodules (also called granulomas) are hubs for bacteria production and distribution. Uninfected macrophages -- the body's frontline soldiers that can eat and destroy many bacteria -- are recruited to the nodules, where they become TB-infected. However, the TB bacteria are able to grow in the macrophages, rather than being killed, likely by dampening the macrophages' defenses.

So by wooing more macrophages into the granuloma, the bacteria can use them to expand further. Some germ-laded macrophages then move to a new location, where they again attract more macrophages. New tubercles form and the scene is repeated.

Ramakrishnan and her research team have identified a molecular mechanism by which the mycobacteria that cause TB induce the body to form these production and distribution nodules. Researchers have long known that TB virulence is associated with a small protein the bacteria secrete, called ESAT-6.

Ramakrishan's group now has found that this secreted bacterial protein induces epithelial cells -- the cells that make up membranous tissue covers inside the body -- to produce an enzyme called MMP9. This enzyme has many functions including breaking down gelatin -- a connective tissue protein -- into its components. In people, the presence of MMP9 is associated with increased susceptibility to infection and worse outcomes. The findings of this new study explain why this might be the case. MMP9 is also implicated in the development of several non-infectious inflammatory conditions, like arthritis, as well as heart disease and cancer.

Epithelial cells were once thought to be bystanders as tuberculosis took hold, according to the research group. However, their latest findings suggest that www.microbiologyworld.com

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secretion of MMP9 by epithelial cells is amplified in the vicinity of a single TB infected macrophage. The activity of this enzyme draws in uninfected macrophages to join the infected macrophage to form and expand the granuloma.

"TB bacteria may have a two-prong strategy," said the first author of the Dec. 10 Science Express report, Dr. Hannah E. Volkman, who recently received her Ph.D. from the UW Molecular and Cellular Biology Program, "whereby the bacteria simultaneously suppress the macrophages inflammatory programs in order to create a hospitable niche inside them, while prodding epithelial cells to signal more macrophages to arrive and be unwitting participants in their home expansion project."

The researchers genetically "knocked out" MMP9 production in zebrafish embryos to see if that made them more resistant to TB. After TB infection, these embryos indeed had greater survival rates, fewer bacteria, and fewer granulomas than their normal, MMP9-producing siblings. This finding suggested that intercepting the production of MMP9 in epithelial cells should be further studied as a possible TB therapy.

"These novel findings," said Dr. William Parks, a UW professor of medicine and director of the UW Center for Lung Biology who was not part of this study, "point to new ways in which the body's resident cells can effect an inflammatory response and may have relevance beyond TB infection. The pathogen-to-epithelium-to-macrophage pathway they uncovered should provide several new avenues that could be targeted for intervention."

Co-authors of the article, "Tuberculous Granuloma Induction via Interaction of a Bacterial Secreted Protein with Host Epithelium," in addition to Volkman and Ramakrishnan, are Tamara C. Pozos, a former UW infectious disease fellow who is now on the faculty of Children's Hospital and Clinics of Minnesota; John Zheng, a UW medical student; J. Muse Davis, an M.D./Ph.D. student at Emory University; and John F. Rawls, assistant professor of cell and molecular physiology, microbiology, and immunology, University of North Carolina, Chapel Hill.

Source: University of Washington www.microbiologyworld.com

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How Simple Can Life Get? It’s Complicated In the pageant of life, we are genetically bloated. The human genome contains around 20,000 protein-coding genes. Many other species get by with a lot less.

The gut microbe Escherichia coli, for example, has just 4,100 genes.

Scientists have long wondered how much further life can be stripped down and still remain alive. Is there a genetic essence of life? The answer seems to be that the true essence of life is not some handful of genes, but coexistence.

(The microbe Escherichia coli has just 4,100 protein-coding genes.

Scientists have found, by systematically shutting those genes off one at a time, that only 302 are absolutely essential to its survival) E. coli has fewer genes than we do, in part because it has a lot fewer things to do. It doesn‘t have to build a brain or a stomach, for example. But E. coli is a versatile organism in its own right, with genes allowing it to feed on many different kinds of sugar, as well as to withstand stresses like starvation and heat.

In recent years, scientists have systematically shut down each of E. coli‘s genes to see which it can live without. Most of its genes turn out to be dispensable.

Only 302 have proved to be absolutely essential. www.microbiologyworld.com

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Those essential genes carry out the same fundamental tasks that take place in our own cells, like copying DNA and building proteins from genes. And yet the 302 genes that are essential to E. coli turn out not to be life‘s minimal genome.

Scientists have come up with lists of essential genes in other microbes, and while the lists overlap, they are not identical. Scientists can also look to nature for species that are closer to the minimal genome. In 1969, they first recognized that a group of disease-causing bacteria called Mycoplasma had remarkably tiny genomes. One species, Mycoplasma genitalium, turned out to have a mere 475 genes — one-fiftieth the number in our own set.

