Extremophiles Life Under Extreme Conditi

2013
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Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

2013
Contents
Page
Topics
No.
Extremophiles: Life Under Extreme Conditions 03
Medical And Biotechnological Applications Of
10
Extremophiles
Survival Of Hyperthermophiles Under Extreme
19
Conditions From Genetical Point Of View
A Talk With
Naowarat Cheeptham : A Renowned Cave 22
Microbiologist
Bacterial Toxins Induce Their Relatives Production 30
Salmonella as a Cancer Fighter 35
Interview of PhD Fellow by We The Microbiologist 36
Periodontal etiology 40
TOP NEWS 42
The Nobel Prize in Physiology or Medicine 2013 44

*NOTE: - THE IMAGE ON THE COVER PAGE IS TAKEN FROM GOOGLE IMAGES
2

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EXTREMOPHILES
LIFE UNDER EXTREME CONDITIONS.
PRINCETEEJAY
DOS MICROBIOLOGY
UNIVERSITYOF MYSORE
princeteejaywigglesworth@yahoo.com
One bright morning, I stepped out of the comfort of my room to start the days
journey; right out there to meet me was a bright sun shining in its brilliance. I
reached to my cell phone and checked the weather forecast; the temperature was
expected to reach 30oC. Thats pretty too hot for the part of the world I am. I knew
I would be cycling on average of 3km; to be comfortable I had to equip myself
with cold water and definitely a towel, my heart reached to my friends in the North
that would be facing a 45oC day time temperature thats really to hot can I ever
survive that?
Then it struck me, as a microbiologist some microbes survives hotter temperature

than that, common how did they do that? And not just temperature, adverse
conditions beyond human imagination, these microbes are there and actively
living; in fact they love it, they wouldnt survive elsewhere and we call them
extremophiles.
Extremophiles got their name from Latin extremus meaning "extreme" and
Greek phili meaning "love", they are organism that thrives in physically or
geochemically extreme conditions that are detrimental to most life on
earth. Extremophiles thrive in extreme environment which includes high
temperature, pH, pressure, and salt concentration; or low temperature, pH, nutrient
concentration, or water availability. Even some extremophiles tolerates extremely
high levels of radiation or toxic compounds.
Let us look into some of them one by one:
THERMOPHILES
Thermophiles are microorganisms that thrive at relatively high temperatures,

between 45C and 80C.They belong to the Domain Archaea and Phylum
3 Crenarchaeota. E.g.: Thermusaquticus, Pyrococcusfuriosus, Pyrococcusabyssi
Habitat

2013
Yellow Stone National Park:
With over 10,000 geothermal features
including hot springs, mud pots, fumaroles, and
geysers, Yellowstone National Park provides vast
habitats for a wide variety of thermo tolerant and
thermophilic organisms.
Kamchatka
Kamchatka is a 1,500 km long

peninsula in far Eastern Russia. With 30
active volcanoes, geothermal features such
as geysers and hot springs, and a constantly
evolving landscape this area is called the
land in the making. Because of its variety
off geothermal features and its pristine
condition, Kamchatka has been recent
hotspot for thermophile research.
Mechanism Of Survival For This Group Of Organisms Include:
Protein Stability: A highly hydrophobic core, which decreases the tendency

of the
he proteins to unfold.Chaperonins are also present which functions to
refold partially denatured proteins.
DNA Stability: High temperature is lethal to DNA as it melts the DNA. A

variety of mechanisms are involved in stabilizing it and this are:
Thermostabilizers.
bilizers.
Reverse Gyrase.
DNA binding proteins.
Lipid Stability: Lipid bilayers consist of branched chain hydrocarbons

linked by ether linkages to glycerol. All thermophiles produce lipids
constructed upon the diphytanyltetraether model which is more thermo
4
tolerant.
Microbiology Today (Oct.-Nov.

Nov. 2013) | We The Microbiologist
2013
ACIDOPHILES
They are microorganisms that grow optimally at pH values of 2.0. In general, the
low pH of the habitat is the consequence of microbial metabolism, and not a
condition imposed by the system, as is the case of other extreme environments.
Acidophiles are able to survive in this acid habitat because its cells pump out
poisonous hydrogen ions fast enough not to damage the DNA inside the nucleus. If
they could not pump out the hydrogen ions, then acidophiles wo
would
uld not be able to
survive
E.g.: Sulfolobusaciocaldarius,
Alicyclobacillusacidocaldarius,
dunaliellaacidophila
Habitat
Tinto River Most of the characterized strict

acidophilic microorganisms have
been isolated from volcanic areas
or acid mine drainage. Acidophiles
are not just present in exotic environments such as Yellowstone National Park or
deep-sea
sea hydrothermal vents. Genera such as Acidithiobacillus and
Leptospirillumbacteria, and Thermoplasmalesarchaea,, are present in syntrophic
relationships in the more abundance environments of concrete sewer pipes and
implicated in the heavy-metal
metal-containing,
containing, sulfurous waters of rivers such as the
Rheidol. Such microorganisms are responsible for the phenomenon of acid mine
drainage (AMD) and thus are important both economically and from a
conservation perspective.
Mechanism of Survival:
1. The cell membrane is

highly impermeable to
protons
5
2. Membrane channels have a
reduced pore size

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3. Excess protons are pumped out of the cell
4. Proton uncoupling by organic acid
5. DNA and protein damage caused by low pH can be can be repaired by

chaperones
6. Intracellular enzymes might be stabilized by iron rivets
ALKALIPHILES
They are microorganisms that grow

optimally at pH values above 9.0, often
with pH optima around 10.0, while
showing little or no growth at near neutral
pH values. Some microbial communities
live at pH of 12.0 in the soda lakes.
E.g.: Natronococcusgregory
Natronococcusgregoryi,
Deinococcusthermus,
Deinococcusradiodurans,
Pyrolobusfumarii.
Iron Mountain Mine
Mechanism of Survival
Under alkaline conditions, the concentrations of hydrogen ions are very low
and cells have trouble using ATP
ATP-synthasee to produce energy and other essential
ions such magnesium and calcium which precipitate out of the water as salts. Base
loving microbes circumvent these problems by actively pumping in these ions and
by exporting others to maintain their interior at near
near-neutrality.
neutrality. Furthermore, the
cell wall of alkaliphiles acts as a defense barrier from extreme environmental
conditions.
6

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HALOPHILES
These extremophiles thrive in environments with have very high concentration of

salt. The name comes from the Greek for "salt
"salt-loving".
loving". They have a capacity to
balance osmotic pressure and resist the denaturing effects of salts.
Classification
Slightly halophile 22-5%
Moderately halophile 55-10%
Extremely halophile 20
20-30%
Non halophile - less than 2%
Halotolerant those that doesnt need high salt to grow but are not affected
by it
The two largest and best-studied

studied hypersaline lakes are the Great Salt Lake, in the
western United States. The Great Salt Lake is
larger (3900km2) and shallower (10 m), and
contains salts that are close in relative
proportion to sea water. The Dead Sea is
smaller (800km2) and deeper (340 m m), and
contains a very high concentration of
magnesium salts. Both of these lakes are close
to neutral pH, although the Great Salt Lake is
slightly alkaline while the Dead Sea is slightly
acidic. While the Sambhar Salt Lake Lake,
Indias largest inland salt, si
sits 96 km south west
of the city of Jaipur along National Highway 8
in Rajasthan. Great Salt Lake located in western USA

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Dense growth of halophilic microorganisms in hypersaline environments, like this saltern

near SanFrancisco, leads to reddening of the brine.
Sambhar Salt Lake in INDIA
Survival Mechanism:
Osmoregulation
Osmosis is the process of flow of solvent from the region of higher to the
lower concentration. Halophiles maintain high solute concentrations inside their
cells. Some types of halophiles have unique chloride pumps that transport chloride
from the external environment to the inside of the cells.
Application
8
All said and done, all this varying extremophiles have been annexed for human
benefit and this includes:

2013
Applications of salt-active enzymes include those that can break down
viscous materials present in oil wells as well as enzymes that can carry out
desirable transformations in highly salted foods.
Cellulose-degrading enzymes a cellulose-utilizing, extremely halophilic

bacterium was first reported by Bolobova et al. (1992). The obligate
anaerobic organism named Halocellacellulolytica is able to utilize cellulose
as a sole carbon source.
Enzymes have been used in detergents since the 1960s. The use of enzymes
in laundry and automatic dish washing detergents provides consumers clear
cleaning performance with lighter burden on environment.
Taq Polymerase enzymes used for PCR obtained from Thermusaquaticus

from yellow stone park
Pfu polymerase from microorganism in hydrothermal vent useful in forensic
Extremophiles have been of very much importance, they have provided useful data
that are basic to molecular biology, including information on protein folding.
These extremophiles have endeared themselves to multibillion dollar industries,
including agriculture, chemical synthesis, laundry detergents and pharmaceuticals.
And the enzymes from these extremophiles are called as extremozymes
Maybe I should look into engineering some of the DNA of thermophiles into my
own gene probably I wont be bothered about the temperature.
References
Raina M. Maier, Ian L. Pepper, Charles P. Gerba. (2009). Environmental
microbiology. Volume 397 of methods in enzymology. Academic press.
Cavicchioli R. and Thomus T. (2000). Extremophiles in Encyclopedia of
Microbiology. Editors Lederberg J et al., pp317-337.volume 2.Academic
press.
9 Methods in Microbiology, volume 35-extremophiles, edited by Fred

