Internshipreport Biotech-412: Tahmina Sattar 2015-Uam-168 B.SC (Hons.) Agriculture
Internshipreport Biotech-412: Tahmina Sattar 2015-Uam-168 B.SC (Hons.) Agriculture
Biotech-412
Submitted By
Tahmina Sattar
2015-Uam-168
B.Sc (Hons.)Agriculture
Approved by:
Internship Supervisor:
_______________________
Dr.Yasir Saleem
(Senior Scientific officer
PCSIR, FBRC Lahore)
Internal Supervisor:
_______________________
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Acknowledgement
At the beginning I would like to convey my sincere appreciation to almighty Allah for giving
me a strength and ability to finish the task within the planned time. Then I would like to
express my gratitude to my parents they contributed towards preparing and making this study
successfully.
I convey my sincere gratitude to my academic supervisor Dr.Zulkurnain khan, Associate
professor of institute of Plant Breeding and Biotechnology, university of Multan. Without his
kind direction and proper guidance this study would have been a little success. In every phase
of the project his guidance and supervision shaped this report to be completed perfectly.
I would also like to express my sincere gratitude to my internship supervisor Dr.Yasir
Saleem, Senior scientific officer, FBRC, PCSIR, Lahore and Director FBRC Dr.Muhamad
Ijaz With their guidance and appreciation I have learned most of the laboratory techniques.
I am humbly thankful to my seniors out there in the molecular biotechnology lab especially
Miss Maryam, Miss Rafia and Mr. Qasim javaid. They were really extremely helpful to
me throughout my internship.
At last but not least I am extremely grateful to our energetic and honourable chairman
Dr.Muhammad Hammad Nadeem Tahir and our hard working coordinator Mr. Ali Sher.
I perceive this opportunity as big milestone in my career development. I will strive to use
gained skills and knowledge in the best possible way, I will continue to work on their
improvement, In order to attain desired career objectives. Hope to continue cooperation with
all of you in future.
TAHMINA SATTAR
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Table of Contents
5 Learning Experience 27
6 SWOT Analysis 29
7 References 32
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1. Executive Summary
I joined internship at Molecular Biotechnology Lab FBRC, PCSIRLahore. Basically, the
project was on testing antibiotic susceptibility pattern of aerobic bacteria isolated from
diabetic foot ulcers. The sample size was 100, collected from diabetic foot ulcer unit from
various hospitals of Lahore. The aim of the project was to identify and isolate diabetic foot
infection and to check antibiotic susceptibility pattern against bacteriocins. Besides this
project two milk testing were also performed. One sample from a branded milk company was
tested for the presence of antibiotics, Beta lactam and Tetracycline while the other sample
from another branded company was evaluated for the presence of lactose. I also witnessed
projects on antimicrobial susceptibility pattern testing through NPs, isolation of internal and
external micro flora of vegetables and Ozone application and Evaluation and identification of
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2. Introduction to PCSIR
In 1953 Pakistan Council of Scientific and Industrial Research (PCSIR) was established with
Pakistan. It has its laboratories situated in all across the Pakistan in various cities including
Hyderabad, Karachi, Skardu, Quetta, Peshawar and Lahore. Its head office is situated in
Islamabad.
PCSIR, Lahore started functioning in 1953 in Punjab University and then got shifted to
PCSIR Lahore has a number of functional research centres under various domains including a
Applied chemistry
Applied physics
Environmental protection
Engineering
Mineral processing
PCSIR, Lahore has a number of international and national recognitions including ISO
(Pakistan), Saudi Arabian Standard Organization and Ministry of health and welfare japan.
In 1977 by emerging biological evaluation and food technology department FBRC came into
improving quality and utilization of food products. It is equipped with all kind of required
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instrumentation including Spectrophometer, High Performance Liquid Chromatography, Gas
Basic hierarchy:
Back in 2016 FBRC brought PCSIR in the international eyes, as a student of it won Queen
Elizabeth II young leaders award for her research on genomic characterization of different
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In the labs of PCSIR, a healthy diverse environment is found. There is a lot of diversity is
found among research fields, research ideas and intellect of researchers making it an ideal
place to do research.
