Tuesday, December 7, 2010
Monday, December 6, 2010
প্রথম আলো - সবচেয়ে ছোট হোটেলে মধুচন্দ্রিমা
প্রথম আলো - সবচেয়ে ছোট হোটেলে মধুচন্দ্রিমা
এটি ২৮২ বছরের পুরোনো একটি হোটেল। নবদম্পতিদের মধুচন্দ্রিমার জন্য সম্প্রতি একটি প্যাকেজ ঘোষণা করেছে হোটেল কর্তৃপক্ষ। এই হোটেলের বিশেষত্ব হচ্ছে, এটি এত ছোট যে, সেখানে একসঙ্গে দুজনের বেশি থাকা যায় না। বিশ্বের সবচেয়ে ‘ছোট’ বলে খ্যাত এই হোটেলে এক রাত কাটাতে খরচ হবে মাত্র ২৪০ ইউরো।
হোটেলটির নাম এহয়জেল (বিয়ের ঘর)। জার্মানির বেভারিয়ান শহরে এটি অবস্থিত। ১৭২৮ সালে নির্মিত এ হোটেলটি মাত্র আড়াই মিটার চওড়া। বেভারিয়ানের তখনকার স্থানীয় শাসক ঘোষণা দিয়েছিলেন সম্পত্তি (ঘরবাড়ি) ছাড়া কোনো দম্পতি বিয়ে করতে পারবে না। এরপর দরিদ্র দম্পতিদের সুবিধার জন্য এ হোটেলটি নির্মাণ করা হয়। এটি এতই ছোট যে, মাত্র এক দম্পতির জায়গা হবে এতে।
হোটেলের মালিকেরা দাবি করেছেন, এটিই বিশ্বের সবচেয়ে ছোট হোটেল। তাঁরা বলেন, হোটেলটি খুবই সাদামাটাভাবে তৈরি করা হয়েছিল। তখনকার রীতি অনুযায়ী নবদম্পতিরা এটি স্বল্প সময়ের জন্য কিনে নিতেন। সেখানে কিছুদিন কাটানোর পর এটি আবার আরেক নবদম্পতির কাছে বিক্রি করে দেওয়া হতো।
দীর্ঘদিন বন্ধ থাকার পর সম্প্রতি হোটেলটি ফের চালু করা হয়েছে। যুগের দাবি মেনে এটি আধুনিকও করা হয়েছে। ওপরে বাড়িয়ে সাততলা করা হয়েছে। পাঁচ তারকা হোটেলের সব সুযোগ-সুবিধা নিশ্চিত করা হয়েছে এতে। ফায়ারপ্লেস ও বিলাসবহুল স্নানাগারও রয়েছে সেখানে।
সম্প্রতি বারবারা ও হাইঞ্জ ভিলহেম নামের সত্তরোর্ধ্ব এক দম্পতি এই হোটেলে রাত কাটিয়েছেন। এই দম্পতি বলেন, ‘পৃথিবীর অনেক হোটেলে আমরা থেকেছি। সেসব হোটেলে আমাদের পাশাপাশি আরও অনেক অতিথি ছিলেন। কিন্তু এই হোটেলে আমরাই কেবল অতিথি।’
হোটেলটির আধুনিক সাজসজ্জার নকশা করেছেন মারিয়ান্না লস। তিনি বলেন, ‘হোটেলটিকে নতুন রূপে সাজানোর ক্ষেত্রে অনেক বাধা পেরোতে হয়েছে। নবদম্পতিদের মধুচন্দ্রিমার ক্ষেত্রে হোটেলে কিছুটা ছাড় দেওয়া হয়েছে।
এটি ২৮২ বছরের পুরোনো একটি হোটেল। নবদম্পতিদের মধুচন্দ্রিমার জন্য সম্প্রতি একটি প্যাকেজ ঘোষণা করেছে হোটেল কর্তৃপক্ষ। এই হোটেলের বিশেষত্ব হচ্ছে, এটি এত ছোট যে, সেখানে একসঙ্গে দুজনের বেশি থাকা যায় না। বিশ্বের সবচেয়ে ‘ছোট’ বলে খ্যাত এই হোটেলে এক রাত কাটাতে খরচ হবে মাত্র ২৪০ ইউরো।
হোটেলটির নাম এহয়জেল (বিয়ের ঘর)। জার্মানির বেভারিয়ান শহরে এটি অবস্থিত। ১৭২৮ সালে নির্মিত এ হোটেলটি মাত্র আড়াই মিটার চওড়া। বেভারিয়ানের তখনকার স্থানীয় শাসক ঘোষণা দিয়েছিলেন সম্পত্তি (ঘরবাড়ি) ছাড়া কোনো দম্পতি বিয়ে করতে পারবে না। এরপর দরিদ্র দম্পতিদের সুবিধার জন্য এ হোটেলটি নির্মাণ করা হয়। এটি এতই ছোট যে, মাত্র এক দম্পতির জায়গা হবে এতে।
হোটেলের মালিকেরা দাবি করেছেন, এটিই বিশ্বের সবচেয়ে ছোট হোটেল। তাঁরা বলেন, হোটেলটি খুবই সাদামাটাভাবে তৈরি করা হয়েছিল। তখনকার রীতি অনুযায়ী নবদম্পতিরা এটি স্বল্প সময়ের জন্য কিনে নিতেন। সেখানে কিছুদিন কাটানোর পর এটি আবার আরেক নবদম্পতির কাছে বিক্রি করে দেওয়া হতো।
দীর্ঘদিন বন্ধ থাকার পর সম্প্রতি হোটেলটি ফের চালু করা হয়েছে। যুগের দাবি মেনে এটি আধুনিকও করা হয়েছে। ওপরে বাড়িয়ে সাততলা করা হয়েছে। পাঁচ তারকা হোটেলের সব সুযোগ-সুবিধা নিশ্চিত করা হয়েছে এতে। ফায়ারপ্লেস ও বিলাসবহুল স্নানাগারও রয়েছে সেখানে।
সম্প্রতি বারবারা ও হাইঞ্জ ভিলহেম নামের সত্তরোর্ধ্ব এক দম্পতি এই হোটেলে রাত কাটিয়েছেন। এই দম্পতি বলেন, ‘পৃথিবীর অনেক হোটেলে আমরা থেকেছি। সেসব হোটেলে আমাদের পাশাপাশি আরও অনেক অতিথি ছিলেন। কিন্তু এই হোটেলে আমরাই কেবল অতিথি।’
হোটেলটির আধুনিক সাজসজ্জার নকশা করেছেন মারিয়ান্না লস। তিনি বলেন, ‘হোটেলটিকে নতুন রূপে সাজানোর ক্ষেত্রে অনেক বাধা পেরোতে হয়েছে। নবদম্পতিদের মধুচন্দ্রিমার ক্ষেত্রে হোটেলে কিছুটা ছাড় দেওয়া হয়েছে।
Friday, December 3, 2010
Top Ten Discoveries of 2010: Nat Geo News's Most Popular
Top Ten Discoveries of 2010: Nat Geo News's Most Popular
A team of evangelical Christian explorers claimed they'd found the remains of Noah's ark beneath snow and volcanic debris on Turkey's Mount Ararat (pictured) in April.
But some archaeologists and historians took the latest claim that Noah's ark had been found about as seriously as they had past ones—not very.
Nat Geo
Thursday, December 2, 2010
Wednesday, December 1, 2010
Monday, November 29, 2010
How to Shine in a Small Biotech Company
So you finally got your PhD (or your masters or batchelor’s) and you are making the big switch to a small biotech company.
You will probably have been hired for the specific skill set that you have built during your training, but now you have to learn to apply those skills to solve real world, commercially-driven scientific problems. The future of your new employer, and your job, will depend on it.
Working in a small biotech company is completely different from academia. There is much less of a support structure around you so have to learn to support yourself and others. You need to tap into the experience and knowledge of those around you, contribute to the knowledgebase and take responsibility for your own development.
A small biotech company needs to be a team much more than an academic group does. They need to pull together to reach their goals. And you need to be an integral player.
More than that, to make sure that you and your career prospects shine, you should set out to be the star player. Here are some tips that I think will help you to do this:
1. Keep the company’s goals in mind
The first thing you should strive to understand is the company’s commercial goals and how your work fits into them. Understanding this will help to keep you motivated, but it will also help you to stay focused in your research. Your company wants results that will build a path towards the profits it needs to make it a success. It does not care about the “interesting” detours and neither should you, but to stay on the path you need to know the intended destination.
2. Don’t assume others know what approach is best
In the first biotech company I worked for, I came straight out of my PhD and landed in an excellent group of people who were all trying to solve the same problem. Within two weeks, I had actually pinpointed a crucial flaw in their approach, but I assumed that I was wrong. 6 months later I started talking about what I thought the problem was and stimulated a discussion that ended up with a radically new, and entirely successful approach. Obviously I should have started talking much earlier as it would have saved a lot of time, money and heartache.
My mistake was that I deferred far to easily to those around me, assuming that they knew much more and had it covered. Thinking like this is not good in any organisation, but is especially damaging in a small biotech company because the team tends to be a lot more threadbare.
It could be that the people who are more experienced than you are having to wear a number of different hats so are more likely to miss small details, or it could be – as it was in the case I just described – that the problem fell between the cracks of the different disciplines being applied to the problem.
Whatever the case, in a small biotech company, perhaps more than in any other early career scientist position, your opinion matters and it is your job to voice it.