A.Rainey and Aharon.
http://en.wikipedia.org/wiki/Extremophile

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Medical and Biotechnological Applications of

Extremophiles
HARSHADA KASAR
MSC MICROBIOLOGY
MICROBIOLOGIST, RANQ REMEDIES PVT LTD.
cool18rinks@gmail.com
Extremophiles were first discovered just 40 years ago in the hot springs of
Yellowstone National Park. Since their discovery, scientists around the world have
worked to find how extremophiles might be useful to humans, and how they might
harm humans. Since extremophiles use proteins in different ways than other
microorganisms do, scientists are working on adding a sixth kingdom in the
classification of life just for the extremophiles. This classification will be called
Archea and it will include all prokaryotic and eukaryotic extremophiles. From a
phylogenetic point of view, extremophiles belong to this newly defined domain of
life, the Archaea, and the term 'Extremophile' is often used synonymously with
them.
R. D. MacElroy first coined the term Extremophile.
Thermophiles were the first extremophile to be discovered, but other extremophiles

have been found living in ice, deep under the surface of the ocean, in salty
environments, and in environments with both high and low pH levels. When these
organisms were found living in harsh environments that would kill any other
organism, scientists began trying to understand how they were able to survive. The
proteins inside extremophiles are adapted to the habitat where the extremophile
lived. It was discovered that each type of extremophile had enzymes that were
resistant to extreme heat, saline, acids, high or low pH, and high barometric
pressure. There are different types of extremophiles, called on the basis of their
habitat.
Xerophiles are the one that live in extreme dry environments.
Acidophiles are microorganisms that can live in acidic environments, usually at

10 pH 2.0 or below.
Thermophiles are microorganisms that live and grow in extremely hot

environments that would kill most other microorganisms. They grow best in

2013
temperatures that are between 50oC/120oF- 70oC/158oF. They will not grow if the
temperature reaches 20oC/68oF.
Alkaliphiles live in alkaline environments like soda lakes, or alkaline soil. The pH
level in alkaline substances is from about 9 to 11 on the pH scale.
Psychrophiles are microorganisms that live and grow better in temperatures that
are about -10 to 20C (14 to 68F).
Halophiles are aerobic microorganisms that live and grow in high saline or salty
environments. The saline content in halophilic environments is usually 10 times
the saline or salt content of normal ocean water. Normal ocean water has a saline
or salt level of 30 percent.
Capnophiles are microorganisms which thrive in the presence of high

concentrations of carbon dioxide.
Piezophile, previously termed Barophiles are microorganisms that can survive

under great pressures. The pressure often exceeds 380 atm (38 MPa).
Metallophiles are extremophilic organisms able to live in the presence of high

metal ion concentrations.
Radiophiles are microorganisms able to live in the presence of high radiation

levels.
Recently extremophiles have earned an important place in Astrobiology, the search

for life in the universe. Indeed, the possibility that life can develop at extreme
conditions of temperature, pressure, pH, high radiation or low moisture levels has
increased the chances of finding life elsewhere in the universe, in systems with
conditions completely different from our planet Earth.
The discovery that many organisms, called extremophiles, live and thrive in
environments considered extreme for human life, led to a great interest in these
organisms and their biomolecules. In fact, proteins and enzymes isolated from
extremophiles are considered useful for a variety of applications, due to their
extraordinary properties to work in hostile conditions.
11
Scientists spent a huge amount of money studying the special characteristics of the
enzymes inside extremophiles. Many different industries would like to use these

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enzymes in making products like artificial sweeteners, stonewashing blue jeans,
and in identifying the makeup of the genes of criminals. Scientists hope that the
enzymes inside extremophiles will replace regular enzymes used in enzyme based
industries.
The medical industry has discovered that there are some uses for extremophiles in
medicine. Scientists are searching for ways that the special proteins inside
extremophiles can be used to fight infectious diseases and genetic diseases.
Enzymes are proteins and are sometimes used as biological catalysts. Enzymes
inside extremophiles have been given the name of extremozymes. These
extremozymes cause chemical reactions in extremophiles that allow them to
survive in deadly environments. Before extremophiles were discovered, regular
proteins had to be protected from breaking down and becoming useless. Scientists
hope that the proteins in extremophiles will not need special treatment like regular
proteins. This will save all industries a great deal of money.
Extremophilic micro-organisms represent a potentially valuable resource in the

development of novel biotechnological processes. Most applications involving
extremophiles are based on the use of their biomolecules, in particular their
enzymes. In fact, enzymes from extremophilic micro-organisms represent versatile
tools for sustainable developments in a variety of industrial applications, as they
show important environmental benefits due to their biodegradability, specific
stability under extreme conditions, improved use of raw materials and decreased
amount of waste products. These enzymes are already in use as biocatalysts in
industrial processes.
Biotechnological applications of enzymes are often hampered by their low stability

to heat, pH, organic solvents and proteolysis (Sthal, 1993, Shoichet et al. 1995).
However, the enzymes that have been isolated from these micro-organisms are
extremely thermostable and usually resistant to the action of chemical denaturants,
detergents, chaotropic agents, organic solvents as well as to the exposure to
extreme values of pH (Nucci et al.1995, DAuria et al.1996, 1998).
Sensing systems that are more and more sensitive and simple are needed in various
12
fields, such as clinical, environmental and food analysis. The development of such
sensing systems requires that proteins be stable under a wide range of
environmental conditions, as their replacement accounts for most of the operating
costs. Examples of recent applications of thermophilic proteins for the

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development of a new class of fluorescence non-consuming substrate biosensors
for monitoring the levels of two analytes of high social interest are glucose and
sodium.
The use of proteins or enzymes from thermophilic organisms represents an

interesting alternative to the efforts to improve stability properties of mesophilic
biomolecules. Enzymes isolated from thermophilic sources are natural examples of
stable biomolecules (Robinson et al. 1992). The most well-known example of a
successful application of a thermophilic enzyme is Taq DNA polymerase isolated
from Thermusaquaticus (Chien et al. 1976; Kaledin et al. 1980). The use of this
enzyme allowed the automation of PCR technology, with a great advantage for
research laboratories and industries. Other widespread biotechnological
applications of thermophilic enzymes include the utilization of amylase for the
production of glucose and xylanase to whiten paper. Furthermore, thermophilic
enzymes have been used for the construction of optical nanosensors, stable and
non-consuming analyte.
A thermostable glucokinase from the thermophilic organism Bacillus

stearothermophilus- use as a reversible glucose sensor (DAuria et al. 2002).The
potential application of glucose dehydrogenase (GD) from the thermoacidophilic
archaeon Thermoplasma acidophilum for glucose sensing was investigated
(DAuria et al. 2000).
The a-amylases of Pyrococcus woesi (Koch et al., 1991) and P. furiosus (Brown et
al., 1990; Koch et al., 1990) are the most thermophilic versions of the protein
known, possessing optimal temperatures of 100C each. Unlike mesophilic a-
amylases, the Pyrococcus enzymes do not require the presence of calcium.
Trehalose is a non-reducing dissacharide, which has found broad use as a

stabilizing agent in numerous industries. Due to the expensive process of trehalose
extraction from bakers yeast, there has been much interest in describing organisms
capable of trehalose biosynthesis. The recent report of thermophilic trehalose-
synthesizing enzymes from S. shibatae could extend the industrial synthesis and
applicability of trehalose (Di Lernia et al., 1998).
Thermostable xylanases have gained interest of late given their roles in enzyme-
13 assisted paper bleaching, an attractive alternative to current chlorine bleaching
techniques (Viikari et al., 1994).