PCSIR has many important achievements on its credit most importantly, establishment of
Asia’s first ever dioxin testing laboratory which is assisting persons related to fisheries and
sea foods to enhance its export to European market. Another big and critical achievement of
PCSIR is the establishment of Halal authentication laboratory to regulate the import and
export of Halal items. PCSIR has a number of products and processes ready for being
fertilizer, phytase enzyme for poultry feed, bio fertilizer, food grade pink dye, Nano filter
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3. Training Program
Foot ulcers are usually hardly irreparable(Singh, Armstrong et al. 2005) erosions on the foot
skin that may get extend deep into tissues(Reiber, Lipsky et al. 1998). Occurrence of foot
patients(Reiber, Lipsky et al. 1998), termed as diabetic foot ulcer. It worsens the already
worse condition of diabetic patient .Diabetic patient having ulcer too has a more chance of
psychologically(Reiber, Lipsky et al. 1998; Boulton, Vileikyte et al. 2005). It most of the
times lead towards amputation of leg It most of the times lead towards amputation of leg
.Only the cost of amputation is US$993 to US$17 519(Boulton, Vileikyte et al. 2005). It
increases mortality rate in diabetic patients up to 2.39%(Boyko, Ahroni et al. 1996). Even
after amputation there is a chance of mortality from it, whose chance varies from country to
country(Reiber, Lipsky et al. 1998; Faglia, Favales et al. 2001) according to availability of
medical facilities in that country(Lee, Lu et al. 1993). Women and old men are more
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A lot of negligence towards identification and treatment of these ulcers has been shown in
Swabbing from wound is done and it is immediately checked for the identification of bacteria
in both aerobic and anaerobic conditions. Diabetic foot ulcer is a complex phenomenon
having involvement of many aerobic/ anaerobic bacteria and gram positive/gram negative
specie, enterococci, Staphylococcus spp. and Escherichia coli(Louie, Bartlett et al. 1976).
The complexity of microbes is kept in mind while selecting antimicrobial therapy from it and
microbes obtained from the results of this identification test(Lipsky 1999; Lipsky and
Berendt 2000).
A special focus on elimination of Staphylococcus spp. has been given. In early times
methicillin was used to cure foot ulcers however bacteria developed resistance against
them(Dang, Prasad et al. 2003) than came the most prolong era of vancomycin usage as
antibiotic for treating ulcers associated with Staphylococcus spp. However Staphylococcus
spp. developed resistance against it too through vanA gene. First case of vancomycin
resistivity was reported in 1997(Control and Prevention 1997) and then a series of reports
start to come out(Rotun, McMath et al. 1999; Smith, Pearson et al. 1999; Hageman, Pegues et
al. 2001; Weinstein and Fridkin 2001). Many modifications were used in this antibiotic to
control Staphylococcus spp. but none of them proved to be effective over a long period of
time. These drug resistance cases were increasing the complications associated with diabetic
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So in these all conditions a new solution to the old problem has been suggested, named as
et al. 2013) secreted by different bacteria and have antimicrobial activity with broad
inhibition spectrum, high specificity, high stability and low toxicity, giving them edge over
antibiotics(Tagg, Dajani et al. 1976; Gálvez, Abriouel et al. 2007; Cotter, Ross et al. 2013). It
3.2. Objective:
To isolate staphylococcus spp. from diabetic foot ulcer and to evaluate potential of
3.3. Hypothesis:
If bacteriocins may have potential against staphylococcus spp. than it will inhibit the growth
Wound swabs of diabetic foot ulcer patients were collected from hospitals of Lahore and
were processed by standard microbiological analysis. After the collection of samples swabs
were placed in a plastic tube.These samples were swabbed on nutrient agar plates and these
plates were incubated at 37C for 24 hours. After the incubation different bacterial strains
were observed on the plates. After the identification,colonies were re-streaked on media for
isolation of strains.
