Amino Acid Composition of New Delhi metallo-beta-lactamase-1 [Escherichia coli]

Amino Acid Composition of New Delhi metallo-beta-lactamase-1 [Escherichia coli]

By,
V.palanivelan.

The sequence details of New Delhi metallo-beta-lactamase-1 [Escherichia coli]
were retrieved from Pubmed (National Center for Biotechnology Information) (Roy,S. and Basu,S.)

The amino acid sequence of New Delhi metallo-beta-lactamase-1 [Escherichia coli] are as follows…

ldmpgfgava snglivrdgg rvlvvdtawt ddqtaqilnw ikqeinlpva lavvthahqd kmggmdalha agiatyanal snqlapqegm vaaqhsltfa angwvepata pnfgplkvfy pgpghtsdni tvgidgtdia fggclikdsk akslgnlg

ProtParam (Gasteiger E et al, Protein Identification and Analysis Tools on the ExPASy Server) was used to predicate amino acid composition, atomic composition, molecular weight, Theoretical pI of the enzyme. The raw sequence of New Delhi metallo-beta-lactamase-1 [Escherichia coli] was used as input file.
The amino Acid composition (Primary Structure) of above enzyme is as follows…


Number of amino acids: 158
Molecular weight: 16.36 kDA.
Theoretical pI: 5.07
Amino acid composition:
Ala (A) 22 13.9%
Arg (R) 2 1.3%
Asn (N) 9 5.7%
Asp (D) 11 7.0%
Cys (C) 1 0.6%
Gln (Q) 7 4.4%
Glu (E) 3 1.9%
Gly (G) 19 12.0%
His (H) 5 3.2%
Ile (I) 9 5.7%
Leu (L) 14 8.9%
Lys (K) 6 3.8%
Met (M) 4 2.5%
Phe (F) 5 3.2%
Pro (P) 8 5.1%
Ser (S) 6 3.8%
Thr (T) 10 6.3%
Trp (W) 3 1.9%
Tyr (Y) 2 1.3%
Val (V) 12 7.6%
Pyl (O) 0 0.0%
Sec (U) 0 0.0%

(B) 0 0.0%
(Z) 0 0.0%
(X) 0 0.0%

Total number of negatively charged residues (Asp + Glu): 14
Total number of positively charged residues (Arg + Lys): 8

Atomic composition:

Carbon C 727
Hydrogen H 1137
Nitrogen N 199
Oxygen O 221
Sulfur S 5

Formula: C727H1137N199O221S5
Total number of atoms: 2289

Ref:
1) http://www.ncbi.nlm.nih.gov/protein/BAJ10873.1
(Roy,S. and Basu,S.NDM-1 like metallobetalactamase in Escherihia coli causing outbreak of bloodstream infection in a neonatal ward, West Bengal, India)
2 ) www. expasy.org/tools/

Bacteria in Earthquake Prediction?

My question in DicCNet ( American Society for Microbiology) on 20/07/2010.
-----------V.Palanivelan.

[divc] Bacteria in Earthquake Prediction?
Tuesday, 20 July, 2010 9:55 PM
From:
"V.Palanivelan."
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To:
"DivC"
Dear Friends,
Since ancient times people have believed that animals can sense impending earthquakes. Animals behavior may be unusual before earthquakes. Example: Chances of earthquake are found high when 1) Dogs start barking and howling unusually,2) Birds start twittering loudly and start flying high towards sky.

Can we use bacteria in earthquake Prediction by monitoring the motility or enzymatic activity of bacterial cells in a particular region? Is it possible?

With Regards,
V.Palanivelan,
Microbiologist,
Hiran Agroceuticals Pvt.Ltd,
Madurai-2
Tamil Nadu,INDIA.

I got two replies for above question from microbiologists around the world.

1) Re: [divc] Bacteria in Earthquake Prediction?
Tuesday, 20 July, 2010 10:15 PM
From:
"John and Lucy James"
Add sender to Contacts
To:
"DivC"
To List-

Magnetotactic bacteria would be a possibility.