2013
Current concerns regarding the ability to produce or purify archaeal extremozymes
in sufficient quantities for industrial use will also be alleviated in the near future.
Presently, heterologous expression of thermo- and hyperthermoarchaeal

extremozymes has shown that, in general, the intrinsic extremophilic properties of
the enzymes are preserved upon transfer to elevated temperatures (Morana et al.,
1995), although examples in which thermotolerance was not preserved following
heterologous expression have been reported (Purcarea et al., 1997). Still,
industrial-scale production of archaeal extremozymes in heterologous hosts and
their subsequent purification is possible (Morana et al., 1995; Miura et al., 1999).
The steady increase in the number of newly isolated extremophilic micro-
organisms and the related discovery of their enzymes document their enormous
potential within the scientific field. Extremophilic enzymes have become model
systems to study enzyme evolution, enzyme stability and activity mechanisms,
protein structurefunction relationships and biocatalysis under extreme conditions.
In particular, enzymes from thermophiles and hyperthermophiles possess a great
potential for biotechnological applications, due to their high resistance not only to
temperature, but also to chemical, organic solvents and extreme pH values.
Ground breaking research on extremophiles continues to this day, with the recently
discovered 22nd genetically encoded amino acid pyrrolysine from the
archaeon, Methanosarcina barkeri, (Hao et al., 2002; Srinivasan et al., 2002).
The major impetus driving extremophile research is the biotechnological potential

associated with them. Indeed, the application of extremophiles in industrial
processes has opened a new era in biotechnology. Each group has unique features
that can be exploited to provide biomolecules with a wide variety of applications.
14

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Table 1.Extremophiles and some examples of their biotechnological products

and applications.
Thermophiles and Hyperthermophiles Applications

DNA polymerases DNA amplification by PCR
Lipases, pullulanases and proteases Detergents
Amylases Baking and brewing
Xylanases Paper bleaching
Halophiles Applications
Bacteriorhodopsin Optical switches and
photocurrent generators
Lipids Liposomes for drug delivery and cosmetics
Compatible solutes e.g. Ectoin Protein, DNA and cell protectants
-Linoleic acid, -carotene and cell extracts, Health foods, dietary supplements,
e.g. Spirulina and Dunaliella food colouring and feedstock
Psychrophiles Applications
Alkaline phosphatase Molecular biology
Proteases, lipases, cellulases and amylases Detergents
Polyunsaturated fatty acids Food additives, dietary supplements
Ice nucleating proteins Artificial snow, food industry e.g. ice
cream
Alkaliphiles and Acidophiles Applications
Proteases, cellulases, lipases and pullulanases Detergents
Elastases, keritinases Hide de-hairing
Cyclodextrins Foodstuffs, chemicals and pharmaceuticals
Acidophiles Fine papers, waste treatment and de-
gumming
Sulphur oxidizing acidophiles Recovery of metals and de-sulphurication
15 of coal
Acidophiles Organic acids and solvents

2013
It is also important to name enzymes isolated from psychrophiles, such as lypases,
proteases and cellulases, which have been used as additives for the preparation of
detergents working at low temperatures, or as additives in the frozen food industry.
Evidence from piezophiles is limited although piezophilic mutants of antibiotic-

producing Actinomyces species have been shown to produce novel antibiotics
when grown under high-pressure (Abe and Horikoshi, 2001).
Halophiles provide the most potential as they are more easily manipulated cell
factories compared with other extremophiles (Rodriguez-Valera, 1992; Das Sarma
and Arora, 2001). Evidently, the haloarchaea Haloferaxmediterranii and
Haloferaxgibbonsii are known to produce halocins, which, like bacteriocins,
inhibit growth of closely related species (Aravalli et al., 1998; Prangishvili et al.,
2000).
Interestingly, a recent paper has highlighted extremophiles as an unexplored

source of antifungal compounds. A novel thermophilic Pseudomonas species was
demonstrated to synthesize an iron-binding compound pyochelin that has
activity against several species of Candida and Aspergillus fumigatus (Phoebe Jr.
et al., 2001).
Other extremophile products may find application in veterinary medicine in the

future. These include enzymes in biosensors, compatible solutes in skin care
products, drug excipients, treatments for respiratory disease, radioprotectants,
peptide antibiotics, archaeal lipids for drug delivery and anti-cancer therapeutics.
Polysaccharides secreted from halophilic archaea could find use in oil exploration
efforts (Rodriguez-Valera, 1992) while secreted haloarchaeal polymers have been
considered as a raw material for biodegradable plastics (Fernandez-Castillo et al.,
1986).
Often, the mere presence of archaeal communities carries considerable economic
value. Methanogenic archaea are the focus of much attention in their capacity as
clean and inexpensive energy sources (Reeve et al., 1997), while acidophilic
archaea have been identified at several acid mine drainage sites where their
mineralsulfide oxidizing abilities play an important role in the geochemical sulfur
cycle
16 (Vaquez et al., 1999; Edwards et al., 2000; Golyshina et al., 2000).
Few Examples of Interesting Extremophiles:

2013
Bacillus infernus - the 'bacillus from hell' was identified as the first anaerobic
member of the bacterial genus Bacillus in 1995. Obtained from depths of
approximately 2700 m below the land surface, this extremophile was found to be
thermophilic (60C), halotolerant (salt concentrations 0.6 M) and slightly
alkaliphilic (pH 7.8; Boone et al., 1995).
Methanococcus jannaschii was the very first archaeon to have its genome
sequenced in 1996. It was isolated in 1983 from the sea floor surface of a Pacific
thermal vent white smoker off the coast of Baja, California. It is
methanogenic (methane producer), thermophilic, strictly anaerobic and autotrophic
(uses CO2 as the sole source of cell carbon), and normally lives at about 2400 m
below sea level, where the pressure is approximately 230 atmospheres (Bult et al.,
1996).
Deinococcusradiodurans is the most radiation-resistant organism known to man.
It can withstand exposure to radiation levels up to 1.5 million rads (500 rads is
lethal to humans).Discovered in 1956, it was first observed in cans of meat that had
been exposed to supposedly sterilizing doses of radiation. The many characteristics
of D. radiodurans include an extreme resistance to genotoxic chemicals, oxidative
damage, high levels of ionizing and ultraviolet radiation, and dehydration. A
recombinant strain has been engineered to degrade organopollutants in radioactive,
mixed waste environments (Cavicchioli& Thomas, 2000).
To date, new microbes are still being discovered and investigated. Most recently,
Karl Stetter and his team of microbiologists discovered the worlds smallest
microorganism Nanoarchaeumequitant (see figure), whose name roughly
translates as ancient dwarf who rides the fire ball from its tendency to latch on to
or ride the surface of the archaeal microbe Ignicoccus (fireball). The discovery
of this nano sized hyperthermophilic archaeon has led to the creation of a new
phylum, Nanoarchaeota (Huber et al., 2002). This extremophile was found in a 120
m depth submarine hydrothermal vent, north of Iceland and thrives in temperatures
close to 100oC. With less than 500 kb in its genome, N. equitans represents the
smallest archaeal genome sequenced to date and has the smallest genetic code of
all living organisms to date.
17

2013
Image provided by Prof Dr KO Stetter and Dr Rachel Reinhard, University of Regensburg. Reprinted with
permission from Nature (citation) copyright 2002-07-02 Macmillan Publishers Ltd)
As improved molecular biology tools for working with Archaea become available,
it will become possible to over express archaeal extremozymes in their native
hosts. Combined with an improved ability to grow Archaea on the reactor-scale
(Krahe et al., 1996; Mukhopadhyay et al., 1999; Schiraldi et al., 1999), the
availability of archaeal extremozymes at levels required by industry will be
improved. Finally, as the structurefunction rules that impart stability to enzymes
under various extreme conditions become better understood (Danson and Hough,
1998), it will be possible to tailor specific extremophilic traits into any protein of
interest by protein engineering or directed evolution (Arnold et al., 2001), possibly
improving upon nature.
18

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SURVIVAL OF HYPERTHERMOPHILES
UNDER EXTREME CONDITIONS FROM
GENETICAL POINT OF VIEW
Bapi Kumar Jha
B.Sc Microbiology ((Univ.of Calcutta)
M.Sc Microbiology (Univ. of Mysore)
Why and How are two wonderful conflicting simple words that always lead all
of us together to find out something that exist and operating beyond our knowledge
in our Universe. Today, Im going to present some genetical point of view on
survival of Hyperthermophiles (A kind of Extremophiles) under extreme
conditions. The pioneering work of Thomas Brock in 1960s and 1970s , Karl
Stetter and co-workers at Regensburgs (Germany) have proceeded to isolate over
30 genera (over
ver 70 species) of Hyperthermophiles. Brock was first to demonstrate,
often using simple but indigenous field of experiments that bacteria present in
boiling hot springs in Yellowstone National Park.
19 Fig: Active deep sea vent chimney, a "Black Smoker

Smoker"" spewing superheated mineral-laden
mineral
black water into the cold deep sea environment. The plume appears like black
"smoke".(Courtesy : Karl O. Stetter Hyperthermophilic Microorganisms)

