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Killing for DNA: A predatory device in the cholera bacterium

Cholera is caused when the bacterium Vibrio cholerae infects the small intestine. The disease is characterized by acute watery diarrhea resulting in severe dehydration. EPFL scientists have now demonstrated that V. cholerae uses a tiny spear to stab and kill neighboring bacteria -- even of its own kind -- and then steal their DNA. This mechanism, known as "horizontal gene transfer," allows the cholera bacterium to become more virulent by absorbing the traits of its prey. The study is published in Science.

The lab of Melanie Blokesch at EPFL has uncovered how V. cholerae uses a predatory killing device to compete with surrounding bacteria and steal their DNA. This molecular killing device a spring-loaded spear that is constantly shooting out. This weapon is called the "type VI secretion system" (T6SS) and is known to exist in many types of bacteria. When V. cholerae comes close to other bacteria, the spear punches a hole into them, leaving them to die and release their genetic material, which the predator pulls into itself.

Killing neighbors and stealing genes

This spear-killing, predatory behavior is triggered by the bacterium's environment. The cholera bacterium naturally lives in water, such as the sea, where it attaches onto small planktonic crustaceans. There, it feeds on the main component of their shells: a sugar polymer called chitin. When chitin is available, V. cholerae goes into an aggressive survival mode called "natural competence." When in this mode, V. cholerae attacks neighboring bacteria with its spear -- even if they are of the same species.

Melanie Blokesch set out to explore how V. cholerae uses this behavior to compete for survival in nature. Her lab tested different strains of the bacterium from all over the world, most of which have been implicated in the 7th cholera pandemic, which began in Indonesia in the 1960's, spread rapidly to Asia, Europe, and Latin America, and still affects populations today.

The researchers grew these bacteria on chitin surfaces that simulated their natural habitat on crustaceans. What they found was that the tiny spear is not only part of V. cholerae's natural survival system, but it also contributed to the transfer of genes that could make the bacterium more resistant to threats, even to antibiotics. The researchers then used genetic and bioimaging techniques to identify, in real time, which mechanisms are involved in this event, which is called "horizontal gene transfer."

"Using this mode of DNA acquisition, a single V. cholerae cell can absorb fragments containing more than 40 genes from another bacterium," says Melanie Blokesch. "That's an enormous amount of new genetic information." This phenomenon is referred to as "horizontal" gene transfer, as opposed to the conventional "vertical" passage of genes from parent to offspring.

The importance of this study lies in the fact that horizontal gene transfer is a widespread phenomenon in bacteria, and it contributes to the dispersal of virulence factors and antibiotic resistances. In addition, the chitin-mediated activation of the spear-killing device most likely renders the bacterium more dangerous to patients when they ingest it, as this molecular spear might also kill protective bacteria in the human gut.

The researchers are now extending their investigation into the interplay between the chitin-induced production of the spear and horizontal gene transfer. "By studying this interplay, we can begin to better understand evolutionary forces that shape human pathogens and maybe also transmission of the disease cholera," says Blokesch.

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New mechanism for Type IV pili retraction in Vibrio cholerae

Type IV pili, essential for many pathogens to cause disease, are hair-like appendages that grow out of and are retracted back into bacteria cells, enabling them to move and adhere to surfaces. Although pathogenic bacteria often rely on a specialized molecular motor to retract their pili, a new study in PLOS Pathogens reveals that a minor pilin protein elicits pilus retraction in the cholera bacterium, Vibrio cholerae.

Bacteria utilize a number of highly sophisticated molecular tools to colonize their hosts. One of the most ubiquitous is a complex nanomachine called the Type IV pilus. This nanomachine has as few as 10 to as many as 30 molecular components, producing exquisitely thin filaments that extend from the bacterial surface and that can be several times the length of the bacteria itself. These pilus filaments have a remarkable array of functions that rely on their ability to (i) adhere to many substrates, including host cell surfaces, pili from nearby bacteria, DNA and bacterial viruses (bacteriophage), and (ii) to depolymerize or retract, which pulls the bacteria along mucosal surfaces, pulls them close together in protective aggregates, and can even draw in substrates like DNA and bacteriophage for nutrition and genetic variation.