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3.4.2. Identification and confirmation of bacterial strain:
The relative number and type of microorganism and host cells were identified by gram-
staining after the formation of smear of all the samples. In the first step of gram-staining one
drop of distilled water was placed on glass slide. Red hot wire loop was used to pick single
colony from plate and smear was formed. After this the bacterial strain was fixed with the
help of burner. The bacterial strain was stained by placing one drop of crystal violet on smear
for one minute and then washing it with distilled water. Then we placed one drop of iodine
on it and again washed it with distilled water. Than we placed one drop of alcohol for 30 sec
and washed it with distilled water. At the end one drop of safranin was placed on it and it was
again washed with distilled water. Then dried glass slideswere observed under 100X power.
A. Catalyse test:
For the confirmation of staphylococcus aureus biochemical test was performed. In catalyse
test, with the help of sterilized wire loop, single colony was picked and was placed on the
clean glass slide and 1-2 drops of hydrogen peroxide(H2O2) were added, bubbling was
checked if bubbling was formed than it was termed as catalyse positive otherwise negative.
B. Oxidase test:
produced by bacterium.We took piece of filter paper and wetted it with distilled paper and
transferred single colony of bacterium on it with the help of sterilized platinum loop. Then we
placed 1-2 drops of oxidase reagent on it and incubatedit for some minutes at room
temperature. Positive test result: Dark blue-purple colour change within 10-30 sec. Negative
test result: No colour change or colour change after more than 30 sec.
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Figure.8 (Oxidase Test)
C. Methyl red test:
In methyl red test, the test bacteria were grown in a broth medium that contained glucose.
Incubate the broth media at 37C for 24 hours. Thenwe took 1 ml of broth medium in an
aliquot and added 3-4 drops of methyl red reagent into the aliquot and observed it, colour
changed from yellow to red. If the inoculated bacteria have the ability to utilizeglucose, it
produced stable acid, changing colour from yellow to red. Positive result: colour changed
from yellow to red (bacteria have the ability to utilized glucose and produced stable acid)
negative result: colour not changed from yellow to red (bacteria don’t have the ability to
3.4.2.3.Selective media:
For the differentiation and isolation of particular organisms selective media were used, they
allow certain type of microorganism to grow and inhibit the growth of other. For the isolation
of staphylococcus spp. MSA media was used as selective medium, that contain high salt
concentration (7.5%), staphylococcus spp. was able to tolerate this salt concentration but
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other gram positive or gram negative bacteria not. That’s way MSA used as a selective
Antimicrobial susceptibility test was done to analyse the antibiogram of the isolates by using
disc diffusion method. The discs of antibiotics used in diabetic foot ulcer treatment were
used, such as, ceftriaxone 30 µg, ceftazidime 30 µg, amoxyclave 30 µg, ampicillin 25 µg, co-
Some of the pictures clicked during antimicrobial susceptibility testing using disc diffusion
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Fig.12, 13 (Different antibiotic susceptibility testing plates having aforementioned
antibiotics in them)
For the isolation of bacillus from soil, 1g soil was measured and then dissolved in 50ml
distilled water and vortexed vigorously to dissolve particles. Then the soil sample was boiled
for 10-15 minutes by using water bath and was allowed to cool. Then serial dilution of
samples were made by dissolving 1ml sample in 9ml distilled water in first dilution and then
ten-fold, hundred-fold and thousand-fold dilution of the re-suspended soil samples were
made. Then we took 0.1ml from each dilution was plated on nutrient agar plates by using
micropipette. The undiluted soil solution was also placed on the nutrient agar plates. Then
incubate these plates at 37C for 24 hours. The colonies were identified by colony morphology
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3.4.5. Bacteriocins extraction and purification
After the identification and characterization of bacteriocins, single colony of Bacillus spp.
was placed in a nutrient broth and incubated it at 37°C at 150rpm/minutes for about 24 hours.