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Fig: Electron micrographs of cells of hyperthermophilic Metallosphaera sedula, freeze

fracturing, bar, 0.2 m. ".(Courtesy : Karl O. Stetter Hyperthermophilic Microorganisms)
Hyperthermophiles are mainly found in water water-containing

containing volcanically and
geothermal heated environments situated mainly along terrestri
terrestrial
al and submarine
tectonic fracture zones where plates are colliding (subduction), Solfataric fields,
fields
deeply originating hot springs and vents etc. To be able to survive or thrive under
such extreme conditions, any biological entity must have either thermo-stable
thermo
membrane integrity, proteins, extremo
extremo-zymes,
zymes, DNA/RNA (Nucleic acids) or
somewhat thermo-stasis
stasis regulatory system to make them heat resistant. Proteins
stay intact and functioning at high temperature by adapting various changes, some
of them are mentioned
tioned below
In Thermus thermophilus HB27, charged residues like Arginine and Lysine
form more ion pairs which create more weak bonds to hold protein
molecules together.
Lactate dehydrogenase in thermophiles Stygiolobus azoricus and
Chlorobium tepidum has more polar amino acids that form hydrogen bonds
within subunits of the enzyme.
In Thermotoga maritima and Pyrodictium occultum,, proteins appear to have
more densely packed cores than proteins in their more moderate temperature
dwelling cousin.
In Sulfolobus
olobus brierleyi and Thermotoga marimati,, presence of shortened and
reduction loops makes them more resistant to temperature.
In Pyrolobusfumarii, proteins structures are highly embraced with disulfide
bond which makes them more thermo
thermo-stable.
20
As above mentioned for Proteins, the Nucleic acids (DNA/RNA) stay intact and
functioning at high temperature by adapting various changes, some of them are
mentioned below.

2013
In Methanopyruskandleri and Methanococcu signeus, salts like potassium
and Magnesium are found at higher levels which protect d/s DNA from
phosphodiesterase bond degradation.
Presence of Polyamines also protect against degradation first studied in

T.Thermophilus and Acidianusinfernus revealed several novel polyamines
roles.
The extensive study and research reveals that: By making extensive level
reverse DNA Gyrase, closed circular DNA makes themselves more resistant
to degradation as compare to negatively super coiled DNA.
The most interesting finding among thermophiles was the existence of Histone-
like-proteins that look like eukaryotic histone proteins; they wind DNA into tight
structures that look-like Nucleosomes and appear to keep DNA d/s at high
temperature. The tiny DNA-binding proteins such as Sac7d found in Archea bend
DNA and increase its denaturation temperature. Some Researchers says molecules
like Sac7d is the earliest stages of Histone evolution in eukaryotes.
The evolutionary changes and its role in above mentioned modifications at
different structural and physiochemical level is still under question for us. In my
view the only truthful answer to it, we dont know at this point in time, But as
long as there are unanswered questions, we will continue in the pursuit of those
answers thats for sure.
21

2013
A Talk With
Naowarat Cheeptham
A Renowned Cave
Microbiologist
conducted by,,
Saumyadip Sarkar,
Sarkar
MD, We The Microbiologist,
Microbiologist
saumyadip@wethemicrobiologist.in
Naowarat Cheeptham,, Ph.D. (aka Ann) http://www.wethemicrobiologist.in/
Associate Professor,
Department of Biological Sciences
Thompson Rivers University, Canada
email: ncheeptham@tru.ca
Q) Dr. Naowarat Cheeptham (aka Ann), the associate professor at Thompson

Rivers University and the adjunct associate professor at Chiang Mai
University, Thailand. Moreover you are known to be renowned cave
microbiologist as your current research. Starting off with your early life, how
you had been in science during your school life in Thailand and who had been
influencing you while you were a kid?
In my early life, I was fortunate to have great parents, Sub and Ubon Cheeptham,
who supported me and my education (they still are my gr greatest
eatest support), and as
rural public school teachers my parents worked very hard to support me through
my education. My parents still helped out when they could in regards to
extracurricular activities. My father studied biology and going out to collect
samples with him fostered my love of biology. Besides my parents, I was
fortunate to have had a number of great teachers, these include Ajarn Chaweewan,
my English teacher at the elementary school I attended; all my high school teachers
at Yupparaj Wittayalai,
alai, Ajarn Prof. Saisamorn Lumyong, my instructor and
research supervisor when I was at Chiang Mai University, without her and other
profs both at CMU and Hokkaido University, Japan I would not have come this
far.
22
Q) At the age of 15, you received a sch
scholarship
olarship under Ministry of Science and
Technology, under government of Thailand to study in a program for youth in

2013
sciences. If you would recall, what was the program about and does it gave
you some impact or zeal to work for science at such early age?
This DPST (Development and Promotion of Science and Technology Talents
Project - Royal Government of Thailand scholarship) program was a special
program designed to produce scientists and researchers to help develop Thailand
and was created in 1982. The scholarship was fiercely competitive across the
country, and in 1985 when I was awarded with this scholarship, it was offered to
only 25 students annually. I do not know how many students applied each year;
however, the students had to have a minimum GPA of 3.5 (out of 4) to be able to
apply and then there was a writing test (throughout the country) following with a
round table interview (by the chosen high school science teachers and prominent
university science professors) only with the students that passed the written test. I
remember that in my year only three students were selected from the Northern
region. Once one was accepted to such prestigious program, the requirement was
that we had to go to the selected high school in the region that offered this program
and maintain a very high GPA of 3.5 and up throughout school years. Besides
taking typical high school curriculum, we were assigned to think like a scientist
and work extensively on scientific research projects with university professors
when we were in high school. Moreover, each summer during high school years
we got to go to Bangkok where all of the other selected students in the same cohort
gathered, and we were at the annual science camp for several weeks meeting with
and talking science with leading scientists in the country. This program helped
shaped me to be a critical thinker and to love working in science as a researcher.
Q) You have completed your undergraduate with Microbiology (Honors with
medals) from Chiang Mai University, you move to Japan to complete your
graduate studies at Hokkaido University. How was this diverse of culture
from Thailand then to Japan? How were you accustomed with the varying
culture? Does it help you now since you are long away to Canada?
My background in obtaining degrees and working in different cultural settings has
made me more open and easily able to adapt. I also spent three months or so doing
research at the University of New South Wales in Australia financially supported
by the Thailand-Australian Government TASEAP fellowship. These experiences
are beneficial to me as a whole person and not just as a scientist, I understand the
challenges one faces as a student and/or a researcher when relocating to a different
country, and this has made me more compassionate and accepting of my fellow
colleagues and students of different backgrounds. In particular, science is a
23 universal language. One cannot underestimate those for whom English is a second
language when they cannot articulate concepts in English. I often am more patient
to hear them as when I was a student I wanted to be heard!

2013
Q) Microbes are prevailing everywhere, not only inside body but places where
people might have not been reached (like on b bed
ed rocks of sea as example).
Microbes in caves, although it sounds very new for many researchers, but
holds many interesting facts which are clearly highlighted in your book. You
had completed your PhD, where you carried your research on drug discovery
from
m extreme microbes. How the concept cave microbiology came to your
mind? How you set your ideas into plan while undergoing your research?
How your guide during your PhD motivated you for such newly research
aspect?
I have to be honest here, I forget
how I started with caves, and I
think it was by chance that I saw
great work done by my colleague
Dr. Diana Northup, though at the
time Diana worked on different
aspects of cave microbiology. It
spoke to me, and I thought
though wow,
what great habitats to look into
finding new drugs and then I got
hooked! Thanks to all those who
have come before me, the trail blazers! And when I think about it again, why not
caves? Caves are not just mysterious, dark and cold (some can be warm)
wa but we
don't know much about microorganisms that not only survive but thrive in caves
(such inhabitable habitats for other living organisms). Often, we think that we
won't see much life in caves given such harsh physical, chemical and biological
factors
rs involved in these habitats; time and time again we are always stunned at
how life thrives in such habitats. Cave microorganisms may hold promises in drug
discovery! [Picture
Picture showing Baylee Out (student of Dr. Ann), a microbiology
student from Thompson Rivers University, takes soil samples in Nakimu
Caves to study for signs of white white-nose
nose syndrome that afflicts hibernating
bats.]
Q) After completing your PhD, you came back to your native country
Thailand as a lecturer in Chiang Mai University. Currently you are associate
professor too. Do you put some interest to your students on cave microbiology
while coming out with topics outside the normal routine syllabus?
Absolutely, I love talking about microorganisms, and the best way to convey my
24
passion to students
ents is to reel them in with real world and relevant concepts like
using cave bacteria to potentially produce novel antimicrobial agents against MDR
pathogens. I love to inspire! I strongly believe that teaching and conducting

