Scientists are combining biochemistry and knot theory, a branch of mathematics, to understand how cells read the tangle of DNA in their central nuclei.
Scientists are combining biochemistry and knot theory, a branch of mathematics, to understand how cells read the tangle of DNA in their central nuclei.

Nature's knotty problem



Knots have been a source of annoyance since at least 333 BCE, when Alexander the Great was confronted by the fabled Gordian Knot during his campaign in Asia Minor. Now they are becoming a focus of fascination among scientists trying to unravel the secrets of life. New research suggests nature discovered the benefits of knowing how to handle knots long before mariners and mountaineers. That's because some of the most basic elements of life are stringy - and thus perfect knot-forming material.

One of the most remarkable scientific facts is that virtually every cell in our bodies contains over a metre of the genetic molecule DNA. Crammed into the central nucleus, its stringlike double helix structure would seem a dead cert for ending up in an unholy tangle, and in 1976 scientists discovered the all too predictable result: knots. Predictable, perhaps - but also perplexing, as the very processes of life depend on cells being able to "read" the genetic sequences strung along DNA. A single mistake can result in potentially fatal diseases, including cancer. But if the instructions are wrapped up in knots, how can a cell read them reliably?

In the search for answers, researchers had to breach academic boundaries and combine biochemistry with knot theory, the branch of mathematics with the tools for making sense of the chaos inside cells. They were rewarded by uncovering one of the most impressive examples of the power of evolution. Over millions of years, cells have developed a set of special enzymes which do for DNA what Alexander the Great did for the knot at Gordium - but with a lot more subtlety. Known as topoisomerases, they are able to home in on the tangles of DNA in cells, break the molecule at precisely the right places, remove any knots or twists, and then put the whole thing back together again.

By allowing DNA to be read properly, these molecular-sized Alexanders are vital to health and well-being. The flip-side of the discovery has proved no less important, by opening up new ways of combating disease. Drugs companies have exploited the critical function of topoisomerases to develop antibiotics such as Ciprofloxacin, which interferes with the ability of bacteria to sort out their own DNA, thus killing them and stopping infection from spreading.

Some new anti-cancer treatments are based on the same idea, and interfere with the notoriously uncontrolled proliferation of cancer cells. Last year GlaxoSmithKline won approval for the use of a topoisomerase inhibitor called Hycamtin for use in treating ovarian and lung cancer. The US National Cancer Institute has another, batracylin, undergoing clinical trials for treating patients with tumours that have spread around their bodies.

Meanwhile, researchers are still uncovering new ways in which nature has equipped cells to deal with the nuisance of knots. While DNA uses topoisomerases to rid itself of unwanted knots, the wonder is that the molecule is not riddled with the things. After all, the risk of stringy objects ending up knotted grows rapidly with length - as we all know from everyday experience (though it took mathematicians until 1988 to actually prove it).

So why is the long, thin DNA molecule relatively free of them? Last July, a team led by Professor Andrzej Stasiak of the Centre for Integrative Genomics at the University of Lausanne, Switzerland, came up with some answers after using computers to simulate how DNA is stored in cells. Molecular biologists have long known that DNA is "supercoiled" into special twisted shapes, which helps cram more of the molecule into cells. In another example of nature's ingenuity, the supercoiling is performed by DNA gyrase, an enzyme that first forms a loop out of the DNA, cuts into it and passes one part over another, introducing twists which force the DNA into braid-like patterns. According to the simulations by Prof Stasiak and his colleagues, these braids are at much lower risk of forming knots - suggesting that supercoiling is about more than just cramming a lot of DNA into a very small space.

While knots are anathema for DNA, new research suggests they are positively welcomed by some of those other molecules vital for life, proteins. Constructed by cells according to the genetic instructions of DNA, proteins emerge from dedicated "factories" as strings of amino acids, which then curl up into complex shapes that dictate what the protein will do. And some proteins end up with a knot buried deep inside.