In collaboration with researchers from Dartmouth College and Simon Fraser University, Dr. Nicolas Biais, Assistant Professor of Biology at Brooklyn College, City University of New York (CUNY), developed an assay in his laboratory that revealed for the first time the V. cholerae Type IV pilus can retract without this molecular motor, and that retraction is necessary for these pili to function. Instead of a molecular motor, a small minor pilin protein triggers pilus retraction. "The magnitude of the forces though is much smaller," said Dr. Biais. "If Neisseria gonorrhoeae can pull roughly 100,000 times its bodyweight, Vibrio cholerae barely makes it to 1,000 times of its bodyweight. This is a new mechanism for retraction that will help understand how other pili and closely related secretion systems can work and potentially help with the design of novel antibiotics."

"This report [...] demonstrates that the bacterium that causes cholera powers a nanomachine required for infection differently than other disease causing bacteria," said Dr. Hank Seifert, Professor of Biomedical Sciences at Feinberg School of Medicine, Northwestern University, who was not involved with the study. "These findings drastically alter our understanding of how these nanomachines function to provide insights into the mechanisms allowing cholera and the development of synthetic nanomachines."

Research on how Type IV pili function not only advances our understanding of V. cholerae pathogenesis, but will also aid in developing future prevention and treatment strategies for cholera.

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How early should I start GMAT preparation?

Your GMAT score can be sent for 5 years, so I would recommend taking it as early as you are prepared, while you are still in school mode.

For those who are already out of school (the majority of GMAT takers), the answer depends on your mode of preparation and starting score.  If you don't know your starting score, take a practice test asap to get your baseline.

Self-studiers:
You'll want to allow at least 2 hours of self-study for every point you need to raise your score.  If you need 100 points, you'll want to allot 200 hours to be safe.  So if you're working full-time and can only devote ~10 hours of study per week, that's 4 or 5 months.  However, you will forget much of what you learned the first 2 months, so if you have more than 50 points to go, you'll want to do something different.

GMAT Class
Students who take GMAT classes don't do that much better than those who put the same amount of self-study in. The difference is on the order of 20 or 30 points.  I actually recommend hiring a private tutor for that amount of money.

Private Tutor
This of course depends on the tutor, but they should multiply your score increase rate by a factor of at least 2.  My students see their scores increase by between 3 and 7 points per tutoring hour (the fastest in the world). To get the most out of private tutoring, you will need to do homework between meetings and bring them only the questions you struggle with, so that you are not paying your tutor for things you could have done on your own.

Source: The World's Best Online GMAT Tutor

Top 10 IELTS Misconceptions That Stop People Getting a High Score

If you spend enough time as an IELTS teacher you will hear some pretty crazy ‘facts’ about the IELTS test. Every term I hear the same myths and below are the top 10.

These misconceptions are not only false, they are dangerous. A big part of doing well in the exam, apart from a high level of English and good test skills, is learning about how the test works and knowing what examiners expect. If you don’t have accurate information about the test you will probably make unnecessary mistakes and lower your band score.

    1. There is one correct answer in the speaking test

Many students I talk to think the speaking test is more like mathematics than English. In reality, there is no right or wrong answer when it comes to content. The examiner is judging you on four areas and four areas only. They are:

• Fluency and coherence
• Lexical resource
• Grammatical range and accuracy
• Pronunciation

For more on these band descriptors see here.

Five different students could give five different answers to a question and they all can get a high score.

Many school systems teach their students from a young age that there is one way to answer a question and one answer only. This is not the case in the IELTS Speaking or Writing test and there are many ‘correct’ answers.

2. The examiner must agree with my opinion

IELTS is not a knowledge test or an opinion test, it is an English test. The examiner could personally disagree with every opinion you have and you can still get a band score of 9. This is because the examiner is judging your ability to speak or write in English, not agree or disagree with you. In the exam write or speak about what you feel comfortable writing or speaking about, don’t worry about the examiner’s opinions or feelings.

Again, this fear comes from traditional school systems where students often have to agree with the teacher’s opinion and independent thought and critical thinking are discouraged. The opposite is true with the IELTS test.