2013
research are complementary. I love learning and I found that teaching and
conducting research help fulfill my curiosity!
Q) Cave Microbiomes: A Novel Resource for Drug Discovery. Can you
please tell about this book?
I was approached by Springer after I gave a selected
Young Investigator" section at the 111th
talk in the "Young
American Society for Microbiology (ASM
(ASM) General
Meeting in New Orleans, LA, USA in May 2011.
This book was published in the Springer Brief
Series which aims to represent an underused and
under-represented field and cave microbiology fits
perfectly - in particular the application aspect of
cave microorganisms. This book also highlights a
unique approach to cave microbiology in regards to
cave microbiomes and their potential in drug
discovery. This book offers a brief insight to look
into what is happening in cave microbiology
research. As is said on the Springer website
This
This book details recent findings in the field of
cave microbiology and builds on fast
fast-paced
paced efforts to exploit an unconventional
and underexplored environment for new microorganisms which may provide an
untapped source of drugs.
Q) Cave microbiomes are extreme microbes, how you comparatively highlight
the habitat of those floras with the microbes which usually not categorized as
extremes?
es? How these microbiomes rise in evolution? Anything you want to
add, please do to extend your conclusion.
First, lets think about why caves are considered extreme habitats for living
organisms (not just microorganisms)! There are a number of physical, chemical
and biological factors that make caves a harsh home to inhabit; these include
darkness, low temperature, less nutrients, high mineral concentrations (often those
presented cations are natural DNA blocking agents), to name a few. In regards to
darkness,
kness, one can ask a question on what kind of implications this physical factor
contributes to as a harsh habitat? Darkness creates lack of photosynthetic process
hence there is no primary producers in caves that can create foods/nutrients for
25 potential living
iving organisms that live in there (of course there are exceptions
depending on the type of cave; for example, caves with bats, organic matters from
bat guano can be used as nutrients for microorganisms residing in the caves). A
great number of caves are very low in nutrients; we often refer to these as almost

2013
starved environment. With this in mind, life in caves as typical bacteria can be
very tough; however, those that have adapted to such harsh homes are thriving,
though in a much slower rate of growth compared to typical
bacteria/microorganisms. Additionally, these bacteria need to be able to adapt to
high concentration of minerals found in cave bed rocks and be able to utilize those
minerals as energy and electron sources. With such uniquely adapted
characteristics to survive and thrive in caves, these cave bacteria could
hypothetically possess very different and unique metabolic pathways that may
potentially produce new drugs for us.
Q) While working with Cave microbial analysis you might have been into
varied controversies. How you used to overcome them and stayed focused in
your work? This will definitely provide a leading understanding and
motivation for young researchers and students.
I do not understand "controversies"" here in
this context. However, whatever it means in
this context, one thing that keeps me going
when things are hard at work is the
understanding of "being able to accept": that
ideas and choices in experiments and
questions are out of our control (when it
comes to others), theyy are not right or wrong,
they are just different with their own
purposes, things are not personal. Nothing is
set in stone. When things are hard and
discouraging at work, I refer back to what is
important in life (my son, husband, family and
friends) andd back to reread my spiritual books
entitled "Awake at Work" by Michael Carroll
and "When things fall apart" by Pema
Chdrn . I am still a work
work-in-progress when
it comes to this department as well.
Q) How well you have been greeted in Canada as an Associate Professor in the
department of Biological Sciences, Thomson Rivers University? American
Society of Microbiology has selected you as one of the biology research
residency scholars
rs for ASMs Biology Research Residency Scholars Program
in Washington DC. Even Canadian Society of Microbiology has well approach
26
towards you. You have been into receiving many awards. How these used to
motivate you being a Thai Researcher working for you
yourr country as well as
internationally?

2013
I would like to think that I have been treated very well and fairly overall. It would
be too sad and disappointing to know that my ethnicity (the way I look and the way
I sound - which I cannot change) and different backgrounds could make people
judge me unfairly. To date, the CSM (Canadian Society of Microbiologists), ASM
(American Society for Microbiology), SfAM (Society for Applied Microbiology,
UK) have welcomed me to join and awarded me with funding and awards. I feel
that I have contributed greatly in both microbiology education and discipline-
orientated research. This has motivated me to contribute even more as a
representative from Thailand and Asia as a whole.
However, I shall not sugar coat this issue either. Sadly, there is still a real glass
ceiling for female scientists and it is compounded if one is a visible minority. I
shall make this clear that this issue exists everywhere, even in my own mother
country, so it is not where we are as a country; it is all about some narrow-minded
individuals who may feel and treat people that way which is unfortunate. And this,
please note, is just a small number of people; however, they can be discouraging
and hurtful. I strongly feel that these individuals are miserable; they are for some
reason often insecure in their own skin and not content at their own life/career.
Therefore, they may find way to make themselves feel better; they may often put
other people down to justify that they are better than others. I strongly believe that
this is the case for such individuals who treat people unfairly.
I am very lucky to have my parents who have taught me to treat others the same
way I want to be treated, with respect. I have practiced it my whole life. Of course
it hurts when I feel that I have to work hard (er) to get heard or to get respect back
from a small number of very close-minded individuals at different stages of my
life. Over time though, I have learned to see that this is not my problem that they
treated me and others that way, it is their problem. As I get older (and hopefully
wiser) I have more sympathy towards these kinds of characters these days. And I
respect them as they come into my life as teachers, to show me lessons to learn
from, to learn to be even kinder (I have to admit that it is hard to feel kind at
times). As an immigrant, just the fact that one uprooted from their own comfort
environment to a different place with different culture, language, values and work
ethics is challenging - this alone could cause uneasy feelings in oneself already.
Professionally, when one moves, one loses established networks and gained-
reputation, thus one has to work hard (er) to get recognized all over again. This is
not an easy task! Lots of immigrants are not fortunate to get back on their
professional careers as they may have had back home. The majority of the time, I
27 have to admit that I have been so fortunate to have a number of great and
compassionate mentors (late Drs Neil Towers and Bob Bandoni), colleagues (Drs.
Julian Davies, Arnold Demain, Gerry Wright, Ken Wagner, Diana Northup, Nancy
Van Wagoner, Kingsley Donkor, Ernest Tsui, Archana Lal, Phil Withfield, and

2013
many more it is impossible to name all), students and friends who have made my
life and work in Canada a fine one. Most importantly, my husband, Joe, and my
six year-old son, Ryder, have been my rocks! I could never have done this without
their unconditional love, unwavering belief and continued support.
Q) What would be your personal message towards young researchers and
students of Microbiology?
Keep your curiosity and dream alive, work and study hard and open to what life
may bring. Give credit where it is due! Be compassionate and learn to forgive and
be kind to yourself and others. Always accept your mistakes (see them as teachers)
and if you are in the wrong (or even when you are right), apologize. Accept that
one does not know everything and never be ashamed of not knowing everything.
Be respectful to everyone no matter who they are or what they do in life.
Q) Finally concluding with the questions, would like to express your life apart
from your work?
I am a mother, a wife, a daughter, a
sister, a friend and much more to
people around me. I would not want
to just be a successful
scientist/microbiologist. I want
people to remember me as who I am
as a whole not just what I do in life.
I love cooking, eating, traveling,
skiing, reading, knitting, learning
new and different languages, and
photography. I could have never
gotten here without my family, friends, teachers, students, mentors, colleagues,
community and everyone else to help me in one way or another along the way.
There are so many names in my thank-you book.
28

2013
A picture attached is Dr. Cheeptham's (aka Ann) former and an current
research students (their family and friends) and her collaborators/colleagues
(June 2013).
Namely: Baylee Out (and Shaun), Erik Prytula, Dr. Ernest Tsui, Dr. Kingsley Donkor,
Donkor Dr. Nancy
Van Wagoner, Timothy Crowe (with son, Everett and wife, Erica), Sue Whitehead, Erika Koeck,
Ariga Avanessian, Travis Orange, Tamara Bandet, Dr. Ann, Tiago Selau Rodrigues, Zafiirah Bibi
Hayfaa Golapkhan, Raniyah Alnadhi and Devon Rule (and Matt
Matt)
We The Microbiologist conducted this interview over email and from the team of
WTM we are privileged to represent Dr. Naowarat Cheeptham in our magazine.
Some Related Links:

1. Antibiotic-resistant
resistant bacteria found in ancient cave could be source of new drugs. [By Sheryl
Ubelacker, The Canadian Press, Globa
Global News]
2. Video Animation of Naowarat Cheepthams work (YouTube)
29