The discovery of these knots, announced in 2000 by Dr William Taylor of the National Institute for Medical Research in London, surprised many. What purpose do they serve, and how are they created? Unlike everyday knots, they can't be the result of blind chance: shape is crucial to the function of proteins, so the knots must be formed with as much care as DNA takes in ridding itself of the things.

Some light has now been cast on the process by Dr Anna Mallam and her colleagues at the University of Cambridge, in experiments with a protein made by a bacterium which ends up with a simple overhand knot trapped inside. The results, published last week in the Proceedings of the National Academy of Sciences, suggest the knot is made as the bacterium forms the chain of amino acids, which form a loop and thread through themselves before the whole protein curls up into its final shape.

This still leaves the question of why some proteins bother to perform such intricate manoeuvres. Like DNA, most proteins seem keen to avoid knots, but some clearly derive benefit from them; one suggestion is that it makes them stronger. The short answer is no one knows - and finding out looks set to keep scientists tied up for some while yet. Robert Matthews is Visiting Reader in Science at Aston University,

Birmingham, England

Greatest of All Time
Starring: Vijay, Sneha, Prashanth, Prabhu Deva, Mohan
Director: Venkat Prabhu
Rating: 2/5
Auron Mein Kahan Dum Tha

Starring: Ajay Devgn, Tabu, Shantanu Maheshwari, Jimmy Shergill, Saiee Manjrekar

Director: Neeraj Pandey

Rating: 2.5/5

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Stuck in a job without a pay rise? Here's what to do

Chris Greaves, the managing director of Hays Gulf Region, says those without a pay rise for an extended period must start asking questions – both of themselves and their employer.

“First, are they happy with that or do they want more?” he says. “Job-seeking is a time-consuming, frustrating and long-winded affair so are they prepared to put themselves through that rigmarole? Before they consider that, they must ask their employer what is happening.”

Most employees bring up pay rise queries at their annual performance appraisal and find out what the company has in store for them from a career perspective.

Those with no formal appraisal system, Mr Greaves says, should ask HR or their line manager for an assessment.

“You want to find out how they value your contribution and where your job could go,” he says. “You’ve got to be brave enough to ask some questions and if you don’t like the answers then you have to develop a strategy or change jobs if you are prepared to go through the job-seeking process.”

For those that do reach the salary negotiation with their current employer, Mr Greaves says there is no point in asking for less than 5 per cent.

“However, this can only really have any chance of success if you can identify where you add value to the business (preferably you can put a monetary value on it), or you can point to a sustained contribution above the call of duty or to other achievements you think your employer will value.”

 

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Who is Ramon Tribulietx?

Born in Spain, Tribulietx took sole charge of Auckland in 2010 and has gone on to lead the club to 14 trophies, including seven successive Oceania Champions League crowns. Has been tipped for the vacant New Zealand national team job following Anthony Hudson's resignation last month. Had previously been considered for the role. 

ENGLAND SQUAD

Team: 15 Mike Brown, 14 Anthony Watson, 13 Ben Te'o, 12 Owen Farrell, 11 Jonny May, 10 George Ford, 9 Ben Youngs, 1 Mako Vunipola, 2 Dylan Hartley, 3 Dan Cole, 4 Joe Launchbury, 5 Maro Itoje, 6 Courtney Lawes, 7 Chris Robshaw, 8 Sam Simmonds

Replacements 16 Jamie George, 17 Alec Hepburn, 18 Harry Williams, 19 George Kruis, 20 Sam Underhill, 21 Danny Care, 22 Jonathan Joseph, 23 Jack Nowell