Then the sample was centrifuged at 10,000 rpm/minutes for 20 minutes, and the supernatant
was collected. Then took 100ml supernatant and chloroform and was stirred vigorously after
this transferred it into a separate funnel. Then the bacteriocins was harvested from the
interface layer between the aqueous and organic phase, by using speed vacuum residual
By using Agar well diffusion method inhibitory activities of partially purified bacteriocins of
all the DFU (Diabetic Foot Ulcer) isolates were done. In this step MHA plates were made, by
using blue tips, wells were formed on plates and dilution of bacteriocins were filled in each
well of the plate. These plates were incubated at 37°C for 24 hours, next day plates were
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Antimicrobial susceptibility testing of staphylococcus spp. using disc diffusion method
Antimicrobial sensitivity test was performed against staphylococcus spp. using bacteriocins
from soil. Bacteriocins showed no activity to resist the growth of staphylococcus spp.
Different dilution of bacteriocins were used, not a single dilution of bacteriocins was able to
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In diabetic foot ulceration multiple factors are involved, like neuropathy, abnormal foot
biomechanics and peripheral arterial diseases. In hospitals patients with diabetic foot
infections had multidrug resistant organisms that showed high level of antibiotic resistance.
organism was increased. To reduce the risk of complications continuous surveillance should
be provided.
The most important bacteria are Bacillus spp. whichproduces various kinds of antimicrobial
proteins that inhibit the growth of gram positive bacteria. So, by the purification, SDS page
analysis, HPLC testing and genotypic identification by 16 S rRNA Bacillus spp. will be used
effectively to kill the staphylococcus spp. strains. Since, the bacteriocins and the strain of
Bacillus spp. are found to be safe for use,so, in humans they can be easily used to treat
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4. Tests Performed Besides Main Work
4.1.Milk antibiotic residues identification kit:
On 21 of March molecular biotechnology lab received two milk samples from a branded
company to test presence of two antibiotics named beta lactam and tetracycline in it. To
Antibiotics are like a gift to the entire mankind. From therapeutic to sub-therapeutic level
they have been beneficial for human beings. But their excess of use could result in the
formation of drug residues(Khaskheli, Malik et al. 2008).The antibiotics present in the milk
are usually the residues of antibiotics being injected in it for curing a particular disease. Beta
lactam is usually used for the treatment of Mastitis in cattle(Bengtsson, Unnerstad et al.
2009).
Antibiotics residues present in the milk not also deteriorates quality and processing of
milk(Ruegg 2013)but also pose a serious threat to human health and can cause severe health
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consumable(Commission 2010)After identification of possible hazards by scientists and EU
regulations, Now The practice of testing milk for the presence of any antibiotic has become a
common practice(Fejzić, Begagić et al. 2014) and in USA its even mandatory now(Moats and
Harik-Khan 1995) while in many other countries it is illegal to have amount of antibiotics
residues more than a limit as discussed by(Kempe, Cederfur et al. 1999) In Pakistan too
studies have been made to detect antibiotic residues in the milk(Khaskheli, Malik et al. 2008)
As most of the antibiotics being used are of Beta lactam origin and to somehow of
tetracycline origin so most of the tests are designed to detect these antibiotics only(Fejzić,
Various techniques have been used throughout the world to detect antibiotic residues in milk
like liquid chromatography (Straub, Linder et al. 1994; Moats and Harik-Khan 1995;
MSPD(Long, Hsieh et al. 1990). A trend of using prepared kits is also getting popular(Harik-
We took two nestle samples and one control sample (having confirmed presence of both
antibiotics) to run in the wells of kit. Corresponding antigens were already present in these
wells. We poured down 200ul of all three samples in three separate wells and incubated them
for 5min for antigen-antibody interaction. After 5 minutes of incubation antibiotic detection
After 5 minutes strips were observed, control strip should have c two visible lines first of b-
lectin and second of tetracycline. We compared the pattern of lines on the control strip with
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4.1.4. Results and discussion:
Sample 1 had b-lectin negative but tetracycline positive line. Sample 2 showed negative
ILO#
B-lectin Tetracycline
608 Negative Positive
609 Negative Negative
Basically the presence of any antibiotic in milk sample can be easily tested using antibiotic
identification kit. It is one pot experiment, by using this type of identification technique we
can easily develop different antibiotic identification kit based on antigen-antibody interaction.
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4.2. Lactose free milk identification through HPLC
4.2.1. Introduction:
On April 5th molecular biotechnology lab received lactose free claimed milk sample from
Day fresh. A test was performed to evaluate the credibility of the claim.