2013
Bacterial Toxins Induce Their Relatives

Production
The Jordanian Society for Microbial Biodiversity
By: Nura A. Abboud
Nura_Abboud@yahoo.com , nura.whe@gmail.com
Evolution forces microbial species to develop mechanisms that would favor the
remaining of these species in the environment. In this evolutionary arms-race
bacteria had to invent reliable, potent defense system that will overcome other
species and allowed them to exploit the limited sources present in the environment.
Bacteria use a wide range of defense systems namely: classical antibiotics, lytic
agents, metabolic by-products, exotoxins, and bacteriocins. Among all known
defense systems, bacteriocins is receiving an increasing attention because of their
widespread distribution among Bacteria and Archaea and the high levels of
diversity they display [96].
Bacteriocins are first choice in defense systems in the microbial worlds. The
first bacteriocin to be identified by Gratia in 1925 was an antimicrobial protein
produced by Escherichia coli .The toxin was named colicin after the producing
species from which it was isolated. [13]. Bacteriocins are naturally occurring
antimicrobial compounds produced to inhibit or kill the growth of bacteria closely
related to the producing species [96], they comprisea large and diverse family of
proteinaceous toxins which has been identified in most microbial species of
bacteria and Archaea with one species producing tens or even hundreds of different
types of bacteriocins. What unites them as a group is that they are all ribosomally
synthesized bactericidal proteins. In addition, unlike most classical antibiotics, they
are active against species that are closely related to the producing strains [1-5].
Bacteriocin genes employing a range of killing mechanisms, including cell wall
interference , cytoplasmic membrane pore formation, and nuclease activity [14,
15]. Bacteriocins high prevalence suggest of their ability to target every known
bacterium [100]. Regardless their precise role is, it was suggested that 99% of all
bacteria produce bacteriocins that are currently unknown simply because they have
not been identified yet [64].
30

2013
Fig 1.1: Inhibition zone observed on LB agar plate by Bacteriocin producing

bacteria,, spread on a lawn of Bacteriocins sensitive strain.
As a family, bacteriocins includes a diversity of proteins in terms of

microbial target, size, immunity mechanisms, mode of action and release, they are
usually classified into two main groups: the toxins produced by Gram-positive
Gram and
their counterparts produced Gram Gram-negative bacteria.
eria. These bacteriocin groups
differ in their size, structure ,regulatory pathway, killing system, and release
mechanism [96]. Gram-positive
positive bacteria produce bacteriocins are smaller than
their counterparts [less than 10 kDa]; and are selfregulated by specific transport
mechanisms; hence they do not rely on their host's regulatory as in the case of the
bacteriocins produced by Gram
Gram-negative
negative bacteria; and, they are mostly active by
creating pores in their targets cell membrane, and, are released through a specific
transport system. A good example are the bacteriocins produced by lactic acid
bacteria that are used in the preservation of meat and milk [5].
The antimicrobial toxins produced by Gr Gram-negative

negative bacteria are usually
invading and killing target cell after recognizes specific surface receptors through
either pores formation or nucleic acid degradation. They are released through cell
lysis casing death to the producing cell and are depend
dependent
ent on the host regulatory
31 pathways, like the SOS regulation; the most extensively studied example of this
group are the colicins[1,
[1, 6, 8]
8].. They evolved their own regulatory networks [100].
Producing strains belongs to both bacteriocin groups possesses specific immunity
toward its bacteriocin [100].
].

2013
Bacteriocin production has been detected in all surveyed lineages of
prokaryotes. Unquestionably , bacteriocins play a critical role in mediating
microbial communities ,maintaining interactions and community dynamics, and in
maintaining microbial diversity [60, 63]. An additional role has recently been
proposed for bacteriocins produced by Gram-positive bacteria, in which they
mediate quorum sensing [1, 5, 6]. From an ecological point of view, bacteriocins
are anticompetitor molecules that enable bacteria to respond to environmental
challenges by enabling the invasion of a strain into an established microbial
community , and reducing competition from sensitive bacterial strains that share
the same ecological niche and have similar nutritional requirements[2, 6, 7]. Also it
was suggested that Gram-positive bacteriocins, may mediate quorum sensing ,it is
likely that whatever roles bacteriocins play, these roles change as biotic and a-
biotic components change of the environment.
In recent years, bacteriocins have been targeted for potential use in human
health, veterinary therapy, food preservation and inhibition of abnormal
proliferation of eukaryotic cells, hence; treating malignant tumours. [8, 21, 40,
41].They may be a part of novel application for replacing classical antibiotics
;They are an attractive focus for drug development because bacteriocins can target
every known human, animal and plant pathogen, they are remarkably stable
proteins and they are not toxic to humans [100]. In addition, many of them display
a narrow range of activity enabling the creation of pathogen-specific designer
drugs. The use of the bacteriocin nisin in food production and colicins E1 and B in
reducing the level of enteric pathogens in livestock lends credence to their
perceived promise in human and veterinary therapy [8, 21, 29, 40, 41, 50, 53, and
119].
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34

2013
Salmonella as a Cancer Fighter

In an interesting twist of events, researchers at the Yale Cancer Center are
using Salmonella bacteria to fight cancer. The first phase of human trials has
started and the Salmonella is currently being administered to patients. In the trials,
the patients are administered a gene
genetically altered form of Salmonella and initially
monitored at a hospital. After administration and subsequent monitoring, the
patients are discharged.
Salmonella is commonly known for its role in food poisoning and septic shock.
sho It
is responsible for millions of food borne illnesses each year. Salmonellosis, an
illness caused by Salmonella
Salmonella,, can be contracted by eating contaminated food.
Symptoms of Salmonella infection include nausea, vomiting, abdominal pain and
diarrhea.
Once inside the body, Salmonella use

several methods to avoid destruction by
the immune system.. These bacteria
excrete a protein that hampers the
body's ability to produce an
inflammatory response.
sponse. This helps the
bacteria avoid detection by the immuimmune
system and gives them enough time to
reproduce throughout the body. The
protein affects cells in the wall of Salmonella Bacteria (red)
the intestines and stomach. Salmonella also excrete proteins that enable them to
take in zinc and other metal ions in spite of the attempts of the immune system to
reduce these vital substances needed for bacterial survival.
Under optimal conditions,ns, bacteria can reproduce rapidly, doubling in population

size in a matter of minutes. Most bacteria reproduce asexually through a process
called binary fission.. During binary fiss
fission,
ion, a single DNA molecule replicates and
both copies attach to the bacterial cell membrane. The cell membrane begins to
grow between the two DNA molecules. Once the bacterium just about doubles its
35
original size, the cell membrane begins to pinch inward. A cell wall then forms
between the two DNA molecules dividing the original cell into two bacterial cells
that are genetically identical. While binary fission is an effective way for bacteria

2013
to reproduce, it does produce problems for the organism. Since the cells produced
through this type of reproduction are identical, they are all susceptible to the same
types of antibiotics.
In the study, scientists altered the "wild type" of Salmonella. It is genetically

modified and stripped of its ability to cause illness. Once stripped, the bacteria
have been successfully used to shrink solid tumors in animals. The modified form
also inhibits the growth of the tumors as well. With its pathogenicity removed,
the Salmonella can target cancer cells with little adverse effects. In the test
animals, scientists were able to substantially increase the life span of the animals
that had melanoma cancer.
Based on the results obtained in the animal trials, the researchers are optimistic
about the expected results in humans. The human trials will consist of several
phases designed to determine if the altered Salmonella can successfully inhibit and
shrink tumors. The patients in the study thus far all have tumors that are in or
beneath the skin.
Virus Cancer Fighters

Bacteria are not the only microbes being used to fight cancer. Scientists and
researchers are also focusing on ways to use viruses to treat cancer. They are
creating genetically modified viruses that specifically target cancer cells. Some of
these viruses infect and replicate in cancer cells, causing the cells to stop growing
or shrink. Other studies focus on using viruses to improve immune system
response. Some of the potential cancers fighting viruses being studied are the
human reovirus, the vesicular stomatitis virus, and the measles virus.
36

2013
Interview of PhD Fellow

By
We The Microbiologist
Name: Deepthi B V
Working as Research Fellow in Department of Studies in Microbiology, University

of Mysore, Manasagangothri, Karnataka, India
From when did you start working?

January 2012
Q) Can you tell us something about yourself?

