Microbiology World Sept Oct, 2013microbiologyworld.com/wp-content/uploads/2014/10/Microbiology... · All around our planet there are microbiologists making a difference to our lives

Microbiology World Sept – Oct, 2013

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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

COUNCIL



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



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.



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.



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.



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).



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



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



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.



Who is father of what?

Subject Father Biology Aristotle

Evolution Charles Darwin

Genetics Gregor Mendel

Microbiology Antonie van Leeuwenhoek and

Louis Pasteur

Molecular biology Linus Pauling

Neuroscience Santiago Ramón 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

Bacteriology Robert Koch, Ferdinand Cohn,

Louis Pasteur, Antonie van

Leeuwenhoek

Immunology Edward Jenner



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.



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



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 gram-

negative 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 50μl of patients‘ 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.



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 penicillin-

insensitive 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.

- Bharat Pangeni



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 1970‘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.



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

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 Parkinson‘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

Fig: Clostridium botulinum spores



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 scientist‘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 – 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.



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



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.



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



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



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.



"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



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



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.



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



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



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.



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.



Funny Microbiology Pictures



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



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 single-

celled 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.



You can also send your articles to

[email protected]

or

[email protected]

Selected ones will be published in

our next issue of Nov-Dec.

Thanks,

Microbiology World Team

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