Scientists demonstrate that an i-motif and a partially folded structure coexist in the C-rich human ILPR oligonucleotides

Soma N Dhakal in JACS

Scientists from Kent State University have demonstrated that an i-motif and a partially folded structure coexisted in the C-rich human ILPR oligonucleotides using laser tweezers. 

This discovery has recently been published as an article titled ‘Coexistence of an ILPR I-Motif and a Partially Folded Structure with Comparable Mechanical Stability Revealed at the Single-Molecule Level" in JACS.’ Here, ILPR stands for Insulin Linked Polymorphic Region which is human insulin gene. The ILPR region is known to regulate the production of insulin, a hormone which is responsible for the metabolism of glucose. When the control of insulin level fails it causes diabetes. Any stable DNA secondary structure formed in ILPR region may affect the transcription regulation of insulin gene causing insulin related health problems. This clarifies the importance of understanding the stability of DNA secondary structure. According to the main author of the article, Soma N Dhakal, a PhD student at Kent State University chemistry department, they have pioneered the mechanical stability of the tetraplex DNA secondary structure called i-motif formed by the cytosine-rich DNA sequence from the human ILPR.

The mechanical stability of i-motif was investigated in single molecule level which was supported by other bulk methods such as CD, UV and footprinting. In case of single-molecule study the DNA molecule containing the region of interest (one of the most prevalent variant of human ILPR sequence) was tethered between two surface-functionalized polystyrene beads (~ 2 um in diameters) which are trapped in two laser focuses. One of the laser focuses was stationary and another was moved apart to create tension in the molecule. This allowed to unfold the i-motif formed in the region of interest. The unfolding force and contour length change were recorded for individual molecule. 

Although the single molecular methods like laser tweezers take a while for data collection, it is very impressive in terms of studying individual molecules which is not possible in any bulk techniques like Circular Dichroism (CD), NMR, electrophoresis etc. This is one of the biggest advantages of single molecular methods.

The formation of an i-motif is decreased with increasing pH, while that of partially folded structure is pH independent. Both the i-motif and the partially folded structure have unfolding forces higher than the stall forces of RNA polymerases, suggesting either of the structure can stop transcription from a mechanical perspective alone. Authors have claimed that this is the first time that single molecular investigation on i-motif structures has been done. 

Send Your CV for Nepal Government's "National Science Mapping" Program

Ministry of Science and Technology (Government of Nepal) is collecting information about Nepali researchers (M. Sc. and above in pure science and Bachelor's degree and above in technical fields). For details visit http://planeta-observatory.gov.np/science.mapping.php?. 

They already have data of hundreds of Nepali Researchers and a 'profile' is being prepared. The info is going to be edited soon and will publish the profile.

National Science Mapping program has requested you to send your info.


Deadline: June 2010.

You can send your CURRICULUM VITAE as early as possible to plasmanepal@hotmail.com or to planetarium@most.gov.np

Also, you can submit online form at: http://planeta-observatory.gov.np/form.submit.php?

or you can download PDF version of the form, fill it and send. PDF version can be downloaded here.

Soma Dhakal receives "University Fellowship Award" at Kent State University

Soma N Dhakal, PhD student at the department of chemistry of Kent State University received University Fellowship Award recently for his outstanding performance in graduate research.

University Fellowship award is one of the prestigious awards that is awarded to PhD student by the Graduate School. Scientific publication is one of the main criteria to be qualified for this award. However, other factors like academic standing and leadership are also taken care for most of the fellowship awards. Soma was initially nominated by the Department of Chemistry and finally approved by Graduate School on the basis of the recommendations from graduate coordinator and his advisor. He will be financially supported by the Graduate School for the academic year 2010-2011. 

He has authored and co-authored 3 peer reviewed research journal articles.

NepaChem would like to congratulate Soma jee, best wishes for your future success.

Why did the chicken cross the road? Science Jokes

Scientists have different answers for the same question.