I am pursuing Ph. D in the field of Molecular mycology and Food
Microbiology. Research is always interdisciplinary. I am working on
fumonisinmycotoxin and their effect on poultry and animals and to manage
mycotoxin contamination using probiotics thereby enhancing health of poultry and
animals. As a person, I am a workaholic and love to work and learn. I took up
Research because it is a field where there is no end to learn and keeps me occupied
always which gives me immense happiness and satisfaction.
Q) How was your study background, starting from your school life, then
college life? Which subject do you really like most?
I have always been a hard working, sincere student since my school days. I
had healthy competitive environment and determination to study and top the class
which made my journey as a student so wonderful. I completed my Schooling in
Nirmala Convent. I used to study so hard to get the badge of FIRST RANK every
month, which did happen for a few months and then I used to satisfy myself with
the successive Second and Third ranks. College days! Cherishing I would say. I
completed my Pre-University Education at THE Sadvidya Composite PU College.
I was graduated in Biochemistry, Botany and Microbiology (BBM) from
Maharanis Science College for Women, Mysore and Master in Microbiology from
DOS in Microbiology, University of Mysore. My priority has always been to gain
37 knowledge and improve and henceforth to be sincere towards my studies and
overall development.
Biology was my favorite subject since my School days.

2013
Q) What was your motivation to go for Research after you passed your
Graduation?
I wanted to acquire in-depth knowledge in the subject and to implement it in
day-to-day lives of a layman and environment. This made me to opt Research
Field.
Q) What do you think about Research before you joined and what is your
take about it now?
To RE-SEARCH on anything is a difficult task. It takes lot of dedication,
sincerity, logical analysis, practicability and studying the subject. I took up
research with all these in mind and how should I be. But after entering the field, I
realized it is much more difficult than what I thought and I have to update myself
much more and I am happy to say I am in a process of it. And there is no end for
Research, its a continuous process.
Q) What is your family background and how is the motivation from your
family to go for PhD?
I am the elder daughter to my parents and I have a younger sister. My
parents always wanted me to flourish in the education field and they have been
motivating me to do what I like to do. My family environment is very comfortable
and supportive towards my Research and Education.
Q) What is the focus of your research career now?

My research work is the biological management of mycotoxins
contamination in poultry and animals and to enhance their health using probiotics.
On this basis, I want to work more towards the benefit of animals in improving
their health and resistance to disease causing entities.
Q) Do you feel India has got bright future in Biological Research (mainly in
the field of Microbiology and Biotechnology?
Yes, I do. India is growing fast in the Research field. More aspirants are
taking up Biological Research as their Career and are flourishing. There are
internationally well known Biological Research Companies in India serving their
best. India has every potential and resources to succeed in Biological Research
Field too.
Q) What is your plan after completing your PhD?

38
I am working on to pursue Post Doctoral Studies in Germany/ France where
I can work in-depth on my Research topic.

2013
Q) Do you have interest to further your study as PDF or as RA? If yes then
where will you wish to continue in India or abroad?
Yes, I want to research more related to probiotics and animals taking up
PDF in Germany/ France.
Q) What will you advise majority of Indian student, Research or Job?

Indian students have the potential to Master in all fields and Science and
Technology is the hot cake now globally. Its we, who should be determined,
dedicated and sincere to work for our individual development, development of the
firm and ultimately development of our Country.
Q) Please provide some suggestions to upcoming generations who want to go

for PhD, how they should prepare for CSIR-NET, DBT, ICMR-JRF, and
other competitive examinations.
Time management is most important and the most difficult task to do and
follow it every day. But we have become so regularly irregular in doing so. If we
succeed in managing our time in a right manner for the right things, then we
become determined, dedicated, honest, hard working and aware. This brings
success, happiness and satisfaction in the work what we do. It can be studying,
working or any job for that matter.
Preparing mind map is the best way to study, remember and recall and Mind
mapping is the best tool to prepare for competitive examinations i.e., colors,
pictures, flow links, flowcharts, diagrams, important words are more effective than
just black & white letters, words and sentences what we study.
(Refer Tony Buzans books to study, remember and recall in a most possible easy
techniques. He is the Father of Mind Mapping).
Q) Please comment on 'We the Microbiologist"

We the Microbiologist is a very good firm or platform I would rather say,
for the young students and researchers to get exposure and to gain worldwide
knowledge of Science and Technology in the field of Microbiology. I, personally,
got to know many things around us which I was not aware of.
39

2013
Periodontal etiology
A. Sudheer kumar Sarma
Research Scholar- HOD Biology
Group of Institutions
Division of Human Genetics, Dept. of Anthropology
S.V. University
Periodontitis, the disease or disorder of teeth supporting structures - the gingiva,

periodontal ligament and alveolar bone is a resultant of extensive microbial
colonization, making it chronic, degenerative disease which is localized on the
gingiva, periodontal ligament, cementum and alveolar bone. It is generally
accepted that the oral biofilm in association with anaerobic bacteria is the main
etiological factor in periodontal disease and hence the search for the periodontal
pathogens has been underway for more than 100 years, and continues till day.
The oral biofilm consists mainly of microbes and host proteins that adhere to teeth
within minutes of a dental oral hygiene procedure. Over 300 microbial species,
with 301,000 species per site, may be cultured from the periodontal pockets of
different individuals. Healthy gingival sulcus has a flora dominated by equal
proportions of Gram positive cocci, especially Streptococcus spp, and
Actinomuces sp. Later, plaque "matures" resulting in a flora consisting from
facultative anaerobic microorganisms, spirochaetes and motile rods. The
proportions of strict anaerobic, Gram negative and motile organisms increase
significantly in accordance with increasing severity of disease. Disease activity in
periodontal disease may range from slow, chronic, progressive destruction to brief
and acute with varying intensity and duration.
Several hardships at various stages make the identification and characterization of

this microbiota a herculean task for microbiologists. The complexity of the
subgingival microbiota, Sampling techniques and Cultivation issues are few among
them.
The currently recognized key Gram negative periodonto pathogens include:

40 Porphyromonasgingivalis (P.g), Prevotellaintermedia (P.i), Bacteroidesforsythus
(B.f), Aggregatibacteractinomycetemcomitans (A.a), Fusobacteriumnucleatum
(F.n), Capnocytophaga species (C.sp), Campylobacter rectus (C.r).

2013
Also, the following bacteria cou could
ld be isolated: Eubacteriumspp,
Peptostreptococcus micros, Selenomonasspp, Spirochaetes. The range of putative
pathogens has been extended to include not only culti
cultivated
vated bacteria but also non-
non
cultivated bacteria and viruses. A correlation was found between P.g, P.i, C.r,
Eikenellacorrodens, Selenomonassp, Bacteroides species, Spirochetes and adult or
refractory periodontal disease.
These bacteria could be detected by microbial cultural techniques and as well as by

Polymerase Chain Reaction (PCR). This could facilitate in successful antibacterial
treatment. All bacteria in the periodontal pocket could damage periodontal tissues,
and good knowledge of these as well as aan n adequate treatment could be helpful in
treatment of this disease. A full understanding of the microbial factors, their
pathogenicity as well as host factors are of the essential importance for
pathogenesis of periodontal disease. In this way, it could be possible to treat the
periodontal patients adequately.
PREVENTION IS BETTER THAN CURE

This holds good even for this periodontitis
periodontitis.. It is advised, that proper oral and dental
hygienic practices such as brushing twice a day, regular flossing, gargling and
expert dental checkups shall reduce the incidence of periodontal infections.
41

2013
TOP NEWS
1. Beyond Antibiotics: 'PPMOs' Offer New Approach to Bacterial

Infection, Other Diseases:
Researchers at Oregon State University and other institutions today announced the
successful use of a new type of antibacterial agent called a PPMO, which appears
to function as well or better than an antibiotic, but may be more precise and also
solve problems with antibiotic resistance. Read More
[http://www.sciencedaily.com/releases/2013/10/131015134922.htm]
2. Pandoravirus: Missing Link Discovered Between Viruses and Cells
With the discovery of Mimivirus ten years ago and, more recently,
Megaviruschilensis, researchers thought they had reached the farthest corners of
the viral world in terms of size and genetic complexity. With a diameter in the
region of a micrometer and a genome incorporating more than 1,100 genes, these
giant viruses, which infect amoebas of the Acanthamoeba genus, had already
largely encroached on areas previously thought to be the exclusive domain of
bacteria. For the sake of comparison, common viruses such as the influenza or
AIDS viruses only contain around ten genes each. Read More
3. A Bacterium Reveals the Crucible of Its Metallurgical Activity
Magnetotactic bacteria have the ability to synthesize nanocrystals of magnetite
(Fe3O4) enabling them to align themselves with the terrestrial magnetic field in
order to find the position in the water column that is most favorable to their
survival. The alignment of the nanomagnets is similar to that of a compass needle.
The magnetite crystal synthesis process is a complex one, and it is little understood
at the present time. Magnetite is a compound of oxygen and iron in a mixture of
two different oxidation states [Fe (II) Fe (III)2O4]. In this study, the researchers
have described the mechanism by which the bacterium produces these two states,
one of which, Fe(III), is essentially insoluble. Read More
42 4. Cell Growth Discovery Has Implications for Targeting Cancer