For years, M. genitalium held the record for the smallest genome. (Scientists don‘t allow viruses into this contest, since viruses can‘t grow and reproduce on their own.) But in recent years, M. genitalium has lost its minimalist crown.

Today, the record-holder is a microbe called Tremblaya princeps, which contains only 120 protein-coding genes.

Have we found the minimal genome at last? The answer, once again, is no. But the reason for that reveals something else intriguing about life.

Tremblaya lives in one particular place: the body of a mealybug. And the mealybug, in turn, depends on Tremblaya for its survival.

The insect‘s only source of food is the sap that it drinks from trees. On its own, the mealybug couldn‘t survive on this meager diet. Tremblaya transforms the sap into vitamins and amino acids, which the mealybug can then use to build proteins. In exchange for this biological alchemy, mealybugs provide Tremblaya with a steady source of food and shelter.

It‘s not precisely accurate to say that Tremblaya provides this service. It needs help. Scientists have long known that Tremblaya contains mysterious blobs, but it wasn‘t until 2001 that Carol D. von Dohlen of Utah State University and her colleagues discovered that those blobs were a second species of bacteria, living within Tremblaya.

The bacteria, named Moranella endobia, have a genome of their own. It‘s a tiny genome, with just 406 genes, but it‘s more than twice as big as Tremblaya‘s.

Last month in the journal Cell, John McCutcheon of the University of Montana and his colleagues dissected the genes of both Tremblaya and Moranella to get a www.microbiologyworld.com

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better sense of what each one does. The two species split up the work involved in building amino acids and assembling them into proteins. Just as the mealybug cannot live without its microbes, the microbes can‘t live without each other.

Dr. McCutcheon‘s research reveals a baroque history. At some point in the distant past, the ancestors of Tremblaya infected the ancestors of mealybugs.

The microbes gave the insects new metabolic powers, allowing them to feed on an abundant substance — sap — that most other insects couldn‘t touch. In its comfortable environment, Tremblaya cast off most of its genes.

Only later did Moranella invade the mealybug, and then Tremblaya. It took over some of Tremblaya‘s work, opening the way for Tremblaya to lose even more of its DNA, until it was stripped down to a mere 120 genes.

Tremblaya and Moranella are the only bacteria found in a healthy mealybug.

But Dr. McCutcheon and his colleagues also found vestiges of vanished microbes — in the mealybug‘s own DNA. Some of its genes are more closely related to genes found in bacteria than genes found in any animal.

This strange resemblance means that mealybugs were once host to other species of bacteria, and some of the genes from those mystery microbes accidentally ended up incorporated into their own DNA. Six separate species apparently donated genes to the insects. Dr. McCutcheon and his colleagues suspect that the insect uses some of these genes to manage its microbial residents — perhaps using bacteria proteins to extract amino acids from them, for example.

Studies like Dr. McCutcheon‘s show that the concept of a minimal genome, while provocative, is ultimately a dead end. Life does not exist in a laboratory vacuum, where scientists can pare away genes to some Platonic purity. Life exists in a tapestry, and the species with the smallest genomes in the world survive only because they are nestled in life‘s net.

Note: (An earlier version of this article misstated the academic affiliation of Carol D. von Dohlen. Dr. von Dohlen, a biologist, is with Utah State University, not the University of Utah)

- Samir Aga www.microbiologyworld.com

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Microbiology World

Safe Clearance of Salmonella Individuals with an intact complex gut flora are more likely to clear Salmonella after an infection than individuals with an altered, less complex gut flora. This is suggested by results from a mouse model for Salmonella diarrhea asking why certain people become chronic carriers after a salmonella infection.

Salmonella is troublesome – and can become even more so: even long after an infection has been overcome, certain people can become chronic carriers. They feel healthy, no longer notice any signs of the infection and don‘t have diarrhoea. However, they still excrete a large number of the pathogens in their faeces even weeks after recovery and, unintentionally, can thus pass on the intestinal disease.

Wolf-Dietrich Hardt, a professor of microbiology at ETH Zurich, and his team have now discovered the circumstances under which an individual can become a chronic carrier of salmonella in a mouse model.

Immune response not enough by itself In the case of a first infection with a pathogenic salmonella strain, the mouse (and person) affected develops so-called secretory antibodies to fight the germ. In the case of a second infection with the same bacteria strain, these antibodies help rendering the intruders innocuous in the gut lumen.

This standard immune response, however, doesn‘t explain why single individuals become chronic carriers. For instance, the experiments showed that genetically modified mice without the corresponding antibodies cleared the pathogen once and for all.

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Intestinal bacteria dispose of the competition The microbiologists only discovered the clearance mechanism at second glance. Like in the human gut, tens of billions of various types of bacteria also live in mouse intestines – commensal bacteria that grow densely in the gut.

The experiments have now revealed the advantage of mice that are well-equipped with gut flora: if it‘s diverse and complex, salmonella has little chance of settling permanently in the gut, becoming dislodged and disposed of in the faeces.