Archimedes
A1 : To actualize its potential.
A2 : She was buoyant and excited at the thought of new adventures.
A3 : Eureka!

Robert Boyle : She had been under too much pressure at home.

Marie Curie : She was radiating with enthusiasm as she crossed the road.

Albert Einstein : Whether the chicken crossed the road or the road moved beneath the chicken depends upon your point of view. The chicken did not cross the road - it transcended it.


Galileo : To get a better look at the stars.

Newton
1) Chickens at rest tend to stay at rest. Chickens in motion tend to cross the road.
2) It was pushed on the road.
3) It was pushed on the road by another chicken, which went away from the road.
4) It was attracted to a chicken on the other side of the road.

Ohm : There was more resistance on this side of the road.

Wolfgang Pauli : There already was a chicken on this side of the road.

 More here

Humboldt Research Fellowship for Postdoctoral Researchers

Submit an application if you are a researcher from abroad with above average qualifications, at the beginning of your academic career and only completed your doctorate in the last four years. A Humboldt Research Fellowship for postdoctoral researchers allows you to carry out a long-term research project (6-24 months) you have selected yourself in cooperation with an academic host you have selected yourself at a research institution in Germany.

Scientists and scholars of all nationalities and disciplines may apply to the Alexander von Humboldt Foundation directly at any time. The Humboldt Foundation grants approximately 600 Humboldt Research Fellowships for postdoctoral researchers and experienced researchers annually. Short-term study visits, participation in congresses and training courses cannot be financed.

Requirements:

1. Doctorate or comparable academic degree (Ph.D., C.Sc. or equivalent), completed less than four years prior to the date of application. Candidates who have nearly completed their doctoral degrees are eligible to apply provided that they submit the manuscript of their dissertation or publications containing the results of their dissertation.
2. Academic publications reviewed according to international standards and printed in journals and/or by publishing houses.
3. Confirmation that research facilities are available and a detailed expert's report by an academic host at a research institution in Germany. Details of the research project and the proposed timetable must be discussed with the prospective host prior to application.
4. Expert references from the doctoral supervisor and other academics qualified to comment on the applicant's eligibility, preferably including reviewers not working at the applicant's own institute.
5. Language skills: scholars in the humanities or social sciences and physicians must have a good knowledge of German if it is necessary to carry out the project successfully; otherwise a good knowledge of English; scientists and engineers must have a good knowledge of German or English.
6. The applicant may not have spent an extended period in Germany prior to application. Applications to continue a research stay already underway can only be considered in exceptional cases. If in doubt, candidates who have been in Germany for more than six months at the time of application should consult the FAQs and check with the Humboldt Foundation (info@avh.de) whether formal requirements have been met before submitting an application.
7. The Humboldt Foundation assumes that candidates will abide by the Rules of Good Scientific Practice and the ethical rules of the 7th EU Framework Programme during the application and sponsorship periods.

More info: http://www.humboldt-foundation.de/web/humboldt-fellowship-postdoc.html

Chemistry of the World Football Cup Trophy

 

FIFA world cup is going to start soon in South Africa. Each and every teams target is to get the trophy. In this post I will write something about the chemistry of the trophy. Chemically this trophy is quite interesting.

The present day trophy was commissioned in 1974 by FIFA. The trophy stands 36.5 cm tall and is made of 5 kg gold. This means that it is hollow inside. Otherwise it would weigh ~ 70-80 kg, considering high density of gold. The gold used in the trophy is not pure gold. Gold is an unusual metal. Pure gold is very soft. If the trophy was made by pure gold, then when the winner holds it would bend. Thats why they used 18 carat (75%) gold. Other metals are mixed with gold to make it stronger.

This trophy is interesting for second point. There are two stripes of green at the base. These are made from a mineral called malachite, which is a copper compound (basic copper carbonate-Cu2CO3(OH)2.)

Whoever wins the trophy, good luck to every team. Enjoy world cup games. Don't forget to watch video above.