Milk is complete nutrition having many important nutrients like proteins, fats and lactose.
Lactose is the major component of mammalian milk. It is found about 7.2g/100mL in mature
human milk and 4.7 g/100mL in cow’s milk(Solomons 2003). In the body, in intestine,
Lactase enzyme (B-galactosidase, E.C. 3.2.I.23) digests it into simpler sugars(Gilat, Russo et
al. 1972). However its production is vulnerable to intestinal cell damage as it is not found
much deeply into the intestine. Maintenance of lactase in the body is found to be genetically
regulated(Sahi 1974; Lisker, Gonzalez et al. 1975). In almost all mammals except humans,
the production of lactase enzyme is inhibited upon weaning. However in humans too, to an
extent, production of lactase is disturbed and termed as lactose intolerance. Its symptoms may
include Stomach pain, constipation, diarrhoea and bloating after consuming milk or milk
products(Swagerty, Walling et al. 2002). 50 g of lactose in a litter of milk can produce the
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symptoms associated with Lactose intolerance. However contradiction is found regarding
Many studies have been performed throughout the world to check the prevalence of lactose
intolerance (Cook and Al-Torki 1975; Rahimi, Delbrück et al. 1976; Ahmad and Flatz 1984).
There is no definite pattern about its manifestation in humans. It varies not only on
demographic basis but also on geographic one(Simoons 1978; Swagerty, Walling et al.
2002). In Asians and Africans it appears in the early childhood while in America and Europe
it appears after adolescence(Scrimshaw and Murray 1988). Asians especially east Indians are
found to be mostly lactose intolerant(Murthy and Haworth 1970). However the condition in
and India(Rab and Baseer 1976). This phenomenon is also found more commonly among old
people(Vesa, Marteau et al. 2000). Women are found to be more vulnerable to it(Jussila
1969).
So a trend of producing lactose free milk has been started throughout the world(Dahlqvist,
Mattiasson et al. 1973). Modifications producing lactose free milk can be proved much
promising for milk market throughout the world(Jelen and Tossavainen 2003). As only in
USA, according to estimation, there are 50 million consumers for lactose free milk(Sloan
1999)
In order to check the presence of lactose in milk, we performed HPLC after sample
preparation. First of all 0.1% lactose standard was prepared by mixing 0.01g powdered milk,
having lactose, in 10ml dH2O. After this TCA treated milk was prepared by dissolving 1g
TCA in 5ml day fresh milk sample. Then TCA treated milk was centrifuged at
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5000rpm/20min and then we shifted the supernatant into a labelled falcon. In the next step we
washed the cuvette three times each with methanol and H2O. Lactose standard and
supernatant was syringe filtered and 1.5ml from each was put into separate cuvettes. HPLC
Fig.21 (Sample & standard preparation) Fig.22 (HPLC running after sample
placement)
For the calculation of lactose concentration in milk sample standard and sample was run in
HPLC. Then P.A of the standard and average P.A of the sample was noted and by using
above mentioned formula final concentration of the lactose present in the milk sample was
calculated by comparing the peaks of standard and sample in the retention time.
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Calculations:
9066740+2257169= 11,323,909
10071419+3411505 = 13,482,924
11101750+4037963 = 15,139,713
6802544.51+198973355 = 205,775,899.51
=78,132,845.5033
P.A of standard
11,323,909
= 0.112%
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5. Learning Experience
We have learnt slide preparation and microscopy in our Cytogenetics course that helped us to
prepare slides during our internship experiments. In the course of principles of biotechnology
we have learnt basic techniques liked DNA extraction, PCR running and gel electrophoresis
so these techniques helped us. In molecular virology course we have learnt serial dilution,
microbial isolation and identification techniques that helped us a lot during our internship
work. During our course of Nano biotechnology we have learnt about the synthesis and
We learnt equipment handling and basic biosafety rules. Hence, background knowledge
helped us in understanding experimental work during our internship. We have learnt report
writing skills, time management skills, how to work in a group as well as communication
skills there.