3. Go cross-disciplinary
Many biotech companies are trying to solve problems that are interdisciplinary, which means that the solution lies in the no-man’s-land between the disciplines, as was the case in (2) above. It is very difficult for employers to find people who are cross-disciplinary so to prosper in a company like this, you should learn about the other disciplines involved in the project and help to plug the gaps. You can do this by reading or just actively learning from your colleagues.
It takes a lot of effort to do this, but it is worth it because it is in that no-man’s-land that you can help establish yourself as an expert in the problems that the company are trying to solve and become a vital member of the team.
4. Teach others what you know
As well as trying to plug the inter-disciplinary gaps in your own knowledge. It pays to freely share your own knowledge with your colleagues. Think of it as Karma. You help them, they help you and you all benefit, as does the company.
5. Write SOPs
The ultimate way to share your knowledge is through writing standard operating procedures (SOPs) on the procedures you perform. SOPs are vital for ensuring that things are done uniformly across the company, but they are often overlooked because everyone, especially the management, are too busy to think about them.
If you are new to the company, a great thing to do it to start to establish an SOP-culture. It is easy to set up a word template for writing up SOPs, set aside a folder to keep them in, and an Excel file to list them. There are more advanced ways to do it of course, but even this is infinitely better than having no SOPs. Talk about it with your manager and your colleagues to get their buy-in first of course.
6. Ask questions – promote discussion
In any lab meeting or discussion you should aim to actively contribute. Its easy to sit back and listen, but that’s not your job. You should be trying to contribute new ideas or increase the understanding of yourself or others on the subject being discussed.
If you are nervous about this, one great way to get started is to challenge yourself to ask at least one question at each meeting. It does not matter what you ask – just ask something, and you’ll soon get into the habit.
7. Push new technologies and ideas
In a hard-pushed company and without a large community of scientists around it is easy to become isolated from new technologies and ideas. Strive to keep abreast of the new technolgies in your field and if you find something you think is useful, research it carefully to ensure you know what you are talking about and then put it forcefully to the group. Whether or not your idea is taken up you will be doing them a service.
8. Improve your existing skills
I have talked so far about branching out into new areas of knowledge to help become an integral part of your group. But it is also very important to polish your core skills as highly as possible. Whether you were brought in to group because of your specific abilities, or you were given a specific role to learn, your company depends on you to be an expert. You might even be the only one that they have.
9. Keep meticulous records, and make them as accessible as possible
During your PhD your lab book was your own, and if you didn’t keep it well it was only you who suffered. But in your close-knit biotech research team, anyone could need to access your results. And more to the point, your results are the property of the company you work for.
Make a point of keeping your records very accurate and easy to navigate and you will not only be doing a great job, you will also gain a reputation for being accurate and reliable. A simple lab notebook admin system might help.
10. Dress for the part when needed
Whenever you receive visitors, go out to a collaborator or attend a conference you are representing your company so jeans and t-shirt might not be the order of the day. You need to dress for the part, which – shock horror – might involve wearing a suit, or even shining your shoes! Check with your boss what the dress code should be for events like this, and stick to it.
11. Don’t let your science get sloppy
Often your work will not be published when you work in biotech, but it will remain part of the internal knowledge of the company. But just because your work is not peer-reviewed does not mean you can afford to let your science get sloppy. In fact in many ways it is more important than ever to be stringent with your work because the tools you make or the conclusions you draw will become part of the framework upon which your colleagues build.
n=1 is not good enough and neither are plasmids checked only with a quick digest. You have to be meticulous and you should be vocal in ensuring that others in the group are doing so too.
12. Don’t talk about your “results” until they are in the bag
I think I have finally got expression from that plasmid. Oh wait, no, it was just a squashed fly on the gel.
I was very guilty of this when I worked in the lab. I got so excited about possible results that I would blab about them before I had confirmed them. This is not a good strategy because if you do it often enough it will damage your reputation. Keep things under your hat until you are certain about them.
13. Never, ever make your boss look bad
This is true in any job. And the title says it all.
14. Learn to resolve conflict
In any small team, conflicts will arise. Try to work on being the kind of person who snuffs out conflicts at source, rather than the sort who lets things rumble on and on for months or even years. The reduced stress alone will probably add years to your life!
15. Be cheerful
Life can be tough in a small biotech company. There are a lot of pressures, especially when the science isn’t going well. Strive to be cheerful and inspire those around you to do the same. Cheerfulness, even in adversity, is a great attribute to have as a team member, but also marks you out as a great leader for the future.
Those are my tips for prospering in a small biotech company. Do you agree with them, or do you have some of your own? Let us know in the comments.
Nick; BitesizeBio
You will probably have been hired for the specific skill set that you have built during your training, but now you have to learn to apply those skills to solve real world, commercially-driven scientific problems. The future of your new employer, and your job, will depend on it.
Working in a small biotech company is completely different from academia. There is much less of a support structure around you so have to learn to support yourself and others. You need to tap into the experience and knowledge of those around you, contribute to the knowledgebase and take responsibility for your own development.
A small biotech company needs to be a team much more than an academic group does. They need to pull together to reach their goals. And you need to be an integral player.
More than that, to make sure that you and your career prospects shine, you should set out to be the star player. Here are some tips that I think will help you to do this:
1. Keep the company’s goals in mind
The first thing you should strive to understand is the company’s commercial goals and how your work fits into them. Understanding this will help to keep you motivated, but it will also help you to stay focused in your research. Your company wants results that will build a path towards the profits it needs to make it a success. It does not care about the “interesting” detours and neither should you, but to stay on the path you need to know the intended destination.
2. Don’t assume others know what approach is best
In the first biotech company I worked for, I came straight out of my PhD and landed in an excellent group of people who were all trying to solve the same problem. Within two weeks, I had actually pinpointed a crucial flaw in their approach, but I assumed that I was wrong. 6 months later I started talking about what I thought the problem was and stimulated a discussion that ended up with a radically new, and entirely successful approach. Obviously I should have started talking much earlier as it would have saved a lot of time, money and heartache.
My mistake was that I deferred far to easily to those around me, assuming that they knew much more and had it covered. Thinking like this is not good in any organisation, but is especially damaging in a small biotech company because the team tends to be a lot more threadbare.
It could be that the people who are more experienced than you are having to wear a number of different hats so are more likely to miss small details, or it could be – as it was in the case I just described – that the problem fell between the cracks of the different disciplines being applied to the problem.
Whatever the case, in a small biotech company, perhaps more than in any other early career scientist position, your opinion matters and it is your job to voice it.
3. Go cross-disciplinary
Many biotech companies are trying to solve problems that are interdisciplinary, which means that the solution lies in the no-man’s-land between the disciplines, as was the case in (2) above. It is very difficult for employers to find people who are cross-disciplinary so to prosper in a company like this, you should learn about the other disciplines involved in the project and help to plug the gaps. You can do this by reading or just actively learning from your colleagues.
It takes a lot of effort to do this, but it is worth it because it is in that no-man’s-land that you can help establish yourself as an expert in the problems that the company are trying to solve and become a vital member of the team.
4. Teach others what you know
As well as trying to plug the inter-disciplinary gaps in your own knowledge. It pays to freely share your own knowledge with your colleagues. Think of it as Karma. You help them, they help you and you all benefit, as does the company.
5. Write SOPs
The ultimate way to share your knowledge is through writing standard operating procedures (SOPs) on the procedures you perform. SOPs are vital for ensuring that things are done uniformly across the company, but they are often overlooked because everyone, especially the management, are too busy to think about them.
If you are new to the company, a great thing to do it to start to establish an SOP-culture. It is easy to set up a word template for writing up SOPs, set aside a folder to keep them in, and an Excel file to list them. There are more advanced ways to do it of course, but even this is infinitely better than having no SOPs. Talk about it with your manager and your colleagues to get their buy-in first of course.
6. Ask questions – promote discussion
In any lab meeting or discussion you should aim to actively contribute. Its easy to sit back and listen, but that’s not your job. You should be trying to contribute new ideas or increase the understanding of yourself or others on the subject being discussed.
If you are nervous about this, one great way to get started is to challenge yourself to ask at least one question at each meeting. It does not matter what you ask – just ask something, and you’ll soon get into the habit.
7. Push new technologies and ideas
In a hard-pushed company and without a large community of scientists around it is easy to become isolated from new technologies and ideas. Strive to keep abreast of the new technolgies in your field and if you find something you think is useful, research it carefully to ensure you know what you are talking about and then put it forcefully to the group. Whether or not your idea is taken up you will be doing them a service.
8. Improve your existing skills
I have talked so far about branching out into new areas of knowledge to help become an integral part of your group. But it is also very important to polish your core skills as highly as possible. Whether you were brought in to group because of your specific abilities, or you were given a specific role to learn, your company depends on you to be an expert. You might even be the only one that they have.
9. Keep meticulous records, and make them as accessible as possible
During your PhD your lab book was your own, and if you didn’t keep it well it was only you who suffered. But in your close-knit biotech research team, anyone could need to access your results. And more to the point, your results are the property of the company you work for.
Make a point of keeping your records very accurate and easy to navigate and you will not only be doing a great job, you will also gain a reputation for being accurate and reliable. A simple lab notebook admin system might help.
10. Dress for the part when needed
Whenever you receive visitors, go out to a collaborator or attend a conference you are representing your company so jeans and t-shirt might not be the order of the day. You need to dress for the part, which – shock horror – might involve wearing a suit, or even shining your shoes! Check with your boss what the dress code should be for events like this, and stick to it.