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%3Cp%3EThe%20Royal%20Navy%20raid%20is%20the%20latest%20in%20a%20series%20of%20successful%20interceptions%20of%20drugs%20and%20arms%20in%20the%20Gulf%3C%2Fp%3E%0A%3Cp%3E%3Cstrong%3EMay%2011%3A%20%3C%2Fstrong%3EUS%20coastguard%20recovers%20%2480%20million%20heroin%20haul%20from%20fishing%20vessel%20in%20Gulf%20of%20Oman%3C%2Fp%3E%0A%3Cp%3E%3Cstrong%3EMay%208%3A%3C%2Fstrong%3E%20US%20coastguard%20vessel%20USCGC%20Glen%20Harris%20seizes%20heroin%20and%20meth%20worth%20more%20than%20%2430%20million%20from%20a%20fishing%20boat%3C%2Fp%3E%0A%3Cp%3E%3Cstrong%3EMarch%202%3A%3C%2Fstrong%3E%20Anti-tank%20guided%20missiles%20and%20missile%20components%20seized%20by%20HMS%20Lancaster%20from%20a%20small%20boat%20travelling%20from%20Iran%3C%2Fp%3E%0A%3Cp%3E%3Cstrong%3EOctober%209%2C%202022%3A%20%3C%2Fstrong%3ERoyal%20Navy%20frigate%20HMS%20Montrose%20recovers%20drugs%20worth%20%2417.8%20million%20from%20a%20dhow%20in%20Arabian%20Sea%3C%2Fp%3E%0A%3Cp%3E%3Cstrong%3ESeptember%2027%2C%202022%3A%3C%2Fstrong%3E%20US%20Naval%20Forces%20Central%20Command%20reports%20a%20find%20of%202.4%20tonnes%20of%20heroin%20on%20board%20fishing%20boat%20in%20Gulf%20of%20Oman%C2%A0%3C%2Fp%3E%0A
UAE currency: the story behind the money in your pockets
UAE currency: the story behind the money in your pockets
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RACE RESULTS

1. Valtteri Bottas (FIN/Mercedes) 1hr 21min 48.527sec
2. Sebastian Vettel (GER/Ferrari) at 0.658sec
3. Daniel Ricciardo (AUS/Red Bull) 6.012 
4. Lewis Hamilton (GBR/Mercedes) 7.430
5. Kimi Räikkönen (FIN/Ferrari) 20.370
6. Romain Grosjean (FRA/Haas) 1:13.160
7. Sergio Pérez (MEX/Force India) 1 lap
8. Esteban Ocon (FRA/Force India) 1 lap
9. Felipe Massa (BRA/Williams) 1 lap
10. Lance Stroll (CAN/Williams) 1 lap
11. Jolyon Palmer (GBR/Renault) 1 lap
12. Stoffel Vandoorne (BEL/McLaren) 1 lap
13. Nico Hülkenberg (GER/Renault) 1 lap
14. Pascal Wehrlein (GER/Sauber) 1 lap
15. Marcus Ericsson (SWE/Sauber) 2 laps
16. Daniil Kvyat (RUS/Toro Rosso) 3 laps

The specs

Price, base: Dh228,000 / Dh232,000 (est)
Engine: 5.7-litre Hemi V8
Transmission: Eight-speed automatic
Power: 395hp @ 5,600rpm
Torque: 552Nm
Fuel economy, combined: 12.5L / 100km

How to protect yourself when air quality drops

Install an air filter in your home.

Close your windows and turn on the AC.

Shower or bath after being outside.

Wear a face mask.

Stay indoors when conditions are particularly poor.

If driving, turn your engine off when stationary.

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Our legal consultant

Name: Hassan Mohsen Elhais

Position: legal consultant with Al Rowaad Advocates and Legal Consultants

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TRAP

Starring: Josh Hartnett, Saleka Shyamalan, Ariel Donaghue

Director: M Night Shyamalan

Rating: 3/5

The specs

Engine: 1.5-litre 4-cyl turbo

Power: 194hp at 5,600rpm

Torque: 275Nm from 2,000-4,000rpm

Transmission: 6-speed auto

Price: from Dh155,000

On sale: now

Race 3

Produced: Salman Khan Films and Tips Films
Director: Remo D’Souza
Cast: Salman Khan, Anil Kapoor, Jacqueline Fernandez, Bobby Deol, Daisy Shah, Saqib Salem
Rating: 2.5 stars

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if you go

The flights
Emirates flies to Delhi with fares starting from around Dh760 return, while Etihad fares cost about Dh783 return. From Delhi, there are connecting flights to Lucknow. 
Where to stay
It is advisable to stay in Lucknow and make a day trip to Kannauj. A stay at the Lebua Lucknow hotel, a traditional Lucknowi mansion, is recommended. Prices start from Dh300 per night (excluding taxes). 