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The coordinative and friendly environment helped us to work effectively in the lab. The
honest and helpful attitude of the seniors played an important role in our learning. There was
no communication barrier between seniors and juniors. So, it was quite easy for us to
Though my entire internship work at PCSIR was enough challenging but not more
challenging than that day on which I had already 50 MSA plates to be streaked and then my
senior requested me to streak her 70 MSA plates too. It was quite a hectic task but I accepted
the challenge and it took me 6 consecutive hours of work to accomplish this task.
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6. SWOT Analysis
6.1. Strengths:
Well-equipped labs:
The laboratories are well equipped having latest and up-to-date equipment
and all required kits and equipment for any kind of food testing.
Diversified laboratories:
Cooperative environment:
All the scientific officers there are not only highly competent but also much
cooperative. They boost up their interns to think out of the box and ensure the
6.2. Weaknesses:
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Unclean Labs:
Labs here are not kept cleaned. They are not swept on daily basis. One could easily
find a lot of dust on furniture and other equipment of labs. One has to make his/her
The labs here are not well furnished. They are seriously deficient in essentially
required furniture like nonporous stools, chairs tables and wood cabinets
Poor management:
Lab assistant showed non cooperative behaviour with researcher and students. They
There is no log in/log out register present in labs. There is no proper record of
chemicals. The students or interns from other labs took away things or chemicals
6.3. Opportunities:
Diversified ideas:
their ideas with others and they also have an access to diverse fields of research.
Expert Faculty:
It has a competent and world-class faculty. Intellectually saturated mature minds are
available to guide the mentally scattered naïve minds to a straight path. It has
specially a lot of opportunities for students, coming from any background, to research
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Well renowned institute:
PCSIR is a well renowned institute. About 3 years back, A student of it won” Queen
Elizabeth II young leaders award” for her MS research, Making this institute to be
globally recognized.
6.4. Threats:
Biosafety Breaches:
There is a threat of biosafety related issues in the labs. There is no proper arrangement
of waste disposal. Interns use to throw their waste material openly on the roof.
Although there is no such high biosafety level work is going on here but still who
knows when things got out of control.
Careless attitude:
A lot of careless attitude has been seen in the labs. Interns most of the times ignore the
sterilization precautions. Unawareness about threats associated with a chemical, like
Ethidium Bromide, has been also seen. These practices can cost much in the future.
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7. References
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Bengtsson, B., H. E. Unnerstad, et al. (2009). "Antimicrobial susceptibility of udder pathogens from
cases of acute clinical mastitis in dairy cows." Veterinary microbiology136(1-2): 142-149.
Boulton, A. J., L. Vileikyte, et al. (2005). "The global burden of diabetic foot disease." The
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Boyko, E., J. Ahroni, et al. (1996). "Increased mortality associated with diabetic foot ulcer." Diabetic
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Louie, T. J., J. G. Bartlett, et al. (1976). "Aerobic and anaerobic bacteria in diabetic foot ulcers." Ann
Intern Med85(4): 461-463.
Murthy, M. and J. Haworth (1970). "Intestinal lactase deficiency among East Indians: an adaptive
rather than a genetically inherited phenomenon?" Amer. J. Gastroent.53(3): 246-251.
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medical journal1(6007): 436.
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tolerance) in Afghanistan." Human Genetics34(1): 57-62.
Reiber, G., B. Lipsky, et al. (1998). "The burden of diabetic foot ulcers." The American journal of
surgery176(2): 5S-10S.
Rotun, S. S., V. McMath, et al. (1999). "Staphylococcus aureus with reduced susceptibility to
vancomycin isolated from a patient with fatal bacteremia." Emerging infectious diseases5(1): 147.
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dairy farms." University of Winsconsin, Dept. of Dairy Scinece, Madison, Wisconsin.
Sahi, T. (1974). "The inheritance of selective adult-type lactose malabsorption." Scandinavian journal
of gastroenterology. Supplement30: 1.
Simoons, F. J. (1978). "The geographic hypothesis and lactose malabsorption." The American journal
of digestive diseases23(11): 963-980.
Singh, N., D. G. Armstrong, et al. (2005). "Preventing foot ulcers in patients with diabetes."
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