11. Don’t let your science get sloppy
Often your work will not be published when you work in biotech, but it will remain part of the internal knowledge of the company. But just because your work is not peer-reviewed does not mean you can afford to let your science get sloppy. In fact in many ways it is more important than ever to be stringent with your work because the tools you make or the conclusions you draw will become part of the framework upon which your colleagues build.
n=1 is not good enough and neither are plasmids checked only with a quick digest. You have to be meticulous and you should be vocal in ensuring that others in the group are doing so too.
12. Don’t talk about your “results” until they are in the bag
I think I have finally got expression from that plasmid. Oh wait, no, it was just a squashed fly on the gel.
I was very guilty of this when I worked in the lab. I got so excited about possible results that I would blab about them before I had confirmed them. This is not a good strategy because if you do it often enough it will damage your reputation. Keep things under your hat until you are certain about them.
13. Never, ever make your boss look bad
This is true in any job. And the title says it all.
14. Learn to resolve conflict
In any small team, conflicts will arise. Try to work on being the kind of person who snuffs out conflicts at source, rather than the sort who lets things rumble on and on for months or even years. The reduced stress alone will probably add years to your life!
15. Be cheerful
Life can be tough in a small biotech company. There are a lot of pressures, especially when the science isn’t going well. Strive to be cheerful and inspire those around you to do the same. Cheerfulness, even in adversity, is a great attribute to have as a team member, but also marks you out as a great leader for the future.
Those are my tips for prospering in a small biotech company. Do you agree with them, or do you have some of your own? Let us know in the comments.
Nick; BitesizeBio
Sunday, November 28, 2010
Wednesday, November 17, 2010
Tuesday, November 16, 2010
Thursday, October 28, 2010
5 Ways to Use Coffee to Power Up Your Research, Career and Lab Group
Coffee is great stuff. It’s tasty (well I like it) and it can keep you going through long days and nights in the lab. But this article is not about using the chemical effects of coffee to your advantage. It’s about ways in which you can use the habitual and social side of a nice cup of coffee, or whatever your favorite beverage is, to your advantage in the lab.
Here are 5 ways in which you can use coffee to…
1. Insert thinking time into your day
Taking time out to let your thoughts drift each day will make you happier, more productive and more likely to solve the complex scientific problems you are tackling every day.
But getting into the habit of taking time out can be difficult. Most of us hare into work, get started straight away and don’t really stop for breath until it’s time to go home. But luckily, one of the many ways to start a new, good habit is to tack it onto an old one.
So if you have the habit of gulping down a morning and and afternoon coffee while you work, make it a rule that you convert that habit to stopping work, sitting down in a quiet place and relaxing while you have your coffee, allowing your brain some time to wander.
2. Get into the habit of reading more
Reading every day is an essential part of the job, but, again, it’s not always easy to fit it in to your busy day. Instead of converting your coffee break to a brain-wandering session, you could make switching the kettle (or coffee machine) on a trigger for your daily reading session.
3. Let off steam (or just make friends)
Like many people who frequent Bitesize Bio, my PhD was tough. And I needed to vent — mostly about my supervisor — a lot. A special mention in my thesis acknowledgements went to the “Morning Coffee Support Group”, without whom I may never have made it (ok, I’m exaggerating a bit). The morning coffee support group was a group of PhD students from around our building who met most mornings for a coffee and a chat and a communal moan about our lots. The key to meeting regularly was that we all had coffee habits to support. Whether your need is to make friends, vent or just have a nice chat, why not start your own morning coffee group?
4. Build cohesion in your group
Coffee is a remarkably effective tool for building cohesion in your lab group. Setting up a tradition that each group member takes turns to make coffee for the whole group when it’s lab meeting time will give each person the chance to be nice to the whole group. Lovely — but also important for bonding. And if you’re a group leader, buying coffee for the whole lab now and then is a relatively inexpensive way to show your appreciation of your group.
5. Build your network
One of the secrets of networking at a conference to find the people you want to network with, break the ice with a little conversation then cement the relationship by arranging to meet later for a more in-depth chat. And what’s the best, least-threatening way to arrange to chat later? You’ve guessed it — invite your potential network member to meet later for coffee. Actually, here in Scotland a beer would probably work better, but I did say you could substitute in your own favorite beverage.
Of course, many of these ideas are mutually exclusive (either that or you are going to be drinking A LOT of coffee!) but I hope they’ve given you some food (or drink) for thought.
How has coffee helped you in your career?
From: Nick, Bitesizebio
Here are 5 ways in which you can use coffee to…
1. Insert thinking time into your day
Taking time out to let your thoughts drift each day will make you happier, more productive and more likely to solve the complex scientific problems you are tackling every day.
But getting into the habit of taking time out can be difficult. Most of us hare into work, get started straight away and don’t really stop for breath until it’s time to go home. But luckily, one of the many ways to start a new, good habit is to tack it onto an old one.
So if you have the habit of gulping down a morning and and afternoon coffee while you work, make it a rule that you convert that habit to stopping work, sitting down in a quiet place and relaxing while you have your coffee, allowing your brain some time to wander.
2. Get into the habit of reading more
Reading every day is an essential part of the job, but, again, it’s not always easy to fit it in to your busy day. Instead of converting your coffee break to a brain-wandering session, you could make switching the kettle (or coffee machine) on a trigger for your daily reading session.
3. Let off steam (or just make friends)
Like many people who frequent Bitesize Bio, my PhD was tough. And I needed to vent — mostly about my supervisor — a lot. A special mention in my thesis acknowledgements went to the “Morning Coffee Support Group”, without whom I may never have made it (ok, I’m exaggerating a bit). The morning coffee support group was a group of PhD students from around our building who met most mornings for a coffee and a chat and a communal moan about our lots. The key to meeting regularly was that we all had coffee habits to support. Whether your need is to make friends, vent or just have a nice chat, why not start your own morning coffee group?
4. Build cohesion in your group
Coffee is a remarkably effective tool for building cohesion in your lab group. Setting up a tradition that each group member takes turns to make coffee for the whole group when it’s lab meeting time will give each person the chance to be nice to the whole group. Lovely — but also important for bonding. And if you’re a group leader, buying coffee for the whole lab now and then is a relatively inexpensive way to show your appreciation of your group.
5. Build your network
One of the secrets of networking at a conference to find the people you want to network with, break the ice with a little conversation then cement the relationship by arranging to meet later for a more in-depth chat. And what’s the best, least-threatening way to arrange to chat later? You’ve guessed it — invite your potential network member to meet later for coffee. Actually, here in Scotland a beer would probably work better, but I did say you could substitute in your own favorite beverage.
Of course, many of these ideas are mutually exclusive (either that or you are going to be drinking A LOT of coffee!) but I hope they’ve given you some food (or drink) for thought.
How has coffee helped you in your career?
From: Nick, Bitesizebio
Sunday, October 24, 2010
Thursday, October 14, 2010
Wednesday, October 6, 2010
Khan Academy
Khan Academy
It is the online tutorial library that won google prize. Favorite online teacher of bill gates for his children :)
Congratulation Salman Khan.
It is the online tutorial library that won google prize. Favorite online teacher of bill gates for his children :)
Congratulation Salman Khan.
Tuesday, October 5, 2010
Saturday, October 2, 2010
Tuesday, September 14, 2010
Bumper production of flood-tolerant paddies likely this year in Bangladesh
The news is also featured in IRRI bulletin.
The news is also featured in IRRI bulletin.
Friday, September 10, 2010
Friday, September 3, 2010
Monday, August 23, 2010
Monday, August 16, 2010
Photo of the Day: Best Pictures of May 2010, Gallery - National Geographic
check this amazing picture... very simple trick... but one shot like this is a dream for anyone .........
Photo of the Day: Best Pictures of May 2010, Gallery - National Geographic
Photo of the Day: Best Pictures of May 2010, Gallery - National Geographic
Sunday, August 8, 2010
Tuesday, August 3, 2010
Wednesday, July 28, 2010
Pimp your Microcentrifuge
Microcentrifuges are pretty much the epitome of efficiency, but I have a couple of suggestions that may make using this instrument even easier.
Divide by Three
Not only is the number of tubes a microcentrifuge can hold divisible by two, but almost always by three as well. How does this help you? If you have an odd number of tubes, you can now spin them without a balance tube. Here is the rotor from my microcentrifuge:
I have taken a red marker and colored the white numbers that divide the rotor into thirds, allowing me to quickly place three tubes into the microcentrifuge while maintaining balance in the rotor. On other microcentrifuges that did not have a paired position indicator (a white line on this rotor), I have used a different color marker to divide the rotor in half. Now what if you have five tubes?
The orange tubes balance each other, and the green tubes balance themselves. Of course you don’t need to break out the markers to do this, but premarking the rotor helps avoid mistakes when you are working quickly.
Nested Tubes
Some centrifuges come with multiple rotors that fit 2/1.5 ml, 0.5 ml, and 0.2 ml Eppendorf tubes, and it is best to use these when you are going to be spinning your samples hard for an extended period of time. However, changing rotors can be a pain and most of the time we aren’t trying to pellet our samples, but just trying to bring any condensation on the lid or the sides of the tubes down into the bottom. For these short spins, we can spin our smaller tubes in the 2/1.5 ml rotor by using some home-made adapters.