John F. James, Ph.D., MPH, D(ABMM)

Retired Microbiologist
----------------------------

2) RE: [divc] Bacteria in Earthquake Prediction?
Tuesday, 20 July, 2010 10:33 PM
From:
"Garner, Omai"
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To:
"DivC"
This paper suggests that magnetotatic bacteria could be used for earthquake prediction.

http://www.gps.caltech.edu/~jkirschvink/pdfs/earthquakeprediction.pdf



Omai Garner, Ph.D
Postdoctoral Fellow
UCLA Clinical Microbiology Laboratory
P: 310-794-2722
F: 310-794-2765
E: ogarner@mednet.ucla.edu

-------------------------------------------------------

My Research Paper on SEB

My research paper on "Analysis of Staphylococcal Enterotoxin B ( SEB)
using Bioinformatics Tools" published in “The Internet Journal of
Genomics and Proteomics" ( Volume 6 Number 1) . (ISPUB - Internet Scientific Publications)

Abstract of my research paper is follows....

"Staphylococcal Enterotoxin B (SEB) is one of the toxin responsible for
staphylococcal food poisoning. This work was carried out to predicate the
primary, secondary and tertiary structure of SEB protein. And also to predicate
the DNA and RNA sequence which responsible for the translation of SEB protein.
The SEB protein sequence having 238 amino acid residues and molecular weight
of SEB protein is 28.23 kDA. SEB protein having high amount of lysine (13.4%)
and aspartate ( 10.1%). SEB having 22.27 % alpha helix and 39.08 % of random coil.
The potential cleavage site of SEB for enzymes were predicated by using bioinformatics tools. Proteinase K and Pepsin produce 93 and 84 cleavages respectively on SEB protein. The SEB amino acid composition is slightly similar with Staphylococcal Enterotoxin Type C 2and Streptococcal superantigen"

To read my full research paper, please cut the following link and paste in your browser.

http://www.ispub.com/journal/the_internet_journal_of_genomics_and_proteomics/volume_6_number_1_50/article_printable/analysis-of-staphylococcal-enterotoxin-b-seb-using-bioinformatics-tools.html


By,
V.Palanivelan

Cosmetics Microbiology

Cosmetics Microbiology:
By : V.Palanivelan,

Introduction:
Cosmetics are chemical formulation which used to enhance the appearance of skin and/or hair. The cosmetic products are otherwise known as Personal care products. In cosmetics an active ingredient or group of active ingredients are mixed with a ‘base’. The ‘base’ may be Gel, Cream, Lotion, Shampoo, Oil etc. The active ingredient means a chemical substance or herbal extract(s) which having some beneficial effect on skin/hair. For Example, Titanium dioxide (CAS number: 13463-67-7) is used in Sunscreen creams and Neem (Azadirachta indica) extract is used for antiseptic and Acne treatment purpose. In some cosmetics more herbal extracts like Curcuma aromatica, Azadirachta indica, Ocimum basilicum are added. Those types of cosmetics are called as herbal cosmetics. Now herbal cosmetics are very popular in market. People are regularly using cosmetics are as follows,
• Face Cream
• Moisturizing Lotion
• Sun Screen Cream
• Shampoo
• Hair Oil
• Under Eye Gel
• Face Gel etc.