The way cells divide to form new cells -- to support growth, to repair damaged
tissues, or simply to maintain our healthy adult functioning -- is controlled in
previously unsuspected ways UC San Francisco researchers have discovered. The

2013
findings, they said, may lead to new ways to fight cancer. Read More
5. Glowing Antibiotics Reveal Bacterial Infections
Despite surgeons best efforts, bacteria often manage to sneak onto medical
implants such as bone screws, where they can cause severe infections. Research
published today in Nature Communications suggests that using fluorescent
antibiotics could reveal such infections before they become too severe. Read
More [http://www.scientificamerican.com/article.cfm?id=glowing-antibiotics-
reveal-bacterial-infections]
6. Flesh-eating bacteria outbreak triggers warnings along Florida coast
A flesh-eating bacteria has killed 10 people in Florida and infected another 31 this
year, and health officials have issued an alert to some swimmers to stay out of the
water. Vibrio vulnificus is typically contracted by consuming raw, tainted oysters,
but swimmers with open wounds are advised to stay out of the warm coastal waters
where the bacteria thrive. Read More
[http://www.rawstory.com/rs/2013/10/15/flesh-eating-bacteria-outbreak-triggers-
warnings-along-florida-coast/]
7. Bacteria used to produce electricity
Scientists have examined two important bacterial forms, demonstrating their ability
to produce electricity by coordinating their metabolic activities. The remarkable
find is that the light-sensitive green sulfur bacterium Chlorobiumcan act in tandem
with Geobacter, an anode respiring bacterium. The result is a light-responsive form
of electricity generation and the production of a current. Read More
[http://www.digitaljournal.com/article/360290]
8. Gene therapy trial: The virus that could help damaged hearts
Somedays 50-year-old David Palmer can barely get out of bed and walk to the
bathroom as his heart is so badly damaged. Now the father-of-two is hoping a
revolutionary new treatment will come to his rescue. Read More
[http://www.express.co.uk/life-style/health/436739/Gene-therapy-trial-The-virus-
that-could-help-damaged-hearts]
43

2013
The Nobel Prize in Physiology or Medicine

2013
Awards: Three U.S. researchers share prize for work on vesicle transport
For their discoveries related to the machinery that regulates

the cellular transport system, which is critical to cell
functioning, James E.
Rothman
Rothman, Randy W. Schekman,
and Thomas C. Sdhof were awarded
the 2013 Nobel Prize in Physiology or
Medicine. Cells move molecules
Medicine
around
nd using tiny membrane
membrane-enclosed
packages called vesicles.
Rothman
This years Nobel Laureates, who will share the $1.2 million
prize, discovered how cells get those vesicles to their
Schekman
intended destination at the intended time.
The three winners discovered different aspects of the system. Schekman
discovered a set of genes required for vesicle transport. Rothman determined the
proteins that allow vesicles to fuse with their targets
argets and thus transfer materials.
Sdhof discovered thehe signals that tell vesicles when to release their cargo.
Schekman, a cell biologist at the University of California,

Berkeley, developed a genetic screen of the
yeast Saccharomyces cerevisiae to determine the genes that
regulate vesicle trafficking. By using yeast with defective
transport systems, he was able to determine where vesicle
traffic backed up. With this information, he identified 23 key
genes, which can be divided into three classes that control
vesicles at the Golgi complex, tthe
he endoplasmic reticulum, or
the cell surface.
Sdhof
44 Rothman, a cell biologist at Yale University, determined that proteins known as

SNARE (soluble N-ethylmaleimide
ethylmaleimide-sensitive factor-activating
activating protein receptor)
allow vesicles to fuse with their target membranes
membranes.. These proteins had already
been discovered by others, but their function was unknown. Rothman determined

2013
that these proteins interact with high specificity: The SNARE protein on a
particular target membrane is able to interact with only one or a few vesicle
SNARE proteins.
Sdhof, a biochemist at Stanford University, identified the genes that are

responsible for controlling the timing of vesicle fusion, particularly those involved
in the release of neurotransmitters. He discovered how calcium regulates
neurotransmitter release and those two proteinscomplex in and synaptotagmin-
1is key players in calcium-mediated vesicle fusion. Synaptotagmin-1 acts as a
calcium sensor during synaptic fusion. Complexin acts as a clamp during synaptic
fusion to make sure that regulated exocytosis occurs instead of the vesicle simply
being incorporated into the cell membrane.
Glitches in vesicle transport are associated generally with some human diseases,
such as diabetes. Mutations in genes associated with the protein machinery are
involved in specific diseases. For example, mutations in one of the genes are
involved in certain forms of epilepsy.
MOLECULAR MACHINERY
Multiple proteins (orange and purple) control fusion of a vesicle (blue sphere) to a cell membrane.
45

2013
WTM COUNCIL
President: Ms. Harshada Kasar (cool18rinks@gmail.com
cool18rinks@gmail.com)
Principal Secretary: Mr. Bapi Jha(bbapijha@gmail.com
bbapijha@gmail.com)
Managing Director: Mr. Saumyadip Sarkar (saumyadip.gis@gmail.com
saumyadip.gis@gmail.com)
Organizing Secretary: Mr. Trinankur Bhattacharya
(trinankur.bhattacharya@facebook.com
trinankur.bhattacharya@facebook.com)
Chief Editor: Mr. Swapnil Vichare (swapnil@wethemicrobiologist.in
wethemicrobiologist.in )
International Outreach Coordinators:

Mr. Golam Moktadir Khan (gmk025@gmail.com) - Bangladesh
Mr. Bamgbose Princeteejay Timothy Nigeria
Mr. Sajjad Ahmad Pakistan
http://wethemicrobiologist.in/
46

2013
Supporting Society:
Supporting Organization:
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2013

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Bacterial Toxins Induce Their Relatives Production 30

Salmonella as a Cancer Fighter 35

Interview of PhD Fellow by We The Microbiologist 36

The Nobel Prize in Physiology or Medicine 2013 44

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Then it struck me, as a microbiologist some microbes survives hotter temperature

Thermophiles are microorganisms that thrive at relatively high temperatures,

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Kamchatka is a 1,500 km long

Mechanism Of Survival For This Group Of Organisms Include:

Protein Stability: A highly hydrophobic core, which decreases the tendency

DNA Stability: High temperature is lethal to DNA as it melts the DNA. A

Lipid Stability: Lipid bilayers consist of branched chain hydrocarbons

Microbiology Today (Oct.-Nov.

Tinto River Most of the characterized strict

1. The cell membrane is

Microbiology Today (Oct.-Nov.

4. Proton uncoupling by organic acid

5. DNA and protein damage caused by low pH can be can be repaired by

6. Intracellular enzymes might be stabilized by iron rivets

They are microorganisms that grow

Microbiology Today (Oct.-Nov.

These extremophiles thrive in environments with have very high concentration of

Slightly halophile 22-5%

Moderately halophile 55-10%

Non halophile - less than 2%

The two largest and best-studied

Microbiology Today (Oct.-Nov.

Dense growth of halophilic microorganisms in hypersaline environments, like this saltern

Sambhar Salt Lake in INDIA

Microbiology Today (Oct.-Nov.

Cellulose-degrading enzymes a cellulose-utilizing, extremely halophilic

Taq Polymerase enzymes used for PCR obtained from Thermusaquaticus

Pfu polymerase from microorganism in hydrothermal vent useful in forensic

9 Methods in Microbiology, volume 35-extremophiles, edited by Fred

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Medical and Biotechnological Applications of

R. D. MacElroy first coined the term Extremophile.

Thermophiles were the first extremophile to be discovered, but other extremophiles

Xerophiles are the one that live in extreme dry environments.

Acidophiles are microorganisms that can live in acidic environments, usually at

Thermophiles are microorganisms that live and grow in extremely hot

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Capnophiles are microorganisms which thrive in the presence of high

Piezophile, previously termed Barophiles are microorganisms that can survive

Metallophiles are extremophilic organisms able to live in the presence of high

Radiophiles are microorganisms able to live in the presence of high radiation

Recently extremophiles have earned an important place in Astrobiology, the search

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Extremophilic micro-organisms represent a potentially valuable resource in the

Biotechnological applications of enzymes are often hampered by their low stability

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

The use of proteins or enzymes from thermophilic organisms represents an

A thermostable glucokinase from the thermophilic organism Bacillus

Trehalose is a non-reducing dissacharide, which has found broad use as a

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Presently, heterologous expression of thermo- and hyperthermoarchaeal

The major impetus driving extremophile research is the biotechnological potential

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist

Table 1.Extremophiles and some examples of their biotechnological products

Thermophiles and Hyperthermophiles Applications

Microbiology Today (Oct.-Nov. 2013) | We The Microbiologist