By cutting the top off a 1.5 ml Eppendorf tube, we can nest a 0.5ml tube inside it (left). And if we also cut the top off the 0.5 ml tube, a 0.2 tube can nest inside that as well (right). Depending on the particular tubes you are using, these nested configurations can tolerate quite a bit of force. However, if the samples are particularly precious, radioactive (or otherwise dangerous), or if you are going to be spinning them hard and long, you should probably go to the effort of changing the rotor rather than using these adapters.
Stock Balance Tubes
For those times when you just need a balance tube, you can save some time by preparing a selection of tubes with the volume written on the top and keeping them in a rack next to the microcentrifuge. I know this seems really obvious, but most of the people I’ve worked with simply never thought to do this. I can almost always just grab one from this selection rather than having to make up a new one for each occasion. In addition, I find that it saves me from having the collection of unmarked tubes with clear, colorless liquid in them sitting next to the centrifuge that seems to disturb my lab safety officer so much.
Divide by Three
Not only is the number of tubes a microcentrifuge can hold divisible by two, but almost always by three as well. How does this help you? If you have an odd number of tubes, you can now spin them without a balance tube. Here is the rotor from my microcentrifuge:
I have taken a red marker and colored the white numbers that divide the rotor into thirds, allowing me to quickly place three tubes into the microcentrifuge while maintaining balance in the rotor. On other microcentrifuges that did not have a paired position indicator (a white line on this rotor), I have used a different color marker to divide the rotor in half. Now what if you have five tubes?
The orange tubes balance each other, and the green tubes balance themselves. Of course you don’t need to break out the markers to do this, but premarking the rotor helps avoid mistakes when you are working quickly.
Nested Tubes
Some centrifuges come with multiple rotors that fit 2/1.5 ml, 0.5 ml, and 0.2 ml Eppendorf tubes, and it is best to use these when you are going to be spinning your samples hard for an extended period of time. However, changing rotors can be a pain and most of the time we aren’t trying to pellet our samples, but just trying to bring any condensation on the lid or the sides of the tubes down into the bottom. For these short spins, we can spin our smaller tubes in the 2/1.5 ml rotor by using some home-made adapters.
By cutting the top off a 1.5 ml Eppendorf tube, we can nest a 0.5ml tube inside it (left). And if we also cut the top off the 0.5 ml tube, a 0.2 tube can nest inside that as well (right). Depending on the particular tubes you are using, these nested configurations can tolerate quite a bit of force. However, if the samples are particularly precious, radioactive (or otherwise dangerous), or if you are going to be spinning them hard and long, you should probably go to the effort of changing the rotor rather than using these adapters.
Stock Balance Tubes
For those times when you just need a balance tube, you can save some time by preparing a selection of tubes with the volume written on the top and keeping them in a rack next to the microcentrifuge. I know this seems really obvious, but most of the people I’ve worked with simply never thought to do this. I can almost always just grab one from this selection rather than having to make up a new one for each occasion. In addition, I find that it saves me from having the collection of unmarked tubes with clear, colorless liquid in them sitting next to the centrifuge that seems to disturb my lab safety officer so much.
Friday, July 23, 2010
Friday, July 9, 2010
Thursday, July 1, 2010
Jellyfish Fight Terrorists -- Biochemists And Engineers Create Fast-acting Pathogen Sensor
Engineers invented a device to bring air samples into contact with genetically engineered biosensors in the effort to detect dangerous biological agents. The technology uses multiple collections of altered cell antibodies, each collection designed to respond to a specific pathogen by releasing photons of a unique wavelength upon finding it. Detectors measure the photons' wavelengths and interpret the pathogens they represent.ScienceDaily
Wednesday, June 30, 2010
Incredible fish with transparent head | UFun
http://uleven.com/incredible-fish-with-transparent-head/
Monday, June 28, 2010
Ward 50, Dhaka 12, Digital Bangladesh, Digital Citizen - Welcome To Ward No - 50
This is what we can say digital bangladesh. ... amature .. but on the way ............
Ward 50, Dhaka 12, Digital Bangladesh, Digital Citizen - Welcome To Ward No - 50
Ward 50, Dhaka 12, Digital Bangladesh, Digital Citizen - Welcome To Ward No - 50
Wednesday, June 23, 2010
The Couch to 5k in 9 weeks
Are you a couch potato? Want to change your life to fit and healthy one? check this c25k site.
Monday, June 21, 2010
Thursday, June 17, 2010
Wednesday, June 16, 2010
10 Tips For Better DNA Gel Extraction Results
What is it about gel extraction of DNA that makes it a pain? Maybe it's poor product yields or maybe it's because the process uses harsh chemicals (chaotropic salts, ethidium bromide, ethanol, heat) that will damage or denature DNA and potentially decrease cloning success. In this article I share some tips, both from experience and from helping people with the procedure, to help maximize yields of high quality DNA from the gel extraction process. I hope these suggestions help you to obtain high yields and purity of double-stranded DNA.
1. Trim the gel slice as much as possible. Get rid of all the excess gel including in front of or behind the DNA. Most people cut out a square around the gel but don't think to stand it up and trim the gel on front and back. If you poured a thick gel, there will be a lot more gel to remove. The more you can remove encasing your DNA, the higher the yields.
2. Minimize exposure on the UV light. The UV light causes DNA damage that can impact the clonability of the DNA. Cut your gel slice quickly. If you have multiple bands to trim, work with one band at a time on the UV. Don't let the entire gel sit cooking on the UV light while you cut one slice at a time. The DNA sitting the longest will be nicked to shreds. Alternatively, use a visible range stain such as methylene blue or crystal violet. More info in this article on vector preparation tips.
3. Remove all traces of phenol using a “home brew” method. If using phenol to purify the DNA from agarose, carry-over of phenol will not be removed by ethanol precipitation and will inhibit the ligation. To remove traces of phenol from the aqueous phase, warm the supernatant at 65C for 5 minutes to evaporate. Let it cool back to room temperature over 10-20 minutes before precipitating to make sure you have double stranded DNA.
4. Change to a new brand or bottle of agarose. Sometimes, for some reason, agarose actually causes enzyme inhibition. It may be that the agarose is old and the quality is no longer good or may be certain brands. I can't say for sure, but I have seen cases where simply switching to a different bottle of agarose results in cloning success.
5. Run controls to determine if the problem is actually the gel extraction step, try running a control where you digest empty vector cut with a single enzyme, perform the gel extraction, and re-ligate it. A vector cut with one enzyme should re-ligate very easily and provide plenty of colonies on the plate. If it does, then the inability to clone the DNA may be related to some other factor, such as secondary structure of the DNA, repeat sequences causing instability in E.coli, or the DNA cloned codes for a protein that may be toxic in bacteria.
The following apply if you are using commercial silica spin kits:
6. Renature the DNA. The melting step combines high amounts of chaotropic salts with heat. This combination will denature the DNA. If the eluted DNA appears half the expected size (it is now single-stranded), re-nature the DNA by warming up to 95C for a minute and let cool slowly to room temperature.
7. Wash it again. An extra wash step with the ethanol containing wash buffer in the kit will always help get rid of chaotropic salt residue on the membrane. Carry over of the salts will inhibit ligase.
8. Make sure all of the ethanol is gone. The silica membrane must be dry after the ethanol wash step to ensure a good yield and for cloning. To determine if you have ethanol in the final DNA, run a check gel on the eluted sample. If it floats out of the well (even with loading dye), you have ethanol contamination. To enhance the drying step (especially if you live in areas where humidity is high), try centrifuging the spin column with the cap open to maximize air flow through the membrane.
9. Make sure your ethanol is the good stuff. It is critically important to use high quality ethanol in the wash buffer and not denatured alcohol. Denatured alcohol contains chemicals like isopropanol, methanol, and even benzene and these chemicals will not dry from the silica membrane and will carry into the DNA. You used denatured alcohol if you ever noticed that a) your DNA smells funny, b) you DNA won't freeze at -20C, c) you observed the floating phenomenon mentioned above.
10. Elute with hot elution buffer. Heating the elution buffer to 70C before applying it to the column will release more of the DNA from the membrane, resulting in higher yields. Allowing the buffer to sit on the column for 5 minutes before centrifugation can also help.
Extraction of DNA from a gel is a necessary part of most cloning and sequencing projects. It does't have to be the bottleneck for getting to the real work of expressing the protein or genotyping DNA. With these simple tips, you will be on your to ligation success!
Tech Tips from BitesizBio
1. Trim the gel slice as much as possible. Get rid of all the excess gel including in front of or behind the DNA. Most people cut out a square around the gel but don't think to stand it up and trim the gel on front and back. If you poured a thick gel, there will be a lot more gel to remove. The more you can remove encasing your DNA, the higher the yields.
2. Minimize exposure on the UV light. The UV light causes DNA damage that can impact the clonability of the DNA. Cut your gel slice quickly. If you have multiple bands to trim, work with one band at a time on the UV. Don't let the entire gel sit cooking on the UV light while you cut one slice at a time. The DNA sitting the longest will be nicked to shreds. Alternatively, use a visible range stain such as methylene blue or crystal violet. More info in this article on vector preparation tips.
3. Remove all traces of phenol using a “home brew” method. If using phenol to purify the DNA from agarose, carry-over of phenol will not be removed by ethanol precipitation and will inhibit the ligation. To remove traces of phenol from the aqueous phase, warm the supernatant at 65C for 5 minutes to evaporate. Let it cool back to room temperature over 10-20 minutes before precipitating to make sure you have double stranded DNA.