The bio

Favourite vegetable: Broccoli

Favourite food: Seafood

Favourite thing to cook: Duck l'orange

Favourite book: Give and Take by Adam Grant, one of his professors at University of Pennsylvania

Favourite place to travel: Home in Kuwait.

Favourite place in the UAE: Al Qudra lakes

Conservative MPs who have publicly revealed sending letters of no confidence
  1. Steve Baker
  2. Peter Bone
  3. Ben Bradley
  4. Andrew Bridgen
  5. Maria Caulfield​​​​​​​
  6. Simon Clarke 
  7. Philip Davies
  8. Nadine Dorries​​​​​​​
  9. James Duddridge​​​​​​​
  10. Mark Francois 
  11. Chris Green
  12. Adam Holloway
  13. Andrea Jenkyns
  14. Anne-Marie Morris
  15. Sheryll Murray
  16. Jacob Rees-Mogg
  17. Laurence Robertson
  18. Lee Rowley
  19. Henry Smith
  20. Martin Vickers 
  21. John Whittingdale
Timeline

1947
Ferrari’s road-car company is formed and its first badged car, the 125 S, rolls off the assembly line

1962
250 GTO is unveiled

1969
Fiat becomes a Ferrari shareholder, acquiring 50 per cent of the company

1972
The Fiorano circuit, Ferrari’s racetrack for development and testing, opens

1976
First automatic Ferrari, the 400 Automatic, is made

1987
F40 launched

1988
Enzo Ferrari dies; Fiat expands its stake in the company to 90 per cent

2002
The Enzo model is announced

2010
Ferrari World opens in Abu Dhabi

2011
First four-wheel drive Ferrari, the FF, is unveiled

2013
LaFerrari, the first Ferrari hybrid, arrives

2014
Fiat Chrysler announces the split of Ferrari from the parent company

2015
Ferrari launches on Wall Street

2017
812 Superfast unveiled; Ferrari celebrates its 70th anniversary

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10 tips for entry-level job seekers
  • Have an up-to-date, professional LinkedIn profile. If you don’t have a LinkedIn account, set one up today. Avoid poor-quality profile pictures with distracting backgrounds. Include a professional summary and begin to grow your network.
  • Keep track of the job trends in your sector through the news. Apply for job alerts at your dream organisations and the types of jobs you want – LinkedIn uses AI to share similar relevant jobs based on your selections.
  • Double check that you’ve highlighted relevant skills on your resume and LinkedIn profile.
  • For most entry-level jobs, your resume will first be filtered by an applicant tracking system for keywords. Look closely at the description of the job you are applying for and mirror the language as much as possible (while being honest and accurate about your skills and experience).
  • Keep your CV professional and in a simple format – make sure you tailor your cover letter and application to the company and role.
  • Go online and look for details on job specifications for your target position. Make a list of skills required and set yourself some learning goals to tick off all the necessary skills one by one.
  • Don’t be afraid to reach outside your immediate friends and family to other acquaintances and let them know you are looking for new opportunities.
  • Make sure you’ve set your LinkedIn profile to signal that you are “open to opportunities”. Also be sure to use LinkedIn to search for people who are still actively hiring by searching for those that have the headline “I’m hiring” or “We’re hiring” in their profile.
  • Prepare for online interviews using mock interview tools. Even before landing interviews, it can be useful to start practising.
  • Be professional and patient. Always be professional with whoever you are interacting with throughout your search process, this will be remembered. You need to be patient, dedicated and not give up on your search. Candidates need to make sure