3. Some testing centres are easier than others

All testing centres have the same standards and mark you with the same criteria. You have the exact same chance as getting the score you deserve in each centre. IELTS examiners undergo a lot of training in order to give you the correct score. Examiners are also monitored by more senior examiners and their work is checked all the time.

IELTS is a standardised test and it is therefore the same in every centre around the world. This is one of the main reasons that IELTS is accepted by the world’s top universities. If it was not reliable and standardised, no one would accept it.

4. Some examiners are more generous than others

This is not true for the same reasons as the previous point. If an examiner was being overly generous or overly strict they would soon lose their jobs. The determining factor is you, not the examiner or the centre.

Many students have complained to me that they didn’t get a very high score because the examiner was unfriendly or didn’t like them personally. It is not the examiner’s job to be your friend; it is to give you an accurate score. They should be friendly, but if they are not constantly smiling at you it is because they are concentrating on what they are doing, not because they dislike you.

5. I can learn some tricks to ‘cheat’ the exam

Many schools and websites claim to be able to guarantee you a high band score by teaching you ways to ‘cheat’ the exam. This is very misleading and these companies are more concerned about taking your money than getting you a high score. If you see something like this, be very careful.

There are schools and websites (like this one) that offer great advice but there are no ways to cheat the exam. Only go to a school that has a good reputation or has been recommended by a friend.

6. I should just study IELTS to get a high score

This is probably the biggest mistake students make. Learning about the IELTS test and practicing is very important, but your general English ability is more important. If you are not getting the score you need, you probably need to improve your general English first before doing the test again.

I always advise my students to work on their general English first before starting to prepare for the IELTS test. After your general English is at the required level, you can improve your test skills and learn about the test.

Generally, students would need to complete around 200 hours of guided study to improve by one band score, although there are always exceptional students who can do it much quicker. See Cambridge English support site for more information on this.

7. I should learn lots of big words and insert them into my writing test

It is very obvious to an IELTS examiner when students insert ‘complex’ words into their writing because they think this will impress the examiner. If you do this it looks unnatural and your coherence and cohesion suffers. You obviously need to display a wide range of vocabulary but you should do this appropriately. Learning a list of words and then dropping them into your essay, without really thinking about the meaning, will cause you big problems.

If you are not 100% sure about a word don’t use it. You should be aware of not only the meaning of the word, but also its form, collocations and synonyms.

8. I can’t ask the examiner in the Speaking test to repeat the question

The Speaking test is not a listening test and it is perfectly acceptable to ask the examiner to repeat the question. Even native speakers have to ask each other to repeat themselves from time to time. You can also ask the examiner to explain the meaning of a word but only one word per question. Don’t abuse this privilege; only use it when you need to.

I once had a student who had an examiner with a Scottish accent and she found it very difficult to understand her. She had never heard someone from Scotland speak before and it really put her off. Instead of asking the examiner to repeat the question she said nothing. Don’t do this in the exam.

9. I need to have a British or American accent to do well in the Speaking test

Students without British or American accents get 9 in the speaking test every day.

When students ask me about how to speak with a British accent I ask them ‘Which one?’ There are hundreds of British accents and none of them will really help you in the Speaking test.

It is not about which accent you have, but how easy you are to understand. It is about having clear speech and using a range of pronunciation features such as, sentence stress, weak sounds, linking sounds and intonation. Focus your efforts on these, not sounding like the Queen of England.

10. It is better to have a wide range of grammatical structures than be error free

In the writing test you will be judged on two things when it comes to grammar:

• ability to use a wide range of structures
• ability to write error-free sentences.

The problem is that the wider the range of structures you use the more likely you are to make errors. Paradoxically, by staying safe and using only structures you feel very comfortable with, you reduce the amount of structures you use.

In my opinion, it is better to use grammar you are comfortable using and reduce the amount of mistakes you make, rather than trying to insert a wide variety of tenses and structures. Errors will bring your score down much more than lack of complex grammar structures. If you focus on all the other areas of the exam, complex sentences, such as conditional and subordinate clauses will come naturally.