Hardt and his team have created a mouse whose gut flora is extremely simple and species-poor. In these mice, the pathogen can implant itself, regardless of the remaining immune response. Whilst the carrier no longer feels any effects of the infection, traces of the pathogens remain in the faeces even weeks after the infection.

One percent of patients affected Humans, Hardt suspects, should have a similar mechanism to mice. However, chronic carriers are rare in humans: only one percent of patients have salmonella in their faeces long after overcoming the disease. ―In Germany, only 500 in every 50,000 patients would be affected‖, says the ETH-Zurich professor.

For people who work in the food industry, especially meat processing, this is serious; they can‘t work until all traces of salmonella have disappeared. Treatment methods can be quite crude. Patients are sent into quarantine and given antibiotics. If that doesn‘t contain the disease, the gall bladder might be removed. ―That‘s where the salmonella seems to settle more long-term if it can‘t be eliminated altogether‖, says Hardt.

If a way could be found to supplement and stabilise the patients‘ gut flora permanently with a greater variety of bacteria, persistent Salmonella infections might subside without drastic intervention. However, that is still a long way off. For the time being, we still know far too little about how the commensal bacteria work to manipulate or use them specifically for therapeutic purposes.

Reference: Endt K, Stecher B, Chaffron S, Slack E, Tchitchek N, et al. 2010 The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea.

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Funny Microbiology Pictures

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How many viruses on Earth?

How many different viruses are there on planet Earth? Twenty years ago Stephen Morse suggested that there were about one million viruses of vertebrates (he arrived at this calculation by assuming ~20 different viruses in each of the 50,000 vertebrates on the planet). The results of a new study suggest that at least 320,000 different viruses infect mammals.

To estimate unknown viral diversity in mammals, 1,897 samples (urine, throat swabs, feces, roost urine) were collected from the Indian flying fox,Pteropus giganteus, and analyzed for viral sequences by consensus polymerase chain reaction. This bat species was selected for the study because it is known to harbor zoonotic pathogens such as Nipah virus. PCR assays were designed to detect viruses from nine viral families. A total of 985 viral sequences from members of 7 viral families were obtained. These included 11 paramyxoviruses (including Nipah virus and 10 new viruses), 14 adenoviruses (13 novel), 8 novel astroviruses, 4 distinct coronaviruses, 3 novel polyomaviruses, 2 bocaviruses, and many new herpesviruses.

Statistical methods were then used to estimate that P. giganteus likely harbor 58 different viruses, of which 55 were identified in this study. If the 5,486 known mammalian species each harbor 58 viruses, there would be ~320,000 unknown viruses that infect mammals. This is likely to be un under-estimate as only 9 viral families were targeted by the study. In addition, the PCR approach only detects viruses similar to those that we already know. Unbiased approaches, such as deep DNA sequencing, would likely detect more.

Let‘s extend this analysis to additional species, even though it might not be correct to do so. If we assume that the 62,305 known vertebrate species each harbor 58 viruses, the number of unknown viruses rises to 3,613,690 – over three times more than Dr. Morse‘s estimate. The number rises to 100,939,140 www.microbiologyworld.com

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viruses if we include the 1,740,330 known species of vertebrates, invertebrates, plants, lichens, mushrooms, and brown algae.

This number does not include viruses of bacteria, archaea, and other singlecelled organisms. Considering that there are 1031 virus particles in the oceans – mostly bacteriophages – the number is likely to be substantially higher.

Based on the cost to study viruses in P. giganteus ($1.2 million), it would require $6.4 billion to discover all mammalian viruses, or $1.4 billion to discover 85% of them. I believe this would be money well spent, as the information would allow unprecedented study on the diversity and origins of viruses and their evolution. The authors justify this expenditure solely in terms of human health; they note that the cost ―would represent a small fraction of the cost of many pandemic zoonoses‖. However it is not at all clear that knowing all the viruses that could potentially infect humans would have an impact on our ability to prevent disease. Even the authors note that ―these programs will not themselves prevent the emergence of new zoonotic viruses‖. We have known for some time that P. giganteusharbors Nipah virus, yet outbreaks of infection continue to occur each year. While it is not inconceivable that such information could be useful in responding to zoonotic outbreaks, the knowledge of all the viruses on Earth would likely impact human health in ways that cannot be currently imagined.

Update 1: I neglected to point out an assumption made in this study that detection of a PCR product in a bat indicates that the virus is replicating in that animal. As discussed for MERS-CoV, conclusive evidence that a virus is present in a given host requires isolation of infectious virus, or if that is not possible, isolation of full length viral genomes from multiple hosts, together with detection of anti-viral antibodies. Obviously these measures cannot be taken for a study such as the one described above whose aim is to estimate the number of unknown viruses. www.microbiologyworld.com

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You can also send your articles to info@microbiologyworld.com or broneps1@gmail.com Selected ones will be published in our next issue of Nov-Dec. Thanks, Microbiology World Team

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