Microorganisms and Cosmetics:
Microorganisms are ubiquitous in nature. The stability of cosmetics may be disturbed by microbial contamination. Fungal contaminations in cosmetics are more dangerous than bacterial contamination. It will destroy the nature of cosmetics due to their cotton type growth and it may cause the infection on skin. And used cosmetics are having more chance for microbial contamination. Due to improper handling, the cosmetics are contaminated by microbes. For example: Gels are easily contaminated when using wet fingers to apply on the face. And also cosmetics in wild mouth containers are easily contaminated than tubes. A research paper was published by Laila A. Nasser, Riyadh University For Girls -Saudi-Arabia (Saudi Journal of Biological Sciences 15 (1) 121-128 June, 2008) on “Fungal Profiles Isolated from Open and Used Cosmetic Products Collected from Different Localities in Saudi Arabia”. According to Laila, the fungal genus Aspergillus was the most common genus while Aspergillus terreus was the most common species in open and used cosmetic products. Generally preservatives are used to inhibit the growth of microbes in food, beverages, cosmetics etc.
Preservatives:
Preservatives are natural or chemical substance which is used to preserve the materials.
Preservatives are classified in to two groups namely,
Class I Preservatives and
Class II Preservatives.
Class I preservatives are natural substances like sugar, Salt, honey whereas Class II preservatives are chemicals such as Benzoate, Sorbate, Parabens Etc. Class II type preservatives are commonly used in cosmetics to inhibit the microbial growth. The chemicals like potassium sorbate, Salicylic acid, Benzyl alcohol are comes under Class II type preservatives. But ECOCERT (an organic certification organization in France) allows the above chemicals to use as preservatives in natural/organic cosmetics. The following chemicals are commonly used in cosmetics as preservatives.
Potassium Sorbate:
CAS number 24634-61-5
IUPAC name: Potassium (2E,4E)-hexa-2,4-dienoate
Use: It is used to inhibit the growth of yeast and mould.
Benzyl Alcohol:
CAS number 100-51-6
IUPAC name: Phenylmethanol
Use: bacteriostatic.
Methyl Paraben:
CAS number 99-76-3
IUPAC name: Methyl 4-hydroxybenzoate
Use: Anti-Fungal agent.
Propyl Paraben:
CAS number: 94-13-3
IUPAC name: propyl 4-hydroxybenzoate
Use: Anti-Fungal agent.

Methyl paraben Sodium:
CAS number : 5026-62-0
Use: Anti-Microbial

Propyl praben sodium:
CAS number : 35285-69-9
Use: Anti-Microbial

Now some cosmetics manufacturers are not using Parabens as a preservatives. But The European Cosmetics Association (COLIPA) said the parabean are not dangerous when used in cosmetics as preservatives.

List of Preservatives: ( Allowed by COLIPA)

Benzoic acid and its sodium salt
Propionic acid and its salts
Salicylic acid and its salts
Biphenyl-2-ol (o-phenylphenol) and its salts
3-Acetyl-6-methylpyran-2,4(3H)-dione (Dehydroacetic acid) and its salts
Formic acid and its sodium salt
Undec-10-enoic acid and its salts etc

Manufacturing of Cosmetics:

The manufacturing unit should be a GMP (Good Manufacturing Practice) Certified. The raw material should test for chemical and microbiological quality. The approved raw materials only used for manufacturing of products.
To maintain high quality and prevent microbial contamination during manufacturing process the following points should be considered.

• The production area should be clean and dust free.
• The floor of production area should be cleaned by using disinfectants.
• Required persons only allowed with in production area. Excess workers should not be allowed.
• High standard personal hygiene should be maintained.
• Workers should not handle finished cosmetic products in vessels without proper instruction.
• The production area should be fumigated by regular intervals.

Analysis and Specifications:

The COA (Certificate of Analysis) for every purchased raw materials and every batch of finished goods should be maintained. The methodology and Specifications for cosmetic products are released by BIS (BUREAU OF INDIAN STANDARDS) in India. Specification and Methodology for various cosmetics which released by BIS are as follows,
• IS 11377:1985 --- Guidelines for Hygienic Manufacture of Cosmetics.
• IS 14648:1999 --- Methods of Test for Microbiological Examination of Cosmetics.
• IS 66608:2004 --- Skin Creams - Specification.
• IS 7884:2004 --- Shampoo, Surfactant based- Specification.
• IS 5784: 2001 --- Shaving Soap – Specification.
• IS 7123:1993 --- Hair Oil – Specification.
According to IS 14648:1999, Total Viable Count is not more than 1000 cfu/gm in cream products. The sum of Total Bacterial Count and Yeast & Mould count gives Total Viable Count (TVC). Based on IS 14648:1999 only TVC can indicate on a COA. I wish to indicate the both counts ( i.e Bacterial Count and Yeast & Mould count) separately in a COA with individual specifications. Based on my experience in cosmetics industry, the Mould & Yeast counts especially the Mould count should be Zero (0). A COA for every finished cosmetics product may be like following one.


CERTIFICATE OF ANALYSIS
MICROBIOLOGICAL ANALYSIS
Product Name:
B.No:
Mfg.Dt
Exp.Dt.

S.No Test Result Specification
1 Total Bacterial Count ** cfu/gm NMT 100 cfu/gm
2 Yeast and Mould Count
2.1 Yeast Count ** cfu/gm NMT 50 cfu/gm
2.2 Mould Count ** cfu/gm Nil
3 Gram Negative Pathogens Negative Negative


...............
My Thanks to:
Laila A. Nasser, Riyadh University For Girls -Saudi-Arabia.

Public Health Agencies Warn of Outbreaks Related to Drinking Raw Milk

I got a mail from Brent Barrett regarding outbreaks related to drinking raw milk. I wish to post that mail on my blog.

My Thanks to: Brent Barrett
Greenwood, Indiana
salbrent@sbcglobal.net


For Immediate Release: March 26, 2010
Media Inquiries: Siobhan DeLancey, 301-796-4668, siobhan.delancey@fda.hhs.gov
Stephanie Kwisnek, 301-436-1856, stephanie.kwisnek@fda.hhs.gov
Consumer Inquiries: 888-INFO-FDA

Public Health Agencies Warn of Outbreaks Related to Drinking Raw Milk
Latest outbreak of campylobacteriosis in Midwest is linked to unpasteurized product
The U.S. Food and Drug Administration, along with several state
agencies, is alerting consumers to an outbreak of campylobacteriosis
associated with drinking raw milk. At least 12 confirmed illnesses have
been recently reported in Michigan. Symptoms of campylobacteriosis
include diarrhea, abdominal pain and fever.
The FDA is collaborating with the Michigan Department of Community
Health (MDCH), the Illinois Department of Public Health, the Indiana
State Board of Animal Health and the Indiana State Health Department,
to investigate the outbreak. MDCH reports that, as of March 24, 2010,
it received reports of 12 confirmed cases of illness from Campylobacter infections in consumers who drank raw milk. The raw milk originated from Forest Grove Dairy in Middlebury, Ind.
Raw milk is unpasteurized milk from hoofed mammals, such as cows,
sheep, or goats. Raw milk may contain a wide variety of harmful
bacteria – including Salmonella, E. coli O157:H7, Listeria, Campylobacter and Brucella -- that may cause illness and possibly death. Public health
authorities, including FDA and the Centers for Disease Control and
Prevention, have expressed concerns about the hazards of drinking raw
milk for decades.
Symptoms of illness caused by various bacteria commonly found in raw
milk may include vomiting, diarrhea, abdominal pain, fever, headache
and body ache. Most healthy individuals recover quickly from illness
caused by raw milk. However, some people may have more severe illness,
and the harmful bacteria in raw milk can be especially dangerous for
pregnant women, the elderly, infants, young children and people with
weakened immune systems.
If consumers of raw milk are experiencing one or more of these
symptoms after consuming raw milk or food products made from raw milk,
they should contact their health care provider immediately.
Since 1987, the FDA has required all milk packaged for human
consumption to be pasteurized before being delivered for introduction
into interstate commerce. Pasteurization, a process that heats milk to
a specific temperature for a set period of time, kills bacteria
responsible for diseases, such as listeriosis, salmonellosis,
campylobacteriosis, typhoid fever, tuberculosis, diphtheria and
brucellosis. FDA’s pasteurization requirement also applies to other
milk products, with the exception of a few aged cheeses.
From 1998 to 2008, 85 outbreaks of human infections resulting from
consumption of raw milk were reported to CDC. These outbreaks included
a total of 1,614 reported illnesses, 187 hospitalizations and 2 deaths.
Because not all cases of foodborne illness are recognized and reported,
the actual number of illnesses associated with raw milk likely is
greater.
Proponents of drinking raw milk often claim that raw milk is more
nutritious than pasteurized milk and that raw milk is inherently
antimicrobial, thus making pasteurization unnecessary. There is no
meaningful nutritional difference between pasteurized and raw milk, and
raw milk does not contain compounds that will kill harmful bacteria.
For more on the raw milk, please visit www.foodsafety.gov1.