4. Change to a new brand or bottle of agarose. Sometimes, for some reason, agarose actually causes enzyme inhibition. It may be that the agarose is old and the quality is no longer good or may be certain brands. I can't say for sure, but I have seen cases where simply switching to a different bottle of agarose results in cloning success.
5. Run controls to determine if the problem is actually the gel extraction step, try running a control where you digest empty vector cut with a single enzyme, perform the gel extraction, and re-ligate it. A vector cut with one enzyme should re-ligate very easily and provide plenty of colonies on the plate. If it does, then the inability to clone the DNA may be related to some other factor, such as secondary structure of the DNA, repeat sequences causing instability in E.coli, or the DNA cloned codes for a protein that may be toxic in bacteria.
The following apply if you are using commercial silica spin kits:
6. Renature the DNA. The melting step combines high amounts of chaotropic salts with heat. This combination will denature the DNA. If the eluted DNA appears half the expected size (it is now single-stranded), re-nature the DNA by warming up to 95C for a minute and let cool slowly to room temperature.
7. Wash it again. An extra wash step with the ethanol containing wash buffer in the kit will always help get rid of chaotropic salt residue on the membrane. Carry over of the salts will inhibit ligase.
8. Make sure all of the ethanol is gone. The silica membrane must be dry after the ethanol wash step to ensure a good yield and for cloning. To determine if you have ethanol in the final DNA, run a check gel on the eluted sample. If it floats out of the well (even with loading dye), you have ethanol contamination. To enhance the drying step (especially if you live in areas where humidity is high), try centrifuging the spin column with the cap open to maximize air flow through the membrane.
9. Make sure your ethanol is the good stuff. It is critically important to use high quality ethanol in the wash buffer and not denatured alcohol. Denatured alcohol contains chemicals like isopropanol, methanol, and even benzene and these chemicals will not dry from the silica membrane and will carry into the DNA. You used denatured alcohol if you ever noticed that a) your DNA smells funny, b) you DNA won't freeze at -20C, c) you observed the floating phenomenon mentioned above.
10. Elute with hot elution buffer. Heating the elution buffer to 70C before applying it to the column will release more of the DNA from the membrane, resulting in higher yields. Allowing the buffer to sit on the column for 5 minutes before centrifugation can also help.
Extraction of DNA from a gel is a necessary part of most cloning and sequencing projects. It does't have to be the bottleneck for getting to the real work of expressing the protein or genotyping DNA. With these simple tips, you will be on your to ligation success!
Tech Tips from BitesizBio
Cloning: Where to Hit The Pause Button
Here are a few hints on where you can pause in your cloning experiments while working on other projects:
Restriction digests can be left at room temperature over night over even over the weekend. Prolonged digestion occasionally results in star activity, so be aware of this possibility if you encounter subsequent problems with the DNA fragment.
Gel extraction of DNA from an agarose gel can be put off indefinitely. Try storing the gel slice in the fridge overnight, or even melting the slice in buffer and freezing it at -20°C or -80°C. Degradation of the DNA will occur at the same rate and under the same conditions as soluble DNA, so use a colder temperature for longer storage.
Ligations can be done at room temperature or cooler (think 12-16°C) overnight or even for a few days, if you’re really busy. You can also store a ligation in the fridge and take it out later to continue ligating at room temperature for as long as necessary.
Transforming E. coli is usually an overnight procedure. If you incubate the plates at room temperature, however, colonies will appear three days after plating, instead of the usual one day at 37°C -perfect for sneaking in one last experiment on a Friday, without having to come in over the weekend.
We sent a sneak peek of this article to our newsletter subscribers and invited them to add their own tips. Here are a few great ones from John Mackay:
You can keep DNA extraction samples in the fridge once you have added 1) the extraction buffer (e.g. GITC or CTAB) or 2) chloroform (prior to spining) or 3) ethanol for precipitation.
For cloning, PCR reactions are stable in machine over weekend… without a 4degC hold – that’s a good way to bust your machine. I have left reactions on bench for several days before purification etc, although I wouldn’t suggest it for T/A cloning – fresh product is best.
Tech Tips from Bitsize Bio
Restriction digests can be left at room temperature over night over even over the weekend. Prolonged digestion occasionally results in star activity, so be aware of this possibility if you encounter subsequent problems with the DNA fragment.
Gel extraction of DNA from an agarose gel can be put off indefinitely. Try storing the gel slice in the fridge overnight, or even melting the slice in buffer and freezing it at -20°C or -80°C. Degradation of the DNA will occur at the same rate and under the same conditions as soluble DNA, so use a colder temperature for longer storage.
Ligations can be done at room temperature or cooler (think 12-16°C) overnight or even for a few days, if you’re really busy. You can also store a ligation in the fridge and take it out later to continue ligating at room temperature for as long as necessary.
Transforming E. coli is usually an overnight procedure. If you incubate the plates at room temperature, however, colonies will appear three days after plating, instead of the usual one day at 37°C -perfect for sneaking in one last experiment on a Friday, without having to come in over the weekend.
We sent a sneak peek of this article to our newsletter subscribers and invited them to add their own tips. Here are a few great ones from John Mackay:
You can keep DNA extraction samples in the fridge once you have added 1) the extraction buffer (e.g. GITC or CTAB) or 2) chloroform (prior to spining) or 3) ethanol for precipitation.
For cloning, PCR reactions are stable in machine over weekend… without a 4degC hold – that’s a good way to bust your machine. I have left reactions on bench for several days before purification etc, although I wouldn’t suggest it for T/A cloning – fresh product is best.
Tech Tips from Bitsize Bio
Thursday, June 10, 2010
Thursday, May 13, 2010
Ladies should not work in the lab............
Go through the following article I found. I am sure you will agree on the title I gave.
Lab Stuff I wish I could use in my kitchen
Do you ever take a look at what you’re doing in the lab and think, “Wow, this would really come in handy at home?” Here are a few of the things I use in the lab that I would love to have in my kitchen:
1. Stir plates and stir bars would be incredibly useful for cooking those dishes that need to be stirred constantly. Can you imagine making risotto on a stir plate? Just start up the spin function, and you won’t have to stand over a hot pot for 30 minutes just to make a tasty dinner.
2. Parafilm works so much better than saran wrap, I’ve often been tempted to “borrow” a roll for sealing food containers to store in my fridge at home.
3. Liquid nitrogen would be invaluable for flash-freezing veggies and meats to store in the freezer. Imagine making popsicles instantly, and never having to wait for the ice cube tray to freeze!
4. De-ionized water from a tap in my kitchen would seriously decrease the number of times I have to run vinegar through the coffee maker to keep it flowing smoothly.
5. Freezer labels that stay stuck in extreme temperature conditions could eliminate the “mystery meal” phenomenon of pulling an unlabeled tupperware out of the freezer and hoping it’s soup.
6. A vortexer would be an essential party asset for mixing drinks, especially if you could also find conical cocktail glasses!
7. Lab timers can time multiple procedures and have louder buzzers than any kitchen timer I’ve found; they would be perfect for busy cooking days.
8. Freezer racks and boxes would make much better use of freezer storage space at home. What if you could get tupperware containers the same size and shape as freezer boxes, and organize them in those vertical metal racks just like in the -80°C freezer in the lab?
9. A 30°C incubator is the ideal tool for making bread. No more guesswork when it comes to rising times for bread; at the optimal temperature for yeast growth, you know exactly what the doubling time is, and thus exactly when the bread is ready to bake.
10. A desktop autoclave could be really handy for sterilizing baby bottles. I’d also use it to sterilize glasses and flatware after an illness, to make sure the same bug doesn’t make an unwelcome reappearance.
What lab items do you wish you could use in “real life”?
Lab Stuff I wish I could use in my kitchen
Do you ever take a look at what you’re doing in the lab and think, “Wow, this would really come in handy at home?” Here are a few of the things I use in the lab that I would love to have in my kitchen:
1. Stir plates and stir bars would be incredibly useful for cooking those dishes that need to be stirred constantly. Can you imagine making risotto on a stir plate? Just start up the spin function, and you won’t have to stand over a hot pot for 30 minutes just to make a tasty dinner.
2. Parafilm works so much better than saran wrap, I’ve often been tempted to “borrow” a roll for sealing food containers to store in my fridge at home.
3. Liquid nitrogen would be invaluable for flash-freezing veggies and meats to store in the freezer. Imagine making popsicles instantly, and never having to wait for the ice cube tray to freeze!
4. De-ionized water from a tap in my kitchen would seriously decrease the number of times I have to run vinegar through the coffee maker to keep it flowing smoothly.
5. Freezer labels that stay stuck in extreme temperature conditions could eliminate the “mystery meal” phenomenon of pulling an unlabeled tupperware out of the freezer and hoping it’s soup.
6. A vortexer would be an essential party asset for mixing drinks, especially if you could also find conical cocktail glasses!
7. Lab timers can time multiple procedures and have louder buzzers than any kitchen timer I’ve found; they would be perfect for busy cooking days.
8. Freezer racks and boxes would make much better use of freezer storage space at home. What if you could get tupperware containers the same size and shape as freezer boxes, and organize them in those vertical metal racks just like in the -80°C freezer in the lab?
9. A 30°C incubator is the ideal tool for making bread. No more guesswork when it comes to rising times for bread; at the optimal temperature for yeast growth, you know exactly what the doubling time is, and thus exactly when the bread is ready to bake.
10. A desktop autoclave could be really handy for sterilizing baby bottles. I’d also use it to sterilize glasses and flatware after an illness, to make sure the same bug doesn’t make an unwelcome reappearance.
What lab items do you wish you could use in “real life”?
Monday, March 22, 2010
SDS-PAGE: The Easy Way to Find the Wells
If you have ever attempted to load a SDS-PAGE gel only to miss the well, stab the divider, and then watch helplessly as your sample squirts off into the wrong well, then this tip is for you.
The fortunate among us are able to use pre-cast gels with the wells outlined on the gel plate, but home-made gels don’t have this feature. I’ve seen labs with various loading guides printed off on acetate that they stick to the front plate of the gel before loading, which is better than nothing, but only shows you where the well is supposed to be, not where it is. It is true that after loading enough gels you start to develop an eye for finding the wells, but there is an easier way.
The trick is as simple as this: add a bit of bromophenol blue to your stacking gel. If you remember, bromophenol blue is already in your loading dye, so you aren’t adding anything new to the SDS-PAGE equation. I find that adding the dye to 0.003% is enough to color the stacker, but you can adjust the concentration to your liking. To make things even easier, I simply add the dye to my 4X Stacking Gel Buffer (0.5M Tris-HCl pH 6.8, in my case) to a final concentration of 0.012%. Now you don’t even have to add a new line to your recipe. You can see the results below.
Before loading the samples (Yes, I know these are ugly wells.)
Samples Loaded...
...a third of the way into the run...
...and close to the end of the run.
As you can see, the wells are easy to visualize. Once the voltage is applied, all the dye in the gel collapses down into the dye front and the gel runs normally. If the color of the stacking gel is too similar to the color of your protein samples, then you can simply add more bromophenol blue to your concentrated loading buffer (you’ll find that recipes vary on this point anyway). For the sake of the photographs, I ran this gel without the cover – this is potentially dangerous, so don’t try this at home…urr… I mean, your lab.
Courtesy: Jode, Bitesize Bio.
The fortunate among us are able to use pre-cast gels with the wells outlined on the gel plate, but home-made gels don’t have this feature. I’ve seen labs with various loading guides printed off on acetate that they stick to the front plate of the gel before loading, which is better than nothing, but only shows you where the well is supposed to be, not where it is. It is true that after loading enough gels you start to develop an eye for finding the wells, but there is an easier way.
The trick is as simple as this: add a bit of bromophenol blue to your stacking gel. If you remember, bromophenol blue is already in your loading dye, so you aren’t adding anything new to the SDS-PAGE equation. I find that adding the dye to 0.003% is enough to color the stacker, but you can adjust the concentration to your liking. To make things even easier, I simply add the dye to my 4X Stacking Gel Buffer (0.5M Tris-HCl pH 6.8, in my case) to a final concentration of 0.012%. Now you don’t even have to add a new line to your recipe. You can see the results below.
Before loading the samples (Yes, I know these are ugly wells.)
Samples Loaded...
...a third of the way into the run...
...and close to the end of the run.
As you can see, the wells are easy to visualize. Once the voltage is applied, all the dye in the gel collapses down into the dye front and the gel runs normally. If the color of the stacking gel is too similar to the color of your protein samples, then you can simply add more bromophenol blue to your concentrated loading buffer (you’ll find that recipes vary on this point anyway). For the sake of the photographs, I ran this gel without the cover – this is potentially dangerous, so don’t try this at home…urr… I mean, your lab.
Courtesy: Jode, Bitesize Bio.
Saturday, March 20, 2010
Friday, March 12, 2010
How to Build a Plate Centrifuge for $25
A cheap, quick-to-build plate centrifuge that also worked pretty well for a quick spin just before PCR.
Building one is simple
You will need.........
1. A salad spinner – We use the Zyliss brand pull-cord salad spinner.
2. Multi-purpose cable ties found at any hardware store.
3. 96-well plate inserts.
Gathering the components is as complicated as it gets! All you need to do now is use those cable ties to secure the 96-well plate inserts to the inner bowl of the spinner as shown below. Then start using the new mini-plate-fuge!
Building one is simple
You will need.........
1. A salad spinner – We use the Zyliss brand pull-cord salad spinner.
2. Multi-purpose cable ties found at any hardware store.
3. 96-well plate inserts.
Gathering the components is as complicated as it gets! All you need to do now is use those cable ties to secure the 96-well plate inserts to the inner bowl of the spinner as shown below. Then start using the new mini-plate-fuge!
Tuesday, March 2, 2010
A role for cannabinoids in slowing down HIV
We all are very familiar with the effects of cannabinoid receptor stimulation on the body. Relaxation, pain relief, and increased appetite probably come first to mind. These psychoactive effects result from activation of the CB1 receptor found on cells in the brain by tetrahydrocannabinol (THC).
But there is another receptor, called CB2, that can bind THC and other natural ligands for the cannabinoid receptor. The CB2 receptor is found on cells comprising the immune system and have a multitude of anti-inflammatory and immunosuppressive effects upon activation. In most cases, immunosuppressive effects are undesirable, but sometimes that can be beneficial. Today’s article is an example.
New research from the lab of Dr. Guy Cabral at Virginia Commonwealth University shows that stimulation of the CB2 receptor on macrophages inhibits migration of healthy immune cells towards the HIV Tat protein. Tat is an essential viral regulatory protein used by HIV to stimulate inflammatory responses and wreak havoc in the body. Tat protein looks suspiciously like some of our own chemokine proteins and can bind to a variety of receptors on immune cells causing activation of cascades that lead to migration of uninfected macrophages towards the HIV infected cells.
The paper by Erinn S. Raborn and Guy A. Cabral, published in the January 2010 issue of the Journal of Pharmacology and Experimental Therapeutics is titled: Cannabinoid Inhibition of Macrophage Migration to the Tat Protein of HIV-1 is Linked to the CB2 Cannabinoid Receptor. The authors used a macrophage cell line in a migration model system to demonstrate very specifically that when the CB2 receptor is stimulated, macrophages no longer respond to the Tat protein. The chemoattractant effects are abolished.
Here is an summary of their work.
Introduction:
Macrophages are the primary target for HIV infection and once infected, cells begin producing viral Tat (trans activating factor) protein and GP120 protein in addition to stimulating the production of cellular cytokines and chemokines that induce changes in the immunoregulation of the host. The HIV Tat protein has an additional role of acting as a potent chemoattractant for monocytes, thus contributing to the spread of infected cells.
Most drugs of abuse (opiates, cocaine, amphetamines and cannabinoids) have an adverse effect on immunity, increasing susceptibility to infection. The cannabinoids in particular have been shown to have anti-inflammatory properties, downregulating some of the chemokines and cytokines involved in stimulating macrophage to migrate to infections and inhibiting macrophage function. Cannabinoids have also been shown to down-regulate the expression of chemokine receptors, notably CCR5, one of the co-receptors used for HIV entry into cells. Thus, a link between the potential anti-HIV effects of the CB2 cannabinoid receptor has been established.
The purpose of this study was to determine whether cannabinoids exert any effect on the chemoattractant properties of Tat in macrophages. In the presence of cannabinoid agonists delta-9- tetrahydrocannabinol and CP55940, human macrophage-like cells (U937 cells) were inhibited from migrating towards Tat protein and this effect was due specifically to CB2. The results show a clear link between CB2 and the ability of macrophages to respond to the HIV protein in a cell culture system. This work provides the basis for a novel therapeutic target for preventing or reducing HIV associated immunopathology and dissemination in vivo.
Materials and methods:
Cells: The human leukemic monocyte cell line U-937 was used.
Drugs: CB1 and CB2 receptor agonists used were: THC and CP55940. The CB2 specific agonist was O-2137-2 and the CB1 specific agonist was ACEA. The CB1 and CB2 receptor antagonists were SR141716 (SR1) and SR144528 (SR2), respectively. The full names of the drugs and the Ki information is described in the paper.
Tat: Recombinant human HIV Tat protein was obtained from Immunodiagnostics, Inc.
Cell Migration Assay: 35 mm tissue culture plates with upper and lower compartments separated by a polycarbonate 8 micron pore membrane were used. Drug treated or control treated U937 cells were incubated on the top chamber and Tat protein or serum-free media plus vehicle was in the bottom chamber. Migration of cells to the bottom chamber was visualized with an Olympus CK2 inverted microscope connected to a digital video camera. The number of cells were manually enumerated. A greater than 2-fold increase in the number of cells in the presence of chemoattractant compared to no Tat was a positive response. The EC 50 or inhibitory concentration was the concentration of cannabinoid that results in a 50% reduction in macrophage migration.
Knockdown of CB2 expression using siRNA and RT-qPCR: siRNA for the CB2 receptor was used for transient transfection of cells and knock-down shown using Western blot analysis. SYBR Green was used for qPCR analysis after reverse transcription of RNA, qPCR was performed using the SmartCycler. Full details of the experimental design for qPCR and transfection are provided in the paper.
Results:
To begin, the authors first confirmed the expression of the CB2 receptor in U937 cells, both on the RNA and protein level. The CB1 receptor, typically expressed in cells of the brain, was not found in U937 cells using RT-qPCR. Their second set of confirmatory experiments proved that the U937 cells would migrate in response to Tat protein as has been previously described for human monocytes in blood. The migratory response was maximum at 50 nM Tat and so the authors used this concentration for their studies.
The next experiments looked at the migration of macrophages in the presence of the different drugs. All results were compared to vehicle controls (ethanol was used to dilute the drugs). Using vehicle alone with Tat protein in the bottom compartment, migration was the same as with no vehicle. When cells were treated with THC, however, migration of macrophage was inhibited by 50%. And using the agonist CP55940, migration was inhibited by 58%. Using the CB2 receptor specific agonist, the same effect of >50% inhibition was observed, however, but not suprisingly, using a CB1 receptor agonist, ACEA, had no effect on migration.
These results clearly indicate that the CB2 receptor on the human macrophage-like U937 cells plays a role in migration in the presence of the HIV Tat protein and this effect can be blocked when the receptor is activated.
To confirm the effect of migration was due to the CB2 receptor, the receptor antagonists were used to demonstrate that when signalling through the receptor is blocked, the effect is reversed. The antagonist will bind the receptor but not activate the signalling cascade in the cell, thus blocking it from being activated by the ligand CP55940. Using the CB2 specific antagonist SR2 alone, migration in the presence of Tat is the same as controls- it is not inhibited. When CP55940 is combined with the SR2 compound, inhibition of migration is reversed. SR2 prevents the protective anti-migration effect of CP55940.
To further prove the role of CB2 in this effect, siRNA mediated CB2 knockout cells were employed in the cell migration assay. The authors confirmed that neither the transfection reagent nor the siRNA itself had any effect on cell migration. Using the CB2 knockout cells in the presence of THC, migration was observed similarly to untreated cells. This is consistent with the results of blocking the CB2 receptor with antagonist. The CB2 receptor was not available for activation by the THC and thus no protective anti-migration effect was observed.
Discussion:
Chemokines are cytokines that function by directing the flow of inflammatory cells to sites of injury or infection in the body. HIV uses our immune system cascade meant to protect us for its own benefit, by producing the viral Tat protein to bind the receptors meant for chemokines and stimulate the migration of more healthy macrophages to the HIV infected cells, increasing their opportunity to spread. The stimulation of chemokines also increases the number of receptors on the surface, making it easier for HIV to infect new cells.
The ability to slow down the migration of healthy cells towards HIV infected cells and to down regulate the expression of chemokine receptors would slow the progression of HIV associated disease. In this paper, the authors demonstrate a connection between the cannabinoid receptor on immune cells, CB2, and the migration of macrophages towards Hiv Tat protein. When the CB2 receptor is stimulated with an agonist, migration is inhibited. Whether this is due to down regulation of the chemokine receptors used for binding or due to down regulation of chemokines from CB2 activated cells has yet to be determined.
But the fact remains that the cannabinoid receptor CB2 may be a therapeutic target for preventing hyperactivation of the immune system by HIV and potentially, in the future, to help stop widespread infection.
Final note:
I found this paper to be an exciting advance in the fields of HIV and drugs of abuse. A therapy involving cannabinoids would be far less toxic than current drugs used to stop the progression of HIV. With all the ways HIV has found to use our own immune system against us to survive, an approach that counteracts HIV by taking back control of the immune system could be far more effective than developing toxic drugs that target HIV directly or using cytokines that further activate a tired immune system.
But there is another receptor, called CB2, that can bind THC and other natural ligands for the cannabinoid receptor. The CB2 receptor is found on cells comprising the immune system and have a multitude of anti-inflammatory and immunosuppressive effects upon activation. In most cases, immunosuppressive effects are undesirable, but sometimes that can be beneficial. Today’s article is an example.
New research from the lab of Dr. Guy Cabral at Virginia Commonwealth University shows that stimulation of the CB2 receptor on macrophages inhibits migration of healthy immune cells towards the HIV Tat protein. Tat is an essential viral regulatory protein used by HIV to stimulate inflammatory responses and wreak havoc in the body. Tat protein looks suspiciously like some of our own chemokine proteins and can bind to a variety of receptors on immune cells causing activation of cascades that lead to migration of uninfected macrophages towards the HIV infected cells.
The paper by Erinn S. Raborn and Guy A. Cabral, published in the January 2010 issue of the Journal of Pharmacology and Experimental Therapeutics is titled: Cannabinoid Inhibition of Macrophage Migration to the Tat Protein of HIV-1 is Linked to the CB2 Cannabinoid Receptor. The authors used a macrophage cell line in a migration model system to demonstrate very specifically that when the CB2 receptor is stimulated, macrophages no longer respond to the Tat protein. The chemoattractant effects are abolished.
Here is an summary of their work.
Introduction:
Macrophages are the primary target for HIV infection and once infected, cells begin producing viral Tat (trans activating factor) protein and GP120 protein in addition to stimulating the production of cellular cytokines and chemokines that induce changes in the immunoregulation of the host. The HIV Tat protein has an additional role of acting as a potent chemoattractant for monocytes, thus contributing to the spread of infected cells.
Most drugs of abuse (opiates, cocaine, amphetamines and cannabinoids) have an adverse effect on immunity, increasing susceptibility to infection. The cannabinoids in particular have been shown to have anti-inflammatory properties, downregulating some of the chemokines and cytokines involved in stimulating macrophage to migrate to infections and inhibiting macrophage function. Cannabinoids have also been shown to down-regulate the expression of chemokine receptors, notably CCR5, one of the co-receptors used for HIV entry into cells. Thus, a link between the potential anti-HIV effects of the CB2 cannabinoid receptor has been established.
The purpose of this study was to determine whether cannabinoids exert any effect on the chemoattractant properties of Tat in macrophages. In the presence of cannabinoid agonists delta-9- tetrahydrocannabinol and CP55940, human macrophage-like cells (U937 cells) were inhibited from migrating towards Tat protein and this effect was due specifically to CB2. The results show a clear link between CB2 and the ability of macrophages to respond to the HIV protein in a cell culture system. This work provides the basis for a novel therapeutic target for preventing or reducing HIV associated immunopathology and dissemination in vivo.
Materials and methods:
Cells: The human leukemic monocyte cell line U-937 was used.
Drugs: CB1 and CB2 receptor agonists used were: THC and CP55940. The CB2 specific agonist was O-2137-2 and the CB1 specific agonist was ACEA. The CB1 and CB2 receptor antagonists were SR141716 (SR1) and SR144528 (SR2), respectively. The full names of the drugs and the Ki information is described in the paper.
Tat: Recombinant human HIV Tat protein was obtained from Immunodiagnostics, Inc.
Cell Migration Assay: 35 mm tissue culture plates with upper and lower compartments separated by a polycarbonate 8 micron pore membrane were used. Drug treated or control treated U937 cells were incubated on the top chamber and Tat protein or serum-free media plus vehicle was in the bottom chamber. Migration of cells to the bottom chamber was visualized with an Olympus CK2 inverted microscope connected to a digital video camera. The number of cells were manually enumerated. A greater than 2-fold increase in the number of cells in the presence of chemoattractant compared to no Tat was a positive response. The EC 50 or inhibitory concentration was the concentration of cannabinoid that results in a 50% reduction in macrophage migration.
Knockdown of CB2 expression using siRNA and RT-qPCR: siRNA for the CB2 receptor was used for transient transfection of cells and knock-down shown using Western blot analysis. SYBR Green was used for qPCR analysis after reverse transcription of RNA, qPCR was performed using the SmartCycler. Full details of the experimental design for qPCR and transfection are provided in the paper.
Results:
To begin, the authors first confirmed the expression of the CB2 receptor in U937 cells, both on the RNA and protein level. The CB1 receptor, typically expressed in cells of the brain, was not found in U937 cells using RT-qPCR. Their second set of confirmatory experiments proved that the U937 cells would migrate in response to Tat protein as has been previously described for human monocytes in blood. The migratory response was maximum at 50 nM Tat and so the authors used this concentration for their studies.
The next experiments looked at the migration of macrophages in the presence of the different drugs. All results were compared to vehicle controls (ethanol was used to dilute the drugs). Using vehicle alone with Tat protein in the bottom compartment, migration was the same as with no vehicle. When cells were treated with THC, however, migration of macrophage was inhibited by 50%. And using the agonist CP55940, migration was inhibited by 58%. Using the CB2 receptor specific agonist, the same effect of >50% inhibition was observed, however, but not suprisingly, using a CB1 receptor agonist, ACEA, had no effect on migration.
These results clearly indicate that the CB2 receptor on the human macrophage-like U937 cells plays a role in migration in the presence of the HIV Tat protein and this effect can be blocked when the receptor is activated.
To confirm the effect of migration was due to the CB2 receptor, the receptor antagonists were used to demonstrate that when signalling through the receptor is blocked, the effect is reversed. The antagonist will bind the receptor but not activate the signalling cascade in the cell, thus blocking it from being activated by the ligand CP55940. Using the CB2 specific antagonist SR2 alone, migration in the presence of Tat is the same as controls- it is not inhibited. When CP55940 is combined with the SR2 compound, inhibition of migration is reversed. SR2 prevents the protective anti-migration effect of CP55940.
To further prove the role of CB2 in this effect, siRNA mediated CB2 knockout cells were employed in the cell migration assay. The authors confirmed that neither the transfection reagent nor the siRNA itself had any effect on cell migration. Using the CB2 knockout cells in the presence of THC, migration was observed similarly to untreated cells. This is consistent with the results of blocking the CB2 receptor with antagonist. The CB2 receptor was not available for activation by the THC and thus no protective anti-migration effect was observed.
Discussion:
Chemokines are cytokines that function by directing the flow of inflammatory cells to sites of injury or infection in the body. HIV uses our immune system cascade meant to protect us for its own benefit, by producing the viral Tat protein to bind the receptors meant for chemokines and stimulate the migration of more healthy macrophages to the HIV infected cells, increasing their opportunity to spread. The stimulation of chemokines also increases the number of receptors on the surface, making it easier for HIV to infect new cells.
The ability to slow down the migration of healthy cells towards HIV infected cells and to down regulate the expression of chemokine receptors would slow the progression of HIV associated disease. In this paper, the authors demonstrate a connection between the cannabinoid receptor on immune cells, CB2, and the migration of macrophages towards Hiv Tat protein. When the CB2 receptor is stimulated with an agonist, migration is inhibited. Whether this is due to down regulation of the chemokine receptors used for binding or due to down regulation of chemokines from CB2 activated cells has yet to be determined.
But the fact remains that the cannabinoid receptor CB2 may be a therapeutic target for preventing hyperactivation of the immune system by HIV and potentially, in the future, to help stop widespread infection.
Final note:
I found this paper to be an exciting advance in the fields of HIV and drugs of abuse. A therapy involving cannabinoids would be far less toxic than current drugs used to stop the progression of HIV. With all the ways HIV has found to use our own immune system against us to survive, an approach that counteracts HIV by taking back control of the immune system could be far more effective than developing toxic drugs that target HIV directly or using cytokines that further activate a tired immune system.
Friday, February 26, 2010
Protecting Your Professional Image
We all know how important image is to a job search. It’s crucial. This is why we wear a nice suit and print our resumes on thick paper. It’s all about image. And yet, sometimes job seekers fail to remember the image that they are presenting on the internet.
Be careful about what you Tweet!
Pictures and statements of wild parties, drinking or just a friends’ night out on the town may seem fun and innocuous, but they may cost you your next job. More and more articles are appearing citing examples of people whose social networking profiles (i.e. Twitter, Facebook, etc) are causing them to be passed over for job opportunities. A recent study in Time Magazine cited that 70% of HR professionals claim they have passed over a job candidate because of their internet profile. These sites are checked by a growing number of firms and you must be mindful of your public image. None of these are truly private. Most of us have found friends or colleagues’ profiles who were supposed to be “private”. Be mindful of how you present yourself.
Would you “friend” your boss on Facebook?
It’s worth noting that this is not limited to job seekers. Many of us have had a co-worker or boss ask to “friend” us on Facebook. This is a potential minefield. What are your options? Tell them “no” and risk causing an issue? Tell them yes and insist all of your friends keep comments “professional”? (I don’t know about you, but I would worry about what my friends would post if I suggested this!) You could ignore the request..until they ask you about it face-to-face at work
So what’s the solution?
These are the image struggles of the 21st century and they are very real to each of us. The easiest solutions are to stay off of social networking sites or keep them “professional” in content or appearance. But seeing how this is not a realistic option for many, I would suggest that at the very least, you “clean up” your site, remove comments you have made that could reflect poorly, and change out the pictures on your site to make them a bit more conservative until you have started your new job.
I would strongly encourage you to objectively review any of your social networking sites (I am confident your professional networking sites like LinkedIn are already “professional”). If there is anything you would not want your employer, prospective employer, co-workers or your grandmother to see, remove it. If you can’t/won’t/don’t want to do this, you should ensure your accounts are set to the most private settings possible; this will help prevent unwanted visitors to your profile.
The 21st century is full of electronic marvels; just don’t let them interfere with your 21st century career.
Courtesy: Travis, Bitesize Bio.
Be careful about what you Tweet!
Pictures and statements of wild parties, drinking or just a friends’ night out on the town may seem fun and innocuous, but they may cost you your next job. More and more articles are appearing citing examples of people whose social networking profiles (i.e. Twitter, Facebook, etc) are causing them to be passed over for job opportunities. A recent study in Time Magazine cited that 70% of HR professionals claim they have passed over a job candidate because of their internet profile. These sites are checked by a growing number of firms and you must be mindful of your public image. None of these are truly private. Most of us have found friends or colleagues’ profiles who were supposed to be “private”. Be mindful of how you present yourself.
Would you “friend” your boss on Facebook?
It’s worth noting that this is not limited to job seekers. Many of us have had a co-worker or boss ask to “friend” us on Facebook. This is a potential minefield. What are your options? Tell them “no” and risk causing an issue? Tell them yes and insist all of your friends keep comments “professional”? (I don’t know about you, but I would worry about what my friends would post if I suggested this!) You could ignore the request..until they ask you about it face-to-face at work
So what’s the solution?
These are the image struggles of the 21st century and they are very real to each of us. The easiest solutions are to stay off of social networking sites or keep them “professional” in content or appearance. But seeing how this is not a realistic option for many, I would suggest that at the very least, you “clean up” your site, remove comments you have made that could reflect poorly, and change out the pictures on your site to make them a bit more conservative until you have started your new job.
I would strongly encourage you to objectively review any of your social networking sites (I am confident your professional networking sites like LinkedIn are already “professional”). If there is anything you would not want your employer, prospective employer, co-workers or your grandmother to see, remove it. If you can’t/won’t/don’t want to do this, you should ensure your accounts are set to the most private settings possible; this will help prevent unwanted visitors to your profile.
The 21st century is full of electronic marvels; just don’t let them interfere with your 21st century career.
Courtesy: Travis, Bitesize Bio.
Monday, February 15, 2010
15 Reasons to be a scientist ..........
Just for fun, here my top 15 reasons for being a scientist. Add your own reasons in the comments below if you so wish.
1. Not being stuck behind a desk all day every day
2. Conferences… see the world for free
3. Understanding some of the fundamentals of life and the universe
4. Getting paid to do something you can actually enjoy
5. Realising just how little understanding we have of life and the universe
6. Having the freedom to plan & execute your work (If you are a PhD student you may have to wait until you have finished your studies for this one!)
7. People believe what you say (trust me I’m a “doctor”)
8. Not having to wear a suit to work every day (could you imagine that?)
9. Getting paid to think creatively
10. If it doesn’t work, it’s not your fault. Most things don’t work anyway – this is research!
11. Getting paid to think logically and innovate
12. Lab coats – even less need to dress smart for work.
13. You can work in nearly any country in the world that you choose
14. Owning a bunsen burner (or the equivalent gadget for your specialization)
15. Your mother/father/grandmother thinks you are a genius (unless he/she is a scientist too!)
Got any more?… add them below.
Courtesy: Nick, BitesizeBio
1. Not being stuck behind a desk all day every day
2. Conferences… see the world for free
3. Understanding some of the fundamentals of life and the universe
4. Getting paid to do something you can actually enjoy
5. Realising just how little understanding we have of life and the universe
6. Having the freedom to plan & execute your work (If you are a PhD student you may have to wait until you have finished your studies for this one!)
7. People believe what you say (trust me I’m a “doctor”)
8. Not having to wear a suit to work every day (could you imagine that?)
9. Getting paid to think creatively
10. If it doesn’t work, it’s not your fault. Most things don’t work anyway – this is research!
11. Getting paid to think logically and innovate
12. Lab coats – even less need to dress smart for work.
13. You can work in nearly any country in the world that you choose
14. Owning a bunsen burner (or the equivalent gadget for your specialization)
15. Your mother/father/grandmother thinks you are a genius (unless he/she is a scientist too!)
Got any more?… add them below.
Courtesy: Nick, BitesizeBio
SCIENTISTS-ONLY DATING SERVICE!!!!!!!
You know what it’s like. You’re committed to your career, you work long hours so you don’t get to socialise as much as you needed to meet that special someone.
And those people you do meet wouldn’t know their a-factor from their elbow.
So what options are there for the lonely scientist who wants to find someone with whom they can share their copy of Molecular Biology of The Cell?
Well, the Scientist magazine has a scientists-only dating service called Science Connection that can help with that very mission. According to their website:
“The world is a crowded petri dish, and yet for those of an intellectual bent who happen to be single, it’s not easy to find that certain person for a great symbiotic relationship. Enter Science Connection.”
Being scientists we of course need some statistics on how successful this service is and Science Connection duly provides. Their up-to-the-minute stats boast 87 marriages, 69 engagements, 274 “serious relationships” and 303 dating couples out of 15,031 individuals who have joined the service since it began.
Membership fees are only $65/year…Â a small price to pay to find the scientist of your dreams?
Courtesy: Nick, BitesizeBio
And those people you do meet wouldn’t know their a-factor from their elbow.
So what options are there for the lonely scientist who wants to find someone with whom they can share their copy of Molecular Biology of The Cell?
Well, the Scientist magazine has a scientists-only dating service called Science Connection that can help with that very mission. According to their website:
“The world is a crowded petri dish, and yet for those of an intellectual bent who happen to be single, it’s not easy to find that certain person for a great symbiotic relationship. Enter Science Connection.”
Being scientists we of course need some statistics on how successful this service is and Science Connection duly provides. Their up-to-the-minute stats boast 87 marriages, 69 engagements, 274 “serious relationships” and 303 dating couples out of 15,031 individuals who have joined the service since it began.
Membership fees are only $65/year…Â a small price to pay to find the scientist of your dreams?
Courtesy: Nick, BitesizeBio
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