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Taq polymerase storage

May 30, 2013, 1:39 am
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Dear all,
The Taq polymerase storage is usually -20 degree. I have a freezer -40 degree, so my boss didn't agree my order (Taq polymerase) because the temperature storage is not match.
Can we store Taq below -20 degree? and do you have any references to prove the answer?
Thanks all
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Fighting Cancer with Radioactive Listeria-The Lesser of Three Evils?

May 30, 2013, 6:52 am
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Scientists have combined a dangerous pathogen and a radionuclide as a treatment for a yet deadly disease. A group of researchers at the Albert Einstein College of Medicine in New York, claim to successfully defeat Pancreatic Ductal Adenocarcinoma, commonly known as pancreatic cancer, with live attenuated Listeria monocytogenes labelled with a radioactive Rhenium isotope (188 Re). This radioactive bacterium injected into mice in which aggressive pancreatic cancer has been induced, killed the tumor cells without causing severe side effects.

A Silent Killer

Pancreatic cancer, the fourth leading cause of cancer deaths today, is difficult to control due to the distribution of cancer cells to other organs (i.e. metastasis) before the primary tumor is detected. This results in tumors in other parts of the body. These secondary tumors or metastases are resistant to chemotherapy and difficult to remove by resection or external radiation. Therefore, current cancer treatments such as surgery, radiation and adjuvant therapy which are successful against most cancers have not been effective against pancreatic cancer. An effective long-term treatment for this disease is virtually non-existent since the FDA approved-anti-cancer drugs, Gemcitabine and Erlotinib can only increase the survival period by about 6 months.

Targeted-Radionuclide Therapy

Radionuclide therapy is considered a promising treatment against several cancers. Tumor-targeting vehicles such as small molecules, monoclonal antibodies and peptides etc., which are labelled with radioactive elements, can be used to deliver radionuclides to the target tissues where they emit cytotoxic radioactive particles that physically destroy the tumor cells. However, previous trials using tumor-specific antibodies to deliver radionuclides on treating pancreatic cancer with revealed to have limited success. Hence, there exists the need of finding an effective mode of transporting the treatment into the tumors.

A New Delivery Vehicle: Dangerous but Convenient

Listeria monocytogenes is one of the most virulent food-borne pathogen responsible for Listeriosis, a disease that can be fatal. Nonetheless, L. monocytogenes, genetically engineered to remove their virulent factors, have been used as a vector to deliver therapeutics in patients with cystic fibrosis and cervical cancer. In a previous study, the researchers revealed that the attenuated Listeria monocytogenes cells have the ability to selectively accumulate in the tumors and kill the tumor cells by secreting high levels of reactive oxygen species.

Although unable of causing disease, these live attenuated Listeria cells can infect and spread within the cells. Researchers found that the immune system efficiently cleared the attenuated Listeria cells from the normal tissues but in the in metastases and primary tumors where the immunity is suppressed these bacteria piled up considerably. This phenomenon offered a solution as a new means of effectively delivering targeted nuclides into tumors

Radioactive Bugs

In the current study, the attenuated Listeria coupled with radioactive Rhenium isotope were used to treat pancreatic cancer in a mouse model. 188 Re was attached to the bacterial cells using 188 Re-labeled anti-Listeria antigens. 188 Re was the radionuclide of choice due to its short half-life that enabled it to deliver the radiation dose within a shorter time, matching the vigorous growth of the cancer cells.

During the study, it was confirmed that viability and the genetic stability of the attenuated Listeria was not significantly reduced upon labelling with 188 Rh. Furthermore, labelling with radionuclides found to increase the infection rate of the bacteria.

Higher Success Rates

These radioactive Listeria (RL) were then injected into mice in which highly metastatic pancreatic tumors were generated. High levels of radioactivity were observed in metastases while the radioactivity measurements were lower in the primary tumors and normal tissues. One week after the treatment, the radioactive readings in the tissues dropped to lower than detectable levels and the attenuated Listerial cells appeared to be eradicated from the tissues by the immune system.

The scientist declare that the treatment considerably reduce the number of metastases in diseased mice without causing any side effects.

A Note of Caution

The researchers found that the livers and kidneys of the infected mice also accumulated levels of radiation as high as in metastases. They hypothesised that this is because the remnants of radioactive materials which were transferred to the liver following destruction by the immune system, were collected in the kidneys until excretion. However no pathological damage was observed in the liver or kidney cells and liver functions were unaffected.

Nevertheless, more research ought to be carried out before testing the treatment on humans.

Source :

Quispe-Tintaya, W., Chandra, D., Jahangir, A., Harris, M., Casadevall, A., Dadachova, E., & Gravekamp, C. (2013). Nontoxic radioactive Listeriaat is a highly effective therapy against metastatic pancreatic cancer. Proceedings of the National Academy of Sciences, 110(21), 8668-8673.
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Job Oriented Online Clinical SAS Course

May 30, 2013, 7:15 am
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In this online course, you will learn basics and advanced SAS clinical programming concepts to read and manipulate clinical data. Using the clinical features and basic SAS programming concepts of clinical trials, this course shows how to import ADAM, CDISC or other standards for domain structure and contents into the metadata, build clinical domain target table metadata from those standards, create jobs to load clinical domains, to validate the structure and content of the clinical domains based on the standards, and to generate CDISC standard define.xml files describing the domain tables for clinical submissions.

Training type: Online
Duration: 4-5 Weeks
Batch Timings: Morning, Evening and Weekend batches available

Who should attend?

Bioinformatics or Life Science Graduates
Job aspirants with basic understanding of clinical programming concepts or statistics

Clinical SAS Programming is used for Clinical Data Integration, Organizing, Standardizing and Managing clinical research data and metadata. It provides the foundation you need to ensure standard, trusted clinical data to support strategic analyses, such as cross-study and advanced safety analysis. With SAS Clinical Programming, you can gain both speed and efficiency by automating repeatable clinical data integration tasks.

Class size is limited—sign up for this course today!

What you’ll learn?

BASE SAS and Advance SAS:

Basic SAS Concepts
Referencing files, setting Options, Editing and debugging SAS Programs
Creating List Reports and Enhanced List and summary reports
Creating SAS data sets from raw data
Understanding DATA step processing
Creating and applying user defined formats
Producing descriptive Statistics
Creating and managing variables
Reading SAS Data sets
Combining SAS data sets
Transferring Data with SAS functions
Generating Data with DO loops and processing variables with Array
Reading Raw Data in fixed fields
Advanced Base/SAS: Macros and Proc Sql
Advanced Base/SAS: Certification Steps


SAS Clinical Programming

Explanation of organizational aspects of the Biometrics department
Basic concepts of Clinical trials
Phase – I, Phase – II, Phase – III, Phase – IV
Data Management & Statistical Methods in Clinical Trails
Access DICTIONARY Tables using the SQL procedure
Explanation of the Clinical trial process
Protocol development
CRF Design and development, Data Management plan
Principles of 21 CFR Part 11, International Conference on Harmonization, Good Clinical Practices
Edit check specifications document, Edit check programming
Data querying, Paper CRF and E-CRF studies
Database programming and basic understanding of EDC studies
Annotated CRF’s
Data Querying
Lab data handling – procedures and pitfalls
Patient Profiles, Database Lock
MedDRA®: Overview
CDISC (ODM, SDTM, ADaM and Define.XML), SDTM 3.1.2 and ADAM 1.2 Implementation
Clinical SAS Certification Steps
Resume Formatting
Mock Interviews by SAS Clinical Programmers
Job Placement Marketing

For full curriculum and details contact training@serigor.com or visit us at http://www.showtheropes.com/?page_id=223
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Indian Universities/Institutes Offering "Selection Based" Summer Internship Annualy

May 30, 2013, 1:48 pm
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It's not uncommon to face the need of 2-6months internships during the course of one's graduation/degree program. Every B.Tech student is supposed to go for a 2 months training period at the end of second year; and a 6 months major project in the last semester in most of the universities in India. Whereas, the Indian "Educational Market" is full of private institutes and companies that offer "Paid" (Where you need to pay) training programs, it doesn't suit the pocket of many students, who belong to financially weak families. Apart from the money matter, the value and authenticity of such paid trainings isn't considered high, but rather reflects an inability on the part of a student to procure a standard training from an institute/research center of high repute. So, this article is aimed at easing this very problem of the students. I'll be enlisting the names of those institutes/universities/research centers in India that offer summer internships every year, through a structured selection process (and obviously, at most institutes, the internships are Free of Cost, and rather they pay you!).

1. Indian Institute of Technology Delhi (IIT Delhi), Summer Research Fellowship
I don't think IITs need any introduction to any student in India/Abroad. And IIT Delhi, which is Ranked 1 in India, offers a summer research fellowship program to the students who have completed atleast 2 years of their engineering course. The program is stipend based (Rs 500 per week!) and is open to only those students who rank among top 10 in their class in their respective institutes/universities in India/Abroad.

Application Starts: Dec-January

Deadline: March

Result of Selected Candidates: April

Training Period: May-July
Click here for Internship Details


2. Indian Institute of Technology Madras (IIT Madras) Summer Research Fellowship
On the same lines as IIT Delhi, IIT Madras also offers Summer Research Fellowship to Biotech Students. A separate announcement can be seen in the departmental web-page of IIT Madras every year (which is removed after selection is complete). I have attached a cached copy of the list of students selected in this year's SRF program. Also there's a link to the departmental webpage. The stipend paid by IIT Madras is Rs 6500/- for 2 months and the training is open to students who have completed 2 years of B.Tech/BSc or are in 1st year of M.Tech/MSc.

Application Starts: Dec-January

Deadline: March

Result of Selected Candidates: April

Training Period: May-July

IIT Madras Department of Biotech Webpage

List of Selected Students for 2013


3. Indian Institute of Technology, Bomabay (IIT Bombay) Project Work Training to Indian Students

IIT Bombay has a unique and highly structured selection program for summer trainees as well as 6 month project trainees. Stipend given to Summer Trainees is Rs 6000/- for 2 months while to the 6 months project trainees is Rs 15000/- for 6 months! The link to detailed procedure for applying for the internship program(s) is mentioned below:

Detailed Procedure for Application


Application Starts: Dec-January

Deadline: March

Result of Selected Candidates: April

4. Indian Institute of Technology Guwahati (IIT Guwahati) Summer Research Fellowship
IIT Guwahati's Department of Biotechnology offers a paid training program (you have to pay Rs 5000/-) to the Indian students to work for 2 months on a project under any of the following domains:
  • Protein structure, dynamics & aggregation
  • Molecular biophysics
  • Protein engineering & protein function
  • Structural-function-folding relationship
  • Enzyme and Microbial Technology
  • Biocatalysis, Biosensor & Biofuel cell
  • Plant Cell and Tissue Culture
  • Plant Genetic Engineering
  • Gene Therapy for Viral and Metabolic Diseases
  • Biological Control of Insect Pests
  • Biochemistry and Molecular Biology of Carbohydrate Enzymes
  • Fungal Biotechnology and Bio-pesticides
  • Molecular Fingerprinting and Expression Systems in Food Grade bacteria
  • Environmental bioremediation, Bioprocess development (upstream to downstream)
  • Metabolic Engineering
  • Stem Cell Biology
  • Hormone regulated Gene Expression

Application Starts: Dec-January

Deadline: March

Result of Selected Candidates: April

Training Period: May-July

Details of Training Program



5. Indian Institute of Technology Gandhinagar (IIT Gandhinagar) Student Summer Research Internhips (SRIP)
A recently established IIT, IIT Gandhinagar offers large number of internship opportunities with a healthy stipend of Rs 1000/- per week!

Application Starts: Dec-January

Deadline: March

Result of Selected Candidates: April

Training Period: May-July
Details of SRIP


6. Tata Institute of Fundamental Research (TIFR) Summer Internships
Founded by coveted Indian Scientist Dr. Homi Bhabha with support of Sir Dorabji Tata Trust, TIFR is a world renowned research centre! It offers summer training to the students by the name of Visiting Students' Research Programme (VSRP) every year, with a monthly stipend of Rs 7000/-! Sleeper class return railway fare and are provided with shared hostel accommodation too!

Application starts: Sep-November

Deadline: January-February

Result of selected candidates: March-April

Training period: May-July

Details of VSRP



7. Tezpur University Summer Internship Program
Tezpur University Assam offers a four week summer internship program to students of indian universities/institutes. It is a stipend based progrm in which students are paid Rs 2000/- for the training.

Application starts: Februay-march

Deadline: May

Result of selected candidates: May

Training period: June-July

Tezpur Summer Training Program


8. Rajiv Gandhi Centre for Biotechnology (RGCB) Kerala, Training Program(s)
RGCB is a world class research centre in Trivendrum (Kerala) and offers high class trainings (but paid, application fees are very high, starting from Rs 10,000 for 2 month training).
Applications are open throughout the year and have to be made after prior consent of the scientist.

RGCB Training Program Details


9. University of Mumbai, Department of Biotech, Short term/Summer Trainings
Department of Biotech of University of Mumbai is well reputed in India and it's training is worthy of mentioning in your resume! They charge a fee of Rs 2000/- for the registration/

University of Mumbai Short Term Training


10. National Institute of Technology Rourkela (NIT Rourkela) Summer Internship Program (SIP)
NIT Rourkela a renowned NIT in India, offers a stipend based training program to the students, paying Rs 3500/- for a period of two months. B.Tech. as well as B.Sc. and M.Sc. students of different Institutes in India are selected.

Application Starts: Dec-January

Deadline: March

Result of Selected Candidates: April

Training Period: May-July
NIT Rourkela SIP


This was the list of popular internship opportunities every year for the students, about which most of the students stand unaware. Apart from these, following is the list of some coveted Biotechnology research centres in India, which offer "Request/Recommendation" based training/projects. The list is obtained from the publically available information at GNDU's Department of Biotechnology web-page:


Mr. Akhilesh K. Aggarwal,
Administrative Officer,
National Institute of Immunology,
Aruna Asaf Ali Marg,
New Delhi – 110 067.

Prof. Y. D. Sharma,
Professor & Head,
All India Institute of Medical Sciences,
Department of Anatomy,
New Delhi – 110 029.

Dr. K. B. Sainis,
Head Cell Biology Division,
Modular Labs,
Bhabha Atomic Research Centre,
Trombay, Mumbai – 400 085.

Dr. Girish Sahni,
Director,
Institute of Microbial Technology,
Sector – 39-A,
Chandigarh.

Dr. B. D. Bhattacharji,
Scientist RPBD,
Industrial Toxicology Research Centre (ITRC),
Mahatama Gandhi Marg,
P. O. Box No.80,
Lucknow – 226 001.

Prof. G. N. Qazi,
Director,
Indian Institute of Integrated Medicine,
(Regional Research Laboratory),
Canal Road, Jammu Tawi – 180 001.

Prof. J. P. Khurana,
Department of Plant Molecular Biology,
University of Delhi, South Campus,
Benito Juarez Marg, New Delhi.


Prof. Santosh K. Kar,
Centre for Biotechnology,
Jawaharlal Nehru University,
New Delhi.

Dr. Manoj K. Dhar,
Department of Biotechnology,
University of Jammu,
Jammu.

Dr. S. P. S. Khanuja,
Director,
Central Institute of Medicinal and Aromatic Plants,
Kukrail Picnic Spot Road,
P.O. CIMAP, Lucknow – 226 015.

Dr. D. D. Sharma,
Incharge, PME Division,
Centre for Biochemical Technology,
Mall Road, Near Jubilee Hall,
Delhi – 110 007

Dr. K. R. Koundal,
Professor & Head,
Indian Agricultural Research Institute,
Pusa Campus, New Delhi.

Prof. S.S. Gosal,
Department of Plant Breeding
Genetics and Biotechnology,
Punjab Agricultural University,
Ludhiana.

The Head,
Department of Biotechnology,
Central Drug Research Institute,
Chatter Manzil Palace,
Post Box No.173, Lucknow – 226 001.

The Head,
Human Resource,
Ranbaxy Research Lab.,
Gurgaon.

The Manager,
Geno Biosciences Pvt. Ltd.,
A-59, Sector # 57,
Noida – 201 301.

Dr. S. Sinha,
Department of Biochemistry,
All India Institute of Medical Sciences,
Ansari Nagar, New Delhi.

Dr. Y. D. Sharma,
Prof. & Head,
Department of Biotechnology,
All India Institute of Medical Sciences,
Ansari Nagar, New Delhi.

Dr. (Mrs.) Paramjit Khurana,
Department of Plant Molecular Biology,
South Campus, University of Delhi,
Delhi.

Dr. Sita Naik,
Department of Immunology,
SGPGIMS, Raibraily Road,
Lucknow.


The Director,
Rajendra Memorial Research Institute,
Patna – 800 007.

Prof. G. N. Qazi,
Director,
Regional Research Laboratories,
Canal Road. Jammu.

Head,
Department of Biotechnology,
All India Institute of Medical Sciences
Ansari Nagar, New Delhi – 29.

Dr. R.C. Tripathi,
Sr. Assistant Director,
Central Drug Research Institute,
Chattar Manzil, P.O. Box.173,
Lucknow – 226 001

Dr. S. Srivastava,
Senior Research Officer,
Sanjay Gandhi Postgraduate Institute of Medical Sciences,
Raebareli Road, Lucknow – 226 014.

Dr. A. K. Mathur,
Scientist –F/Plant Tissue Culture,
CIMAP,
Lucknow.

Dr. Aparna Mitra Pati,
Scientist & Incharge,
Planning, Project Monitoring & Evaluation,
Institute of Himalayan Bioresource Technology,
Palampur-176 061.

Prof. Indranil Dasgupta,
Department of Plant Molecular Biology,
University of Delhi South Campus,
New Delhi – 110 021.

Prof. S. S. Gosal,
Department of Plant Breeding,
Genetics and Biotechnology,
Punjab Agricultural University,
Ludhiana – 141 004.

Dr. K. P. Mohan Kumar,
Deputy Director,
Division of Neurosciecnes,
Indian Institute of Chemical Biology,
4, Raja S. C. Mullick Road, Jadavpur
Kolkata -700 032.

Prof. Santosh Kar,
School of Biotechnology,
JNU, New Delhi.


Dr. K. P. Mohan Kumar,
Deputy Director,
Division of Neurosciecnes,
Indian Institute of Chemical Biology,
4, Raja S. C. Mullick Road, Jadavpur
Kolkata -700 032.

The Director,
National Centre for Biological Sciences
Tata Institute of Fundamental Research
GKVK, Bellary Road,
Bangalore 560065

The Director,
Central Research Institute,
Kasauli,
Distt-Solan-173 204.

The Director,
Dr. B.R. Ambedkar Center for
Biomedical Research,
University of Delhi,
Delhi - 110 007 INDIA

Hope this information helps. I'll keep you all updated whenever/whatever new information I receive.

Thanks!

All the Best!
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Microbial Cellulases: From a Rotting Cartridge Belt to Designer Jeans

June 1, 2013, 4:54 am
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An Invisible Enemy

During the Second World War, the American military units stationed in the South Pacific jungles had to face a different kind of threat: deterioration of their clothing and equipment made out of cotton. A strain of Trichoderma viride, possessing strong cellulose-degrading abilities was isolated from a rotting cartridge belt during the studies that were carried out to understand the deterioration process.

This focused attention on Trichoderma strains, which, to this day are among the most efficient producers of extracellular cellulases.

A Jack of all Trades

Since early 1980s, cellulases have been used in many industrial applications including food and feed, wine and brewery, textile and laundry, pulp and paper etc. Nowadays, the focus is on cellulases due to their ability of converting cellulosic biomass into glucose, enabling the biofuel production. This article provides an overall summery of some of the current industrial applications and the biotechnological production of cellulases.

What are cellulases?

Cellulases are a family of enzymes including three major groups of members, namely, endoglucanases, exoglucanases (cellobiohydrolases) and beta-glucosidases (Cellobiase) that catalyses the hydrolysis of cellulose, i.e. cellulolysis.

Cellulase in the Textile and Laundry Industry

Cellulases are widely used in the production of denim blue jeans in a process called bio-stoning which gives the garment a softer texture and a fashionable “stone-washed” look. In this process, cellulases digest cellulose fibres on the cotton surface and loosen the indigo dye, giving the fabric a faded look. Cellulase based bio-stoning has many advantages over the traditional use of pumice stones in the stone-washing process; such as reduced wear and tear of the fabrics, short treatment times, less damages to the washing machines and improved quality of garments, etc.

Cellulase enzymes are also being used in textile processing for desizing and bio-polishing of the textiles. Desizing is the process of removing ‘size’ --an adhesive composed of starch, vegetable gum and water-soluble cellulose derivatives, which is added to reinforce the cotton threads-- prior to dyeing, bleaching and printing of the fabric. Enzyme treatment has replaced the conventional use of acids, alkali or oxidising agents in this process thereby eliminating the corrosion of the fibres. During bio-polishing, short cotton fibres that give a surface fuzziness to the fabric are digested by the enzyme, thus giving a smooth and glossy appearance with improved colour brightness.

In many commercial detergents cellulases are used to remove the dirt, restore the colour and soften the garments. This is achieved by removing the partially detached microfibrils on the surface of garments that traps the dirt particles.

Cellulases in the Food Industry

A complex cocktail of enzymes consist of cellulases , hemicellulases and pectinases — collectively called macerating enzymes—are used in the extraction and clarification of fruit and vegetable juices. These enzymes remove the water insoluble plant particles such as fibres, cellulose, hemicellulose, pectin, starch etc. which make the extracted fruit juices turbid. Removing these substances is essential to avoid further turbidity and precipitation and to improve sensory attributes.

In addition, cellulases are added during extraction of juices from particular fruits as black current and red grapes, to improve the release of colour compounds from the skins of the fruit. Furthermore, celluloses, together with pectinases liquefy the plant tissue making it possible to filter juice straight from the pulp without the need for pressing.

Another application of cellulases in food industry is in extraction of olive oil. Macerating enzyme mixture decomposes the cell wall allowing efficient maceration and extraction of oil from olives, increases the oil yield. Macerating enzymes increase the anti-oxidants such as vitamin E, in extra-virgin olive oil thus reducing the rancidity of oil.

Cellulases in the Wine and Brewing Industry

During the production of ethanolic beverages, glucanases are added to hydrolyse glucan which forms gels during the brewing process leading to poor filtration of the wort, low yields and the cloudiness of the final product. Microbial beta-glucanases, added either during mashing or primary fermentation reduce the viscosity of the wort and releases reducing sugars during primary fermentation improving fermentation efficiency, filtration and quality of beer. The commonly used beta-glucanases are from Penicillium emersonii, Aspergillus niger, Bacillus subtilis and Trichoderma reesei.

In the production of red wines, addition of glucanases in combination with other enzymes such as pectinases and hemicellulases, improve the skin maceration and extraction of colour from the grape skins during pressing consequently enhancing the quality, stability, filtration and clarification of wines.

Cellulases in the Paper and Pulp Industry

Cellulases are used widely in the paper and pulp industry for bio-mechanical pulping, de-inking i.e. partial hydrolysis of carbohydrate molecules and the release of ink from fibre surfaces.

Apart from these applications, cellulases are extensively being used in waste management, pharmaceutical industry, agriculture and in various research applications. With the recent developments in the biofuel researches, there will soon be increased applications of cellulases for converting lignocellulose biomass into ethanol.

Cellulase Producing Microorganisms

A large array of microorganisms including both fungi and bacteria produce cellulases. Among them most extensively studied cellulase producers include bacteria such as Clostridium thermocellum (an anaerobe) Cellulomonas (an aerobe) and fungal species like Trichoderma, Phanerochaete and Aspergillus.

Improvement of microbial strains for the production of elevated amounts of cellulases is of vital important as the amount of enzyes produced by the wild-type strains of microorganisms is too low for sustainable industrial operations. Researches carried out to improve the cellulase production by mutagenesis and selection of cellulolytic microorganisms have yielded mutants with enhanced characteristics such as increased efficiency and reaction rates, higher glucose tolerance, greater tolerance to elevated temperature and pressure conditions used in industrial processes etc.
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Antimicrobial Enzymes: Modern Weaponry against Microbes

June 3, 2013, 8:58 am
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The Same Old Story- Drug Resistance and Biofilms

In the age-old war between humans and microbes, we are losing grounds fast. Those so called magic bullets have long since proved unsuccessful due to the evolution of drug resistance in microorganisms. Bacterial biofilms further strengthen their line of defence acting as a protective shield against antimicrobials and host immunity.

A New Treatment Strategy: Antimicrobial Enzymes

Scientists studying new methods of controlling these invisible enemies have focused their attention on a new approach which has demonstrated promising potential thus far-antimicrobial enzymes.

Antimicrobial enzymes are a major component of the immune system of many living organisms that fight against pathogenic microorganisms. These enzymes act through various mechanisms. They may attack the microbial cells by degrading major structural components of the microorganisms or they may induce the production of antimicrobial substances. They may either prevent biofilm formation or disrupt the existing biofilms by degrading the compounds (mainly the exopolysaccharides) that hold the cells together, thus making the individual cells susceptible to antibiotics. Another group of enzymes may interrupt bacterial quorum sensing, thus preventing the cell aggregation and production of virulence compounds.

Antimicrobial enzymes are being currently used in many formulations such as cleaning liquids, polymer substances, ointments and even toothpastes. These preparations may contain a single enzyme, a combination of two or more enzymes or enzymes combined with another antimicrobial agent.

Hydrolysing Enzymes

These enzymes inhibit microbial growth either by directly attacking the major constituents of the cell wall or by degrading the compounds that glue the cells to each other and solid surfaces.

Proteolytic enzymes such as subtilisins, that hydrolyse adhesins--proteins which are essential for bacterial attachment in biofilms--are widely in use as antimicrobial agents. Subtilisins have particularly shown to be effective against species such as Pseudomonas, Bacillus, Streptococcus and, Listeria monocytogenes. Another protein hydrolysing enzyme that has antibacterial capacity is lysostaphin-an enzyme that disrupts Staphylococci cell walls, thus demonstrating immense potential in controlling Staphylococcus species including multi-drug-resistant MRSA which is the main cause of many nosocomial infections.

Polysaccharide-hydrolysing enzymes are also important in controlling microorganisms. Alpha-amylase has been proven to inhibit the formation of biofilms MRSA, Vibrio cholerae and Pseudomonas aeruginosa. This enzyme was also effective in destroying the preformed mature biofilm by disrupting the exopolysaccharide layers in biofilm matrix. Dispersin B is another important glycoside hydrolase enzyme that catalyses the hydrolysis of poly-N-acetylglucosamine, a sticky extracellular polysaccharide which is important in biofilm attachment. Chitinases and beta-glucanases act as antifungal enzymes by degrading chitin and beta-1,3-glucan, the main components in fungal cell wall. Lysozyme, abundantly found in tears, saliva, human milk, and mucus is another antimicrobial enzyme that attacks the cell walls of Gram positive bacteria by hydrolysing the beta-1,4-glucosidic bonds in the peptidoglycan cell wall. Another polysaccharide degrading enzyme, alginate lyase that degrades bacterial alginate polymer has also been successfully used against Pseudomonas aeruginosa.

Apart from these enzymes, DNases are also being used as antibiofilm enzymes. These DNases digest extracellular DNA in the biofilm matrix which are important for the biofilm formation and stability, thus preventing the initiation of biofilms and disrupting the existing ones.

Bacteriophage lysins are another group of enzymes that target the peptidoglycan layer of the bacterial cell walls. Phage lysins are widely used to control many bacterial pathogens including Listeria monocytogenes, Escherichia coli, Streptococcus pyrogenes, Bacillus anthracis and Bacillus cereus.

Oxidative Enzymes

Enzymes such as glucose oxidase, cellobiose dehydrogenase and superoxide dismutase elicit antimicrobial reactions through the production of hydrogen peroxide which is cytotoxic. Still another type of oxidative enzymes, haloperoxidases, oxidise halides or pseudohalides into toxic compounds. Myeloperoxidase, lactoperoxidase and horseradish peroxidase are commonly known members of this group. Lactoperoxidase, found in milk, saliva and other mucosal secretions, oxidises bromide, iodide and thiocyanate ions into powerful bactericides.


Quorum-Quenching Enzymes

Such enzymes including AHL-lactonase, AHL-acylase and paraoxonases interfere with bacterial cell-to-cell communication, i.e. quorum sensing, by degrading AHL (acylhomoserine lactone), the signal molecules. Inhibition of quorum sensing eliminates the ability of the pathogen to produce virulence compounds and initiate biofilms, thus allowing the host defences to eradicate the pathogen.

Pros and Cons

The antimicrobial enzymes possess many advantages over antibiotics and disinfectants. Many of the enzymes are specific for a particular pathogen, therefore do not disturb the normal flora and bacterial resistance to antimicrobial enzymes is very rare. Furthermore,these enzymes are natural, nonreactive, and nontoxic thus they offer a safe alternative to the antibiotics and chemical disinfectants which are currently in use without causing adverse health effects or corrosion of surfaces.

However, the cost of production and purification of these enzymes are comparatively high. Moreover, these enzymes, being proteins, tend to denature at extreme conditions.

Future Potential

Genetic engineering and synthetic biology approaches are being developed to explore the possibilities of overcoming these hindering factors thereby boosting the use this comparatively novel technology in areas such as food production, agriculture, healthcare and medical fields.
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Dental Care Clinics for Children

June 4, 2013, 1:59 am
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Dental care should be started at a very early age. Most parents are concerned about the fact that when they should start the dental appointments of their child. Actually your child’s first visit to a Dental Care Clinic should be within 6 months after the first tooth start appearing. The dentist will examine your child’s teeth to see if there are any signs of tooth decay or any infections. A good dentist can check if your child is prone to tooth infections by verifying the early signs in the tooth structure. He can also show you the best way to clean your child’s tooth.

After the first visit, go for dental appointments once in 6 months. This will help your child’s oral health and his risk of getting cavities in future. If the dentist diagnoses your child with tooth problems then he may ask for more frequent visits. Another common problem with the baby teeth is the weakness of the enamel. You may have to do a fluoride treatment to avoid further problems due to this. If there are fissures in their teeth the dentist may fill it with sealants to avoid the accumulation of plaque.

It is the responsibility of the parents and the staff at the dental care clinics to make each visit pleasant for a child. This will make them come back again and will aid for good oral health. If necessary look for a pediatric dentist who is specially trained to welcome anxious kids. Now there are special Pediatric dental care clinics for kids.
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Is GLYX- 13 A Possible Antidepressant Without Side Effects?

June 4, 2013, 1:35 pm
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GLYX- 13 is ketamine molecular cousin. This tetrapeptide is a NMDA receptor partial agonist. It's neuroprotective effects delay death of CA- 3, CA- 1 under hypoxia and hypoglycemia conditions.

This tetrapeptide has similar influence on human brain like ketamin. However, ketamine is used in many cases such as analgesia, anesthesia, elevated blood pressure and other indications. GLYX- 13 has antidepressant effects without side effects.

Ketamine has shown effectiveness in depression treatment in patients with bipolar disorder. Persons with major depressive disorder have shown good response when they took ketamine drug.

Limitations of major depressive disorder drugs

Ten percent of population is affected with major depression syndrome. According to World health organisation, this disorder is second syndrome that leads to disability in modern world. This fact was involved in creation of big number and several classes of antidepressant drugs. However, not everyone is responsive to these drugs. Several researches revealed that up to 40% of population is unresponsive to any kind of treatment. Moreover, selective serotonin reuptake inhibitors take weeks to be effective, thus suicide is not so rare in this period of few weeks.

Function of NMDA receptors

NMDA receptors were linked to memory and learning by scientist for thirty years ago. Soon after that, pharmaceutical companies tried to block these receptors in order to prevent stroke. However, this experiment led to an unordinary consequence- expansion of cardiovascular disease. These experiments and researches were slowed down, but ketamine, already widely used medication for anesthesia began revolution in depression treatments.

Ketamine properties and disadvantages

Ketamine presented a real revolution in depression treatment. It needs only two hours to take effect, while SSRI needs two weeks. That is significant result in depression treatment. But, not every single thing about ketamine is positive. It has vast of side effects like hallucinations, excessive sleeping disorder and substance abuse behavior.

GLYX- 13 is very different from ketamine. There is a crucial difference between these two drugs, and it is blocking of ion channel. GLYX- 13 does not block this ion channel, and this is maybe the answer why this drug has not same side effects.

Previous studies have shown that GLYX- 13 improved memory and learning in rats. Also, GLYX- 13 showed analgesic effects. These properties are not common for GLYX- 13 and ketamine, they are only properties of GLYX- 13.

Accidental development of GLYX- 13

Researchers developed GLYX- 13 accidentally. One of researchers created, monoclonal antibodies, specific molecules in order to use them in various experiments. These experiments were planned for understanding the pathways of memory and learning. Of course, some of these antibodies were created for NMDA researches. After a certain number of unsuccessful experiments, they began conversion of these antibodies to small protein molecules. One of these molecules is GLYX- 13 molecule, created of only four amino acids.

Experiments with GLYX- 13, ketamine and fluoxetine

Researches and results of researches on four compounds: GLYX- 13, inactive form of GLYX- 13, ketamine and fluoxetine (SSRI drug). Ketamine and GLYX- 13 gave rapid effects within one hour. Also, antidepressant-like effects lasted 24 hours. SSRI typical drug, fluoxetine, did not produce rapid effect on patients. It took two to four weeks for effects expression. Last one, scrambled GLYX- 13, showed no antidepressant-like results.

An increase of NMDA receptor NR2B and chemical messenger glutamate receptor called AMPA in hippocampus was presented in protein studies. Moreover, electrophysiology studies pointed that ketamine and GLYX- 13 supported long lasting transmission of signals in hippocampus. This promotion of signals is also called long term potentiation or simply- synaptic plasticity. This process is very important in memory and learning process.

There are some theories how GLYX- 13 works. One of the theories proposes theory of NR2B receptor activation by GLYX- 13. After this activation, few events like intracellular calcium influx and the expression of AMPA occur. These events are responsible for increased communication between neural cells.

Evaluation of results

Results from these researches are similar to results from phase two from a recent clinical study. This results showed that only one administration of GLYX- 13 gave significant reduction of depression in patients with major depressive disorder. This is maybe greater achievement, because these patients had failed treatment with conventional drugs.

Administration of a single dose of GLYX- 13 gave significant results in 24 hours, and they lasted nearly a week. Application of GLYX- 13 is well tolerated. One of big advances in this therapy is lack of schizophrenia- like symptoms, which may occur in treatments with conventional NMDA receptor modulating agents.

A molecule each of amino acid chemical messengers glutamate and glycine is needed for NMDA receptors to become activated. There are speculations that GLYX- 13 directly binds to the NMDA receptors glycine`s site. Other speculations say that GLYX- 13 modulates how glycine and receptor works together indirectly. By these assumptions, antidepressant effects are caused by previously mentioned activation of NMDA and AMPA receptors, involved in learning and memory. On the other hand, ketamine has different way of functioning. It only blocks NMDA receptors, but increases activation of AMPA receptors. This results could help us in understanding of major depression disorder and development of new generation of antidepressant drugs.

Future of GLYX- 13 research

Nowadays, GLYX- 13 is being tested in clinical trials phase two where scientist have plan to find out which dose of this modern antidepressant drug is needed for humans. Another questions are waiting to be answered: does GLYX- 13 have power to regulate twenty receptor subtypes and is this GLYX- 13 protein able to give positive effects in other disorders like: schizophrenia, autism and attention- deficit hyperactivity disorder? These question could be answered soon, because research started in 1983 could give important answers to scientists.
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Crest award idea?

June 7, 2013, 2:33 pm
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Hi guys.

I want to do a gold level CREST award next year and I want to do an experimental projects(which unfortunately I have to do it in my school's lab) on a biotech topic.

I'm thinking about doing something in bio-washing powders and ecological issues 'cause this seems like the only thing I can do in a school lab.

Can you guys give me some ideas?

Thanks in advance Big Grin
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Bioplastics: Microbial Production of Polyhydroxyalkanoates (PHAs)

June 7, 2013, 5:51 pm
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Conventional Plastics

Plastics are everywhere. They have outdone many of the traditional materials with their durability, flexibility and water-resistance among numerous other useful characteristics.

However, despite their versatility in various domestic, industrial and medical applications, plastics bring forth a myriad of environment-related problems. These plastics are mostly synthetic and are derived from petroleum-based chemicals. The rate of exhaustion of the mineral oil resources is one of greatest concerns regarding the production of these synthetic plastics. Furthermore, owing to their non- or slow- biodegradability, the accumulation of the plastic wastes in the environment has become an increasing problem.

Bioplastics

In the light of such situation, biomass-derived biodegradable bioplastics have gained the interest of many scientists as a more sustainable material. Bioplastics can be of many types and are obtained from various biological sources including plants and microbes. This article focuses on one such material, polyhydroxyalkanoates-commonly known as PHAs- and their microbial biosynthesis.

Polyhydroxyalkanoates (PHAs)

Polyhydroxyalkanoates are fully biodegradable and biocompatible. Their properties are similar to those of petrochemical-based traditional plastics and they are available in a variety of polymers depending on the number of monomer units, thus displaying a wide selection of physical and chemical properties.

PHAs are linear polyoxoesters of R-hydroxyalkanoic acid (HA) monomers, with a number of carbon atoms ranging from 4-14. They are classified based on the number of carbons and the type of monomeric units producing homopolymers or heteropolymers.

[Image: phas.h4.gif]

Short chain length PHAs (SCL-PHAs) such as poly(3-hydroxybutyrate) or P(3HB) and poly(4-hydroxybutyrate) or P(4HB) contain 3–5 carbon atoms. Medium chain length PHAs (MCL-PHAs) such as homopolymers poly (3-hydroxyhexanoate) or P(3HHx), poly(3-hydroxyoctanoate) or P(3HO) and heteropolymers such as P(3HHx-co-3HO) contain 6-14 carbon atoms.

Applications of PHAs in Industry

PHAs are currently being used in many industrial purposes such as packaging materials (mostly cosmetic containers and food packaging material), moisture barrier in sanitary towels and nappies, etc.

Owing to their immunological inertness, PHAs are considered a good candidate to be used in medical applications such as cardiovascular products, prodrugs, dental and maxillofacial treatment, drug delivery vehicles, wound sutures and dressings etc.

Biosynthesis of PHAs

Many living organisms, mainly plants and bacteria produce PHAs. However, microorganisms are more suitable for the industrial production of PHAs due to the fact that plant cells can only accumulate low yields of PHAs i.e. less than 10% (w/w) without adversely affecting their growth. In contrast, bacteria are known to store up PHAs at levels as high as 90% (w/w) of their dry cell weight.

A wide range of Gram-positive and Gram-negative bacteria including Aeromonas hydrophila, Alcaligenes latus, Pseudomonas sp, Bacillus sp, and Methylobacterium sp naturally synthesise PHAs. These bacteria produce PHA as a carbon and energy storage compounds under imbalanced nutritional conditions. When carbon is in excess and the other nutrients such as nitrogen or phosphorous or oxygen is limited, PHA is accumulated in the form of water-insoluble granules in their cytoplasms.

[Image: Fig1.jpg]

Industrial-Scale Production of PHA

Fermentation of PHA is carried out in a two-stage fed-batch process. The first stage, which is aimed to increase the cell density of the bacterial culture, is operated in nutrient-rich media that supports the growth. In the second–stage the aim is to increase the PHA concentrations by the depletion of a nutrient such as nitrogen. Other parameters such as temperature, pH, etc. depend on the choice of microorganisms.

After fermentation, bacterial cells containing PHAs are separated from the medium by centrifugation. Various methods for the recovery of intracellular PHA have been studied including solvent extraction, cell disruption, pre-treatment of cells, chemical or enzymatic digestion of substances other than polyhydroxyalkanoates in the system, extraction using supercritical CO2, however, an economical, safe and industrially feasible process is yet to be exploited in order to maximise the recovery yields.

Future Possibilities

Despite their environmental friendly characteristics and potential usage in many different purposes, the cost of production is still high compare to the conventional petrochemical-based plastics. Therefore, researches are being carried out on reducing the production cost allowing a more viable large-scale production of PHAs. The key areas under study are the use of cheap carbon sources including wastes and byproducts, recombinant microbial strains, increasing fermentation efficiency, efficient recovery and purification processes etc.

[Image: image2.png]

Source

Keshavarz, T., & Roy, I. (2010). Polyhydroxyalkanoates: bioplastics with a green agenda. Current opinion in microbiology, 13(3), 321-326.
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Advanced Algal Technologies Limited is a technology provider

June 10, 2013, 10:10 am
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There are many technology providers in Biotechnology Industry. Those company which are focusing on the production of industrial biomass production using patented technology which helps it in commercial production of biomass. Through This Process Helps its user companies to reduce costs through Carbon emission abatement and simultaneously facilitates a commercial revenue stream. Their Technology systems is a low-cost, extensive open pond raceway system designed for producing protein rich content for livestock feed industry. It has varied application in industries pertaining to animal feeds, health food sector, syngas and co-generation electricity, etc. Advanced Algal Technologies Limited is one of those technology providers.
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Annual Internships In Foreign Universities for Indian & International Students

June 10, 2013, 5:05 pm
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My previous article was focused on providing information about the Summer Internship/Training Opportunities for the Indian Students in India. This article will provide information on one of the most sought after opportunities-An internship "abroad"! Though, most of the Indian (and non-Indians of-course) students dream of going to a foreign University/Institute for a summer/winter internship, the dream remains a dream due to three reasons:

(i). Random application to scientists in randomly selected universities
(ii). If a random application somehow gets a response, then the idea is forgotten after knowing the 'expenses' for training and living in the foreign country!
(iii). Lack of knowledge about the annual "scholarship based" training opportunities in foreign countries.

Considering the fact that the first two problems actually arise because of the third problem basically, so the objective of this article is to let you people get rid of the ignorance about the opportunities that exist.

Every year, numerous global universities/government bodies open-up summer/winter internship opportunities for International students (some specifically for Indians only), that last for 2-6 months, with an aim to improve ties with the country, as well as to conduct a "student exchange program" that might enable their students to get exposed to their biotechnological research base and thrusts. Following is a brief on some of the most coveted scholarship based training opportunities, that can actually change the anatomy of a student's biotechnological career! :

1. Khorana Scholars Program
Khorana Scholars Program is probably the most revered and popular summer internship program, specifically designed for Indo-US students by the collaborative action of the University of Wisconsin-Madison (UW) US, the Government of India (DBT), and Indo-US Science and Technology Forum (IUSSTF), as a dedication to the Noble Laureate late Dr. Hargobind Khorana (world renowned Genetic Engineer). Every year nearly 30-50 Indian Students are exchanged with nearly 15-20 US students, for a 2 month Life Sciences research. The program is fully funded, including the traveling/staying expenses too! Apart from that, a healthy stipend is paid to the students(depending upon the institute you get selected into).

Application Starts: October Every Year

Application Ends: November 30 every year

Program Duration: Mid May-Mid July

Eligibility: Indian Scholars enrolled in M.Tech, B.Tech, or M.Sc.programs at any academic institution in India

Participating US Institutes/Universities:
a) University of Wisconsin-Madison
b) University of Illinois at Urbana-Champaign
c) University of Iowa
d) University of Michigan
e) Michigan State University
f) University of Minnesota
g) Indiana University - Bloomington
h) Georgetown University
i) Massachusetts Institute of Technology
j) University of Nebraska - Lincoln

Click Here for Khorana Program Details


2. Laboratory Training Programme @ CNIO
The Spanish National Cancer Research Centre (CNIO; Centro Nacional de Investigaciones Oncológicas) offers summer research program to undergraduate students of any country in the world for a period of two months. It covers the travelling (airfare) and meal expenses of the students during their stay at CNIO. Upto 8-10 students are selected.

Application Starts:[/u] February End Every Year

Application Ends: April every year

Program Duration: Mid June-Mid August

Eligibility: Open to undergraduate students of any nationality who are in their final two years of studies in the Life Sciences or related subjects (e.g. Biology, Biomedicine, Biochemistry, Pharmacology, Bioinformatics).

Click here for CNIO Training Program Details

3. Summer Research Program @ EPFL
Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland is a leading University of the world, with a highly reputed Life Sciences research base. Every year EPFL offers summer research program to the international undergraduate students of Life Sciences. A financial compensation for living and housing expenses are provided for all successful candidates, apart from the airfare expenses too. Upto 25 students are selected every year.

Application Starts: November Every Year

Application Ends: January every year

Program Duration:July-August

Eligibility: Open to undergraduate students enrolled in a degree program in biology, physics, chemistry, bio-engineering, or computational sciences and plan on pursuing a career in the life sciences. Basic Life Sciences backgound is essential.

Participating Institutes:
a) Brain Mind Instutute (BMI)
b) Institute of Bioengineering (IBI)
c) Global Health Institute (GHI)
d) Swiss Institute for Experimental Cancer Research (ISREC)
Click here for EPFL Summer Research Program Details



4. DAAD Research Internships in Science and Engineering (RISE)
DAAD is a German Academic Exchange Service, which establishes academic research collaborations of various global Universities/Research centres with coveted German Universities under the DAAD authorization. RISE is one of DAAD's various scholarship based internship opportunities for the Indian Research groups, laboratories, professors, postdoctoral and PhD students employed by or affiliated with an accredited academic institution or a non-profit research institution in India. Scholarships are awarded to the successful candidates.

Application Starts: October Every Year

Application Ends: November every year

Program Duration:June-October

Click here for DAAD RISE Details


Click here for Other DAAD Scholarships




5. Stanford-India Biodesign Intern
Stanford-India Biodesign is a result of collaborative funding of the Stanford University and DBT India, in bringing out the Biomedical Engineers and Designers in India. It is administered in New Delhi as a collaboration between Stanford University, the Indian Institute of Technology Delhi, and the All India Institute of Medical Sciences (AIIMS) in partnership with the Indo-US Science & Technology Forum (IUSSTF). A portion of the fellowship is spent at Stanford University and the remainder in India. The SIB fellows are offered training at AIIMS (New Delhi) with foreign trips during the training. Fellows receive tuition, stipend, and international travel support (for trips required for the fellowship.)

Application Starts: March Every Year

Application Ends: June every year

Program Duration:Begins January Every Year for upto 4 months

Eligibility: Open to advanced degree holders (including B.Tech with experience/related projects) and/or significant work experience. University faculty are strongly encouraged to apply.

Click here for Stanford-India BioDesign Details




6. University of Queensland Winter Research Program
University of Queensland, Australia offers Winter Research Internship to the undergraduate students of various fields (including Biology) from various countries of the world. A Winter Research Grant ($1,000) is offered to the selected candidates. Students can check available projects under the Faculty of Health Sciences as well as the Faculty of Sciences.

Application Starts: February Every Year

Application Ends: April every year

Program Duration:Mid June-End July

Click here for Queensland Winter Research Details


7. ITRI Summer Internship
Industrial Technology Research Institute (ITRI), Taiwan offers International Internship program to undergraduate students across the globe in the field of biological and engineering research. This program is open to graduate and undergraduate students currently enrolled at accredited colleges and universities. A healthy stipend of NT $30,000-35000 is paid per month along with free accommodation and accidental insurance.

Application Starts: Jan-February Every Year

Application Ends: March every year

Program Duration:May-July & June-August

Click here for ITRI Summer Internship Details



8. University of Zurich Summer School
University of Zurich and ETH Zurich, Switzerland offer the International Biology Undergraduate Summer School to the undergraduate students of the universities across the globe. The program covers travel expenses and housing costs of international participants.


Application Starts: Jan-February Every Year

Application Ends: March every year

Program Duration:July Start-August End

Click here for University of Zurich & ETH Summer School Details



9. National Tsing Hua University Internship Program
National Tsing Hua University (NTHU), Taiwan has a dedicated internship program for the 3rd year and above undergraduate students of IIT Madras, IIT Delhi, University of Delhi, Anna University, and IISc Bangalore, India. It's a 2 month all expense paid summer research internship program. It includes a Stipend of NT$5,000/month + Round trip airfare + Visa fees + Insurance

Application Starts: November Every Year

Application Ends: December every year

Program Duration: Mid May-Mid July and Mid June-Mid August

Click here for NTHU Taiwan Summer Internship Details



10. International Summer Internship Max Planck Institute
The Max-Planck-Institute of Immunobiology and Epigenetics, Germany offers Summer Internship Program to students across the globe. Interns are provided with a stipend to cover their living expenses and accommodation in the institute's guesthouse.

Application Starts: December Every Year

Application Ends: January end every year

Program Duration: May-September

Eligibility: Students in their 3rd or 4th year of study toward a Bachelor degree in Immunobiology, Genetics, Molecular Biology, Cell Biology, Developmental Biology, Bioinformatics or related fields. Master degree students can also apply, but a valid certificate of enrolment is required.

Click here for International Max Planck Research Internship Details


So, these were some of the highly renowned and coveted internship opportunities, which are open to all Indian students (and most International students too). These are selection based opportunities, so they don't ask for payments, but rather provide the interns with stipends to cover all their expenses! I sincerely hope that this article will help you all, and I wish someone amongst the readers might land-up in one of the listed Universities for an internship program in near future!
All the best!
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Synthetic Microbes as Efficient Cell Factories

June 12, 2013, 12:13 am
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Scientists are trying to play God, it seems.

Rather than replicating existing genomes and modifying existing microorganisms, scientists now aim to create “synthetic life” from scratch.

They are conducting researches on the construction of custom-made microorganisms which are pre-designed to efficiently carry out specific tasks. These microbes will carry programmed genomes which will make them behave in a predictable manner similar to that of synthetic machinery. These ‘biological machines’ will be more competent than genetically engineered microorganisms and will be able to perform a vast range of metabolic activities which are not yet achievable with the natural or genetically altered microorganisms.

A Minimal Genome

In fact, scientists have come halfway through their goal. They have already identified the genes which are crucial for the basic cellular functions of a bacterium. This ‘minimal genome’ enables the bacterium to survive, grow and reproduce without involving in other non-essential energy wasting cell functions. Insertion of another few pre-programmed genes will convert such minimal bacterium into an efficient biological machine capable of self-replication and self-assembly while accomplishing the desired tasks with maximum productivity.

In 1995, a group of researchers at the J. Craig Venter Institute, California completely sequenced the genome of the bacterium Mycoplasma genitalium, the smallest genome of a natural free living organism. They identified that of some 500 genes only 206 genes, approximately, are required for the viability of the cell.

A Man-made Genome

In 2010, they succeeded in the construction of a ‘semi-synthetic bacterium’ by transplanting a synthetic genome into a host bacterial cell.
In the process of creating this bacterium, the scientists first sequenced the genome of the donor bacterium, Mycoplasma mycoides and then designed a computer model of a new genome by purposely deleting some of its genes and adding a few ‘watermark genes’ which enabled to distinguish between the synthetic and natural genomes. Then they chemically synthesised this genome in the lab in the form of several gene fragments with sticky ends. These gene fragments were then put together to form the complete genome. The re-assembly was done in yeast cells.
This completed synthetic chromosome was inserted into another host bacterium of the same genus, M. capricolum, where it replaced the natural genome and replicated successfully.

Read the complete process of the “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Gnome” in detail.

Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., ... & Venter, J. C. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. science, 329(5987), 52-56. 

An Ideal Cell Factory

Equipped with this knowledge, scientists are currently conducting research with the hope of manufacturing an ideal microbial cell factory to be used industrially. This model cell will contain a collection of genes that are essential for the metabolism, growth and reproduction of the microbe along with the tailored genes for carrying out the required job.

Such a cell is hoped to maximise bioprocess efficiency by eliminating unnecessary cellular processes and focusing only on the essential activities. For instance, deleting the genes required for alternative metabolic pathways will make product formation a favourable condition to the cell viability, thus enhancing production efficiency.

A smaller genome will also be beneficial since it will reduce the rate of mutations- probably due to the removal of transposons- consequently increasing the genetic stability of the strain.

Another favourable characteristic will be improved resistance of the bacterium to the physical and stresses such as sheer force or osmotic stress as well as resistance to toxicity by products or substrates. For example, an ideal microbe designed to be used in ethanol fermentation will have higher alcohol tolerance; hence will be able to produce higher ethanol yields without being suppressed by elevated alcohol concentrations.

This perfect microbial machine will be programmed in such a way that its reproduction will be carried out in an effective manner without generating waste biomass i.e., non-viable, non-product forming daughter cells. This will result in higher product yields per unit mass of substrate. Furthermore, it will have higher growth rates accounting for short productions runs, ultimately boosting the overall productivity.

A Dream Come True

The array of possibilities a programmed organism offers is unimaginable.
This will open up new avenues of research and industrial processes such as biofuel research, production of industrial enzymes, pharmaceuticals, bio-based chemicals, etc. These man-made organisms can be programmed with higher resistance to the toxins making them suitable for clearing up chemical spills.

There will be microorganisms with laboratory-designed metabolic pathways capable of utilising new, renewable substrates. And those microbes will have increased resistance for products and inhibitors thus resulting in improved product yields. Moreover, new microorganisms will be constructed to manufacture completely new end products.

Such a microorganism is the dream of industrialists as well as the researchers. With the advancement of technology, this dream will be realised sooner or later. For instance, the ‘de novo’ construction (meaning from the beginning) of the synthetic DNA which cost more than 20 years and approximately $40 million in 2010 is now feasible at a much lower price today and takes much lesser time.

Research On-going

However, the ever inquisitive scientific mind is not satisfied with the creation of a semi-synthetic bacterium. Researches are being conducted to construct an entirely man-made ‘biological machine’ with a complete set of programmed genes as well as a synthetic ‘chassis’ housing those genes. Such a framework will be more durable than the delicate bacterial outer membranes and will have improved features including selective permeability and affinity.

Source:

Foley, P. L., & Shuler, M. L. (2010). Considerations for the design and construction of a synthetic platform cell for biotechnological applications. Biotechnology and bioengineering, 105(1), 26-36.
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How Antibiotics Kill? Mechanism of Action of Various Antibiotics

June 12, 2013, 6:46 am
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Today, there exist a variety of antibiotics for a variety of pathogenic micro-organisms. Each antibiotics is peculiar in it's traits of spectrum, shelf-life, half-life, toxicity, dispersal and mechanism of action. Despite the plethora of antibiotics already existing today, the scientists are always in a pursuit to discover more and better kinds of antibiotics, which might act fast and effect more for a longer period of time, without any resistance from the target microbe. In-fact, the resistance developed in the target microbe towards the existing antiobiotic after a prolonged use, is actually what triggers the research towards developing new antibiotics. But no matter what class or kind of antibiotics exists or is discovered, all of them operate by one of the following mechanisms:

1). Inhibition of cell wall synthesis
2). Inhibition of protein synthesis
3). Inhibition of membrane function
4). Disruption of Metabolism
5). Inhibition of nucleic acid synthesis

The Cell Wall Synthesis Inhibitors
It includes those antibiotics which inhibit the synthesis of microbial cell wall (mostly bacteria, which possess cell walls). There are three mechanisms of inhibition of cell wall, and hence three classes of antibiotics in this regard:

a. Inhibition of peptidoglycan (the structural unit of bacterial cell wall) synthesis
Beta-Lactams is the class of antibiotics that act by this mechanism. Examples of antibiotics in this class are Penicillins (Ampicillin, Amoxicillin, Methicillin etc) , Cephalosporins, Monobactams, Carbapenems etc.

b. Inhibitors/Disruptors of peptidoglycan cross-linkage (making the structural framework of bacterial cell wall)
Glycopeptide class of antibiotics act by this mechanism. Most common example includes Vancomycin. Other are teicoplanin, telavancin, bleomycin, ramoplanin etc

c. Disruptors of Precursor Movement
This class of antibiotics block the movement of precursors required for peptidoglycan. Cyclic polypeptides like Bacitracin include such antibiotics. They are mostly used as ointments (topical use) because of their toxicity and poor bioavailability when taken through oral route.

The inhibitors of Protein Synthesis
It includes those antibiotics which inhibit the synthesis of proteins/enzymes vital for normal functioning of microbial cells. Since translation (protein synthesis) has numerous steps and components involved, there are almost equal number of mechanism of action of antibiotics as mentioned below:

a. Ribosome Subunit Binders
Bacterial ribosomes have 30S and 50S subunits. Both of which are involved in different steps of translation. There are classes of antibiotics which tend to bind to these subunits reversibly/irreversibly, blocking the assembly of ribosomes, or inhibiting elongation and hence translation:
(i) 30S Binders
Aminoglycosides like Gentamicin, Amikacin, Tobramycin etc come into this category which bind irreversibly to 30S subunit of ribosomes.

(ii) 50S Binders
50S binders can bind to 50S subunit in following ways:
  • Binding to peptidyl transferase
Some antibiotics bind to the peptidyl transferase component of 50S ribosome, blocking peptide elongation. Example include Chloramphenicol
  • Inhibitors of amino acid-acyl-tRNA Complex binding
It includes those antibiotics which bind to 50S subunit in such a way that they block the binding of amino acid-acyl-tRNA complex and hence inhibit peptidyl transferase action and hence peptide elongation. Example Clindamycin.
  • Reverible Binders
These bind to 50S subunit in a reversible manner to temporarily block peptide elongation (hence these are bacteriostatic). Example: Macrolides like Azithromycin, Erythromycin, Roxithromycin, Clarithromycin etc

b. t-RNA binding blockers
This class of antibiotics block the binding of tRNA to 30S ribosome-mRNA complex. Tetracyclines like doxycycline, minocycline, plain tetracycline etc.

The Disruptors of Membrane Function
There are the class of antibiotics that render the microbial cell membranes disfunctional by inducing random pores by detergent like activity. This leads to the disruption of osmotic balance causing leakage of cellular molecules, inhibition of respiration and incr eased water uptake leading to cell death. Gram-positive bacteria possessing a thick cell wall are naturally resistant to such antibiotics.
Example: Lipopeptides like Polymyxins belong to this call of antibiotics.

The Disruptors of Metabolism (Folate Pathway Inhibitors)
This class of antibiotics inhibit the pathway responsible for the synthesis of folic acid which is essential for the synthesis of adenine and thymine (important nucleic acids for DNA and RNA synthesis; thymine is not required for RNA though, but required for DNA). And, since humans donot synthesize folic acid, so these antibiotics donot have an inhibitory toxic effect on humans.
The folic acid synthesis inhibition can take place by:
a. Inhibition of the enzyme dihydrofolate reductase required for folic acid synthesis. Example: Trimethoprim/Sulfamethoxazole acts by inhibiting dihydrofolate reductase.

b. Substrate competition with p-aminobenzoic acid (PABA)thereby preventing synthesis of folic acid. Example: Sulfonamides & Dapsone.

The inhibitors of Nucleic Acid Synthesis
Depending upon the target Nucleic Acid, the antibiotics may be:

a. DNA Inhibitors
The antibiotics may act on the DNA synthesis process of the microbes by:
  • Inhibiting DNA gyrases
DNA gyrases (Type II Topoisomerases) are responsible for relieving the positive supercoils in the DNA (or introducing negative supercoils) ahead of the moving DNA polymerase, thereby enabling the availability of relaxed DNA strands for continuation of replication, as well as the compaction (negative supercoiling) of the large strands of newly synthesized DNA to pack them in the bacterial cell. Some antibiotics form a stable complex with these DNA gyrases, thereby inhibiting the DNA replication.
Example: Quinolones like Cinoxacin, Ciprofloxacin, Levofloxacin, Norfloxacin, Ofloxacin act by this way.
  • DNA damagers
This class of antibiotics are metabolized in the microbial cell to generate toxic and highly active byproducts that attack ribosomal proteins,DNA, respiration, pyruvate metabollism and other macromolecules within the cell.
Examples: Metronidazole, and furanes like Nitrofurantoin.

b. RNA inhibitors
This class of antibiotics block the initiation and thus the synthesis of RNA in microbial cells.
Example: Rifampin and Rifabutin which bind toDNA-dependent RNA polymerase, thereby inhibiting the initiation of transcription.

Following is a diagrammatic summary of the mechanisms of action of various antibiotics:
[Image: antibiotic_targets_web.gif]


So, there might exist numerous antibiotics in the market today, most of them act in one of the above described ways. I hope the next time you are prescribed an antibiotic for an infection, you should know the mechanism of it's action!
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Glowing Plants: The Street Lights of Future?

June 12, 2013, 3:30 pm
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Recently, a highly ambitious project aimed at replacing the streetlamps with glowing trees caught the attention of the entire globe-let alone the biotechnological world! The project, directed by Antony Evans(an MBA with Distinction from INSEAD, an MA in Maths from the University of Cambridge and is a graduate of Singularity University’s GSP program), with Omri Amirav-Drory (PhD, the founder and CEO of Genome Compiler Corp., a synthetic biology venture) and Kyle Taylor (a young scientist with a PhD in Cell and Molecular Biology from Stanford University) in the team, was named as "The Glowing Plant Project".
[Image: glowing_plant_square.jpg]
Logo: Glowing Plant Project (Open Source)

About the Project and How They Claim to Achieve it:
In the words of the Glowing Plant Project team, " The project seeks to engineer the thale cress Arabidopsis thaliana to emit weak, green-blue light by endowing it with genetic circuitry from fireflies. If the non-commercial project succeeds, thousands of supporters will receive seeds to plant the hardy weed wherever they wish." The target sequence of both the luciferase and luciferin were designed in a genome compiling software, which can be printed and inserted in the Arabidopsis thaliana geonome by gene gun.

The group aimed at using this simple and novel ambition as a motivational factor for generating awareness among the common public about synthetic biology and hence decided to launch it on a large scale, wherein the common masses would be delivered the GM Arabidopsis thaliana plantlets that would glow!

In order to achieve this goal, a fund raising campaign was launched that aimed at generating $65,000, so that bulk amounts of designed sequence could be printed for insertion in the plantlets. The fundraiser was held between April 23, 2013-June 7, 2013 and astonishingly collected $484,013 (well above the goal of $65,000!!). Following is an overview of the vision of the team (open source), followed by that there's an interactive video of an interview of the Founder and the Co-Founder of this project, that sheds laboratory details of the project, as described above:
[Image: medium_7MYbDmf0SPq30YMdPlnM]



History of similar attempts:
Making glowing plant is not a new concept. It started in 1980s with the engineering of the world's first glowing plant. It was a tobacco plant with firefly luciferase gene inserted into it. So, when luciferin protein was sprayed onto it, the plant started glowing.
Followed by that, in 1989, Luciferin-Luciferase gene system was sequenced, so now scientists could insert the whole system gene into an organism. Luminous Zebra Fish with such a system became popular in the past. So, was the completely self luminous bacteria engineered by the iGEM team of the University of Cambridge. But, taking it to plants on a self-sustained way, and that too at large scale, was something not thought of in the past!


The Resistance to the Project and The Cause of it:
Though the project has received massive from the public at large, as is evident from the funds raised for the ambitious goal, there are groups (scientific and social), that resist this initiative for some reasons (both scientific and social).

Though on a lighter note, but scientists have put forward the thought that such a GM plant/organism isn't a good tool to light the awareness of the people about the advantages of synthetic biology. Infact, this project would hardly make any good use of synthetic biology for the public at large, a use in treating a disease or food problem, would have served the society better. They regard it as a "publicity garnering'' naive approach to synthetic biology!

Then, there are analysts and scientists working on transgenic organisms who fear a problematic future created by the widespread and open use of such an unusually modified plant. There always exists the uncontrolled flow of genetic information in the wild (especially considering the weed nature of Arabidopsis spp.! And using the plants as streetlamps appear a highly immature idea!

Apart from that, there are plant biologists who doubt the feasibility of the claim of using the glowing plant(s) as streetlamps/sustainable light source, considering the limitations on a plant’s ability to harvest energy from the Sun and convert it back into light. It would be an unusual venting of harvested sunlight back into light energy, which not only seems unfeasible on continuous basis, but also it may pose some abnormalities in normal growth of plant.

The Challenges it Might Face in Execution
There are two key challenges that might face this project:
(i) The first and the foremost is "meeting the expectations of the hype already created". It is very less probable that the plants will sustainably emit light, and that too at levels that might make them useful for night lighting! It needs some hyper expression of the system, which is not possible as per the strategy proposed, at this stage.

(ii) Then there exists the fear of the complete wipe-out of this project by the regulatory affairs, as the team aims at launching it at public scale! And, considering the widespread awareness of this action, those who are against such a move, have already filed complaints against the project's scale.

Conclusion:
The project does seem very novel and very exciting considering the scale targeted. With the huge amounts of funds already raised in a very short period of time, the expectations have been peaking over the results of the same. At the same time, there are speculations over the harmful effects of wide-spread use of such a transgenic plant, which might lead to a turnaround of it's prospects. At current stage, it is progressing at a very fast pace, which does bring that very curious question in mind:

"Will the glowing plants really replace the street lamps in near future??"

All I can say is, "Let's see!"

To know all the updates on the project, visit: http://glowingplant.com
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Drug Used in Diabetes Treatment Could Help in Neurodegenerative Disease Treatment

June 13, 2013, 3:48 pm
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The big group of diseases known as leukodystrophies are described and known as progressive loss of the myelin sheath which is the fatty cover that acts as an insulator around nerve fibres. Damage of the myelin sheath blocks or make unstable the conduction of signals in the affected nerve fibres and leads to many severe locomotor problems.

There is no cure for neurodegenerative disease in presence. Various diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease present huge problem for modern medicine, because drug used in these diseases treatment are not efficient, and they can only be used symptomatic.

Spanish scientists have done some experiments with a drug used to control diabetes type II. They have discovered recently that it can help healing of the mice spinal cords suffering from adrenoleukodystrophy disease, which, untreated, leads surely to a paralysis, a vegetative state and death of an organism. They are sure that their research results may be relevant to other neurodegenerative diseases. This drug is currently being tested in a clinical phase II.

The discovery of this drug is an important step in development of neurodegenerative diseases treatment. Current treatment options are very rare and they are just partially effective in treatment.

ABCD1 protein and peroxisomes


Researcher from the Neurometabolic Diseases Laboratory at IDIBELL, Barcelona, Spain, tried to reveal the role of mitochondria, special cell's organelle. This mitochondria, the power plant of the cell, had unknown role in adrenoleukodystrophy, a neurodegenerative disease provoked by the inactivation of the ABCD1 transporter. This transporter has transport function of fatty acids in peroxisomes. This process inactivation leads to the severe accumulation of fatty acids in human body. Mainly they are accumulated in organs and blood plasma, and these accumulations can cause degeneration of the spinal cord.

Mitochondrial role in adrenoleukodystrophy diseases

ABCD1 protein is a transport protein located in the peroxisomes. These peroxisomes are compartments of the cell that have function to detoxify chemicals and lipids, and because of that mitochondrial role in such a neurodegenerative disease was not obvious at all. But, beside that they didn’t know the role of mitochondria in neurodegenerative disease, researchers knew from latest research that oxidative stress role was involved in mitochondrial presence and influence. In human body, in organs or tissues with increased production of chemically active oxygen-containing molecules, there was obviously significant lack in the effectiveness of the body's antioxidant defenses, mitochondrial presence and involvement was present.

Scientists were also familiar with fact that bioenergetic failure appears to happen before symptoms of disease. Because of that and some more facts, they were determined to investigate the role of the mitochondria in neurodegenerative diseases.

Guidelines for research

Because scientists knew effects of oxidative stress damage and dysfunction of bioenergy are responsible for degeneration of nerve fibres, they began a study on mice. They used study on mouse model of X-linked adrenoleukodystrophy (X-ALD) , the most frequently inherited leukodystrophy. When they found good medium, they began to look at mitochondria for further clues. After that research, they found out that the X- linked adrenoleukodystrophy mice showed a loss of mitochondria at age of 12 months. This discovery wasn’t enough to reveal direct consequence of the disease, but it was enough to reveal that that mitochondrial loss could be a contributing factor. Scientists have discovered that mitochondrial loss could be possibly treated with one of frequently used drugs in diabetes disease. This drug, pioglitazone, has showed good results in mice with adrenoleukodystrophy disease treatment.

Pioglitazone adrenoleukodystrophy disease treatment mechanism

Pioglitazone drug is capable to stop the nerve fibre degeneration. This mechanism is based on prevention of the mitochondrial loss, and inhibiting oxidative stress and metabolic failure in the treated mice. Because of this mechanism locomotor disabilities could be prevented, or when started halted. The scientists are able to prove this through two ways. First way is to prove this through analysis of spinal cords post mortem, and second way is in vivo test. This in vivo test is obtained by putting the mice through a number of physical tests.

X- adrenoleukodystrophy is a pretty rare disease. It has minimum incidence of 1 in 17 000 males. But there are different neurodegenerative disorders caused by degeneration myelin sheath. The most frequent neurodegenerative disease is multiple sclerosis, but there are many other diseases where impaired bioenergetics combined with oxidative stress and axons degeneration are known to be involved. The other neurodegenerative diseases include Parkinson's, Huntington's, and Alzheimer's. Scientists from University of Barcelona will not be surprised if these findings appear to be relevant to these other neurodegenerative diseases as well.

Future expectations of Pioglitazone

According to these promising results, together with other researchers, scientists will shortly be starting a multi- centre phase II clinical trial. In this trial they will follow effects of pioglitazone in adult patients suffering from a late beginning of a variant of adrenoleukodystrophy. They are sure that it will be possible to monitor the biological effects of the drug by tracking the biomarkers of oxidative damage in plasma or blood cells. However, scientists are very happy to have made a huge contribution in finding an effective and, of course, very simple treatment to a very severe neurodegenerative diseases, and they are optimistic in way of new researches.

Conslusion

Neurodegenerative diseases are very severe diseases for human population. Loss of nerve fibres could be prevented or even stopped. This well known drug, pioglitazone, is possibly solution for those who suffer from neurodegenerative diseases. These research results are very good news for both doctors and patients with these neurodegenerative diseases. Even if it is still on clinical phase II trial, it is very certain that it will be a revolutionary discovery as soon as clinical trial ends. We can only expect that it is only the beginning of neurodegenerative diseases researches era.
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Biofilms- Bacteria in a Fortress

June 14, 2013, 12:03 pm
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Many bacterial species that are clinical pathogens or industrial contaminants are capable of forming biofilms. These biofilms provide a safe haven to bacteria, protecting them from the attack of antimicrobials, host defences and other microorganisms hence making it practically impossible to eradicate them with the available control strategies.

Biofilms may form on any surface inert or living. Biofilms on industrial pipelines, such as industrial or potable water system piping or pipelines of the oil and gas industry can lead to corrosion problems causing considerable economic losses. When formed on food contact surfaces and food-processing equipment, biofilms may pose a significant risk to the safety and microbiological quality of food products, resulting in food-borne diseases and food spoilage. Biofilms are a serious health threat when formed on catheters, orthopaedic devices and other clinical surfaces aw well as on living tissues such as teeth, heart valves, middle ear and lungs of cystic fibrosis patients etc.

These biofilms resist removal by physical abrasion and are not susceptible to chemical biocides such as antibiotics and disinfectants. For this reason, study of biofilm structure and the mechanisms by which they resist antimicrobials has become an area of immense importance in order to come up with successful methods of control.

Biofilm formation and Architecture

A biofilm is initiated when a planktonic (i.e. free-moving) bacterial cell reversibly attaches to a surface through van der Waals forces. This cell then irreversibly binds to the surface and begins multiplication forming a microcolony on the surface. Bacterial cells in the microcolony continue to multiply and produce a polymer matrix around the colony; a process which is known as the maturation of the biofilm. This biofilm continues to mature further, often trapping other microorganisms such as other bacteria, algae and protozoa in the sticky matrix during the process. This leads to the formation of a complex microbial community, each of these groups serving a specialized function. The biofilm provides a significant survival advantage to the microorganisms entrapped. A fully mature biofilm is often a mushroom-like or tower-like structure and exhibits maximum resistance. When the biofilm is matured, some of the biofilm cells may detach from the structure and initiate a new biofilm by attaching to a new surface, a stage known as biofilm dispersion.

[Image: lifecycle.png]

See also:
Microbial Biofilms: Sticking together for success

A Protective Fortress

Biofilm bacteria are more resistant to antimicrobials and host defenses than their free-floating colleagues. The structure of the biofilm itself and specific genetic mechanisms of the cells contribute to this recalcitrance. This article summarises some of the main strategies that are important for the antimicrobial resistance (and tolerance) of biofilms.

A Drug-Proof Shield

The extracellular polymer matrix is the first line of defence of the biofilm inhabitants against the antibiotics. This matrix, composed mainly of polysaccharide along with other components such as adhesive proteins and DNA, acts as a physical barrier against the diffusion of antimicrobial compounds. The compounds in the external polymeric matrix either react with these chemical agents or bind to them, thus restricting the penetration of the drug molecules into the interior.

Slow Growth Rates

Biofilm bacteria grow at slower rates than planktonic bacteria due to the limited availability of nutrients. Since the antimicrobials usually target rapidly growing cells, this slower growth rate is a major factor contributing to the increased tolerance to the antibiotics of biofilms.

A Stratified Assembly

Due to the multi-layered structure of the biofilm, there exists a gradient of essential growth factors such as oxygen and nutrients. The gene expression depends on the environmental conditions and this gives rise to phenotypically distinct cells in different growth stages with different metabolic activities. The activity levels are higher at the surface of the biofilm and gradually reduce towards the centre. The cells at the core of the biofilm show very low or no activity. As a result, the susceptibility to the biocides of bacteria within the structure greatly varies, thus making it difficult to eradicate the biofilm by any given antibiotic.

Responding to Stress

Another proposed mechanism of antibiotic resistance is the expression of the stress-response genes by the slow growing cells in the biofilm community. It is suggested that RpoS-mediated stress responses- which induce physiological alterations that protect the cells from various environmental stresses- may also play a role in conferring antibiotic resistance to the biofilm bacteria.

Persisters - The Selfless Warriors

Increased number of persister cells - cells that cease proliferation and growth in the presence of antibiotics- than in a planktonic colony is another hypothesis that explains the elevated resilience of the biofilms.

These persisters, though genetically similar to the other bacteria in the biofilm, are resistant to antibiotics. However, they are distinctly different from the drug resistant mutants. Their recalcitrance is thought to occur due to their induction of dormancy and the over-expression of toxin–antitoxin systems which blocks the important cellular functions targeted by the drugs. These “toxins”, conflicting with their name, act to protect the cell form destruction by biocides. The persisters may resume growth once the antimicrobial is removed from the system.

[Image: nrmicro1557-f4.jpg]

You can learn more about persister cells here: and here

 
In Addition

Along with those mechanisms, general drug resistant strategies such as efflux pumps, mutations in target molecules and quorum-sensing also play a significant role in the persistence of biofilms. For instance, the increased incidence of mutation and horizontal gene transfer in a biofilm community account for the multidrug resistance of biofilm-associated bacteria.

Bringing Down the Fortress

Armed with this knowledge, scientists are trying to come up with new, more effective strategies to eradicate biofilms. Use of anti-biofilm enzymes, quorum-sensing inhibitors and bacteriophages as novel therapeutics to prevent formation of new biofilms and destroy the existing ones is being considered currently.

The following image sums up the above described mechanisms:

[Image: 2005930132829_307.jpg]

Sources:

1.Høiby, N., Bjarnsholt, T., Givskov, M., Molin, S., & Ciofu, O. (2010). Antibiotic resistance of bacterial biofilms. International journal of antimicrobial agents, 35(4), 322-332.

2.Lewis, K. (2001). Riddle of biofilm resistance. Antimicrobial agents and chemotherapy, 45(4), 999-1007.

3.Lewis, K. (2001). Riddle of biofilm resistance. Antimicrobial agents and chemotherapy, 45(4), 999-1007.

4.López, D., Vlamakis, H., & Kolter, R. (2010). Biofilms. Cold Spring Harbor perspectives in biology, 2(7).
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Immunotherapy: A New Hope for Cancer Treatment

June 14, 2013, 11:48 pm
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Cancer, the uncontrolled proliferation of cells of the body, which may or may not invade other tissues/organs, is a long feared disease among the humans. The death of the patient it guarantees in most of the cases, is probably what makes it a fearing disease! Those who are at the initial stages of cancer and have a hope of getting treated, don't have a happy life either! The nature of the rigorous treatment regimes of Chemotherapy (Concentrated chemical mediated treatment) and radiotherapy (Use of high frequency radiations) leaves a patient weak and immune-compromised. Intensive care and pre-cautions need to be taken for the patients undergoing Chemo/Radiotherapy. And, despite all the treatments, it never guarantees that the cancer won't re-appear! Following is a nice animation of basic concept of Cancer:[/align]





The current scenario of the magnum nature of cancer and poor plight of the patients undergoing treatment, asks for a new, gentle, simple but yet effective way(s) of treating this deadly disease. A recent hope that has emerged in this regard is "Immunotherapy". Immunotherapy works on the principle of using human immune system as a tool to tackle cancer. This article focuses on this new dimension of Cancer Treatment called Immunotherrapy which has recently emerged and has rather raised expectations after some successful human trials!

The new branch of Immunotherapy aims at boosting the response of a person's own immune system to fight back the cancerous cells! The boosting is achieved in two ways generally:

a. Monoclonal Antibody Based Immunotherapy
It involves the strategy of administering concentrates of Cancer/Tumor cell specific MAbs. The MAbs then recruit the immune system cells to the site of cancer, thereby triggering the clearance of cancerous cells.

b. Immune-Cell Mediated Immunotherapy
This strategy involves the immune cells like Natural killer Cells (NKCs), Cytotoxic T Lymphocytes(CTLs), Dendritic Cells (DCs), etc., which are activated against the Cancer cells. The activation is brought about by administering of certain cytokines such as Interleukins. Also, in the case of compromised immune system, wherein the activation is not-possible, the immune cells may be isolated, enriched and then transfused into the patient's body (just like administration of concentrated MAbs) to fight the cancerous cells.

There is yet another way, Immunization Against Cancer (or simply Cancer Vaccine) which might enable a person's immune system to recognize the cancer cells and scavenge them off! (But the rates and instances of such successes are very meager).

The above mentioned modes constitute the very basis of the entire scope of Immunotherapy, and following are some of the recent success stories associated with this approach:

Yervoy (Ipilimumab)
Yervoy is probably one of the first Immunotherapic drugs "approved" by FDA! As is clear from it's name, it is a Monoclonal Antibodies based drug, which is used against Melanoma, and has been proved effective even in some cases of Advanced Melanoma. Made by Bristol-Myers Squibb (New York, US), it's remark-ability lies in its ability to recess the Cancer for upto years by just 3-4 months treatment!
It acts by blocking the inhibitory signal that prevents the action of Tumor-killing T Cells on cancer cells. The blockage enables the T-cells to recognize the Cancer cells and clear them off! Yervoy binds on the CTLA-4 receptors on T-cells, which is actually the site for binding of the inhibitory signal. In the presence of Yervoy, the inhibitory signal can no more exert its effect! So, the case of Yervoy is an ideal example of the real world application of Immunotherapy in treating Cancers. (Especially considering the fact that its FDA approved!). Following is a highly informative video on Yervoy (its side effects, treatment profile etc):
[align=center]


Provenge (Sipuleucel-T)
Provenge is the first ever FDA approved Cancer Vaccine against Prostrate Cancer, produced by Dendreon Corporation. Prostatic acid phosphatase (PAP) the antigen present in 95% of prostate cancer cells is incubated into patient's Antigen Presenting Cells (APCs) which are extracted by leukapheresis of patient. Along with PAP, GM-CSF is also incubated into the APCs that helps them to mature. The APCs are re-infused into the patient, generating an immune response against the prostrate cancer cells carrying the PAP antigen. Provenge has shown an extension of life by upto 4 months in the target patients in even final stages of the cancer.

The Cost Factor
Immunotherapic Treatments are highly cost bearing. Yervoy's monthy treatment costs US $45,000! and it's as high as US $95,000 for Provenge! But, the high prices may be attributed to the fact that the use of these drugs is currently limited to a very small market yet. Once the market expands, the prices should shrink.
As per the forecasts of the health care analysts, in 10 years or so, Immunotherapy will be treating 60% of the Cancers with a market cap of over US$35 billion a year!!

The Conjugated Treatments:
Oncologists have started the observation of the efficacy of Immunotherapy Conjugated Chemo/Radiotherapy. Patients show better response to the combined therapy than to Immuno/Chemo/Radiotherapy alone.

Summary:
A lot can be done in the field of Immunotherapy with further research on the signal pathways of cancer cells. Search for more Immunological markers associated with Cancer cells can spur the development of yet more Immunotherapeutic drugs. Immunotherapy can fill the gap left by Chemo/Radiotherapy and in conjugation with them, it possesses the capability to over run the advancement of cancers, especially the early stage detections. Drugs like Yervoy and Provenge have shown promising extensions of life of even terminal stage cancer patients, which greatly highlights the untapped potential of Immunotherapy.

At the same time, the high prices of such treatments remains a big concern and hurdle for the welfare of society at large. Expansion of market might dip the prices a bit, but still the support of government in subsidizing these therapies for average and below average economic classes will be greatly needed in future, otherwise these drugs will remain a savior of the Rich only, while a dream of the poor!
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AstraZeneca Latest Updates And Job Opportunities

June 29, 2013, 7:16 pm
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AstraZeneca, found in 1999, is one of the renowned UK based pharmaceutical company, with Headquarters in London. AstraZeneca is mainly involved in the development of healthcare drugs. It emerged out of the merger of two companies, Astra AB of Sweden and Zeneca Group PLC of the UK. It has marked its strong presence in market by its brilliant work on drugs against cardiovascular, metabolic, respiratory, inflammation, autoimmune, oncology, infection and neuroscience diseases. Having partners all across the world, AstraZeneca has a wide global reach.

Here are some recent updates about the company, along with job vacancies:
  • AstraZeneca Signs Agreement with Karolinska Institutet
AstraZeneca signed an agreement with Karolinska Institutet, an academic institution, for joint research on cardiovascular and metabolic diseases, thus leading to the formation of a new center "Karolinska Institutet/AstraZeneca Integrated Cardio Metabolic Centre”, aiming at the rapid research work. The process for recruitment of the Director of center has been started. About 20-30 scientists from both the institutes will work at the center as full time employees.

For Details Click here

  • AstraZeneca and Roche launch data sharing consortium

This collaboration of data sharing is a new step taken by two companies to accelerate the research leading to rapid discovery of high quality compounds and aiming at better service to patients. Modifications will be keyed out using a technology named Matched Molecular Pair Analysis, MMPA. These modifications can be used by both the companies and can apply them to their compound structures without revealing any classified information about these chemical structures. Other large companies can also join this consortium to ameliorate their resources.

For Details Click Here

  • Collaborative work of Cancer Research Technology, The University of Manchester and AstraZeneca on new cancer drugs
This collaboration of AstraZeneca involves two agreements with The University Of Manchester. According to the first one, AstraZeneca will provide basic compounds for the drug development, which will be carried out by the scientists at the Cancer Research UK Paterson Institute for Cancer Research at the University of Manchester. In the second agreement AstraZeneca has invited the other party to test a potential drug target against AstraZeneca’s compound collection to see if any could potentially work as a new cancer drug.

For Details Click Here

  • Current Job Openings
Following are the vacancies for United Kingdom R&D Centers. Kindly see the list below and apply on the company website.

[Image: jobds.png]

Thanks For reading!

Ruchika
Self Employed
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Pfizer Inc. Latest News & Job Openings

June 30, 2013, 2:48 am
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Headquartered in New York (USA), Pfizer Inc. a global giant in Pharmaceutical industry holds one of the most experienced portfolio (founded in 1849) in therapeutic drugs and services across the world. With an aim to address the diverse healthcare medical needs of the patients around the world, Pfizer has kept expanding it's R&D base and hence the product lines round the clock. From Lipitor, Idamycin, Cardura to Viagra etc almost every product of Pfizer has dominated the market post-launch.

Here is a brief overview of the recent developments at Pfizer Inc, with the information on latest job opportunities in this esteemed pharmaceutical firm.
  • Results of Zoetis Inc. Exchange Offer Declared
Pfizer Inc., the owner of common stocks of Zoetis Inc. had offered a share exchange offer, wherein the Zoetis common stock shares could be exchanged with Pfizer common stock shares. The exchange offer had expired at 00:00 hrs, NY City time, June 21, 2013. And, the results of the exchange offer were declared on Thursday, June 27, 2013. As per the declaration 0.9898 shares of Zoetis common stock were exchanged for every 1 share of Pfizer common stock.

For Details on the declaration Click here
  • TEVA and Sun Pharmaceuticals Settle for $2.15 billion penalty for Infringement of Pfizer's Protonix® Patent
After a long legal battle of nearly 10 years, Pfizer (and Pfizer’s subsidiary Wyeth and Takeda) have successfully obtained the settlement of $2.15 billion from TEVA Pharmaceuticals and Sun Pharmaceutical Industries, Limited for the infringement of the patent for their blockbuster medicine Protonix®, by launching the generics before the expiry of the patent in January 2011. As a part of the settlement, Teva will pay $1.6 billion and Sun will pay $550 million to Pfizer and Takeda.

For Details on the story, Click here
  • FDA Accepts Pfizer's Application for Reviewing and Expanding the XELJANZ® Labeling
Pfizer announced on June 21, 2013 that FDA has accepted to review it's application for expanding the labeling of XELJANZ® (tofacitinib citrate), used for severely active Rheumatoid Arthritis to include it's efficacy in inhibition of Progression of Structural Damage too. XELJANZ is the first FDA approved medicine in the class of Janus kinase (JAK) inhibitors, and is effective in treating the patients unresponsive or intolerant to Methotrexate (MTX).

For Details, Click here

Following are the recent job openings at Pfizer in United States:

Note down the JOB ID and Apply here

A. Quality Assurance:
[Image: pfizer_quality.png]

B. Research & Development
[Image: rnd_pfizer.png]

Keep an eye on this thread for further updates.


Thanks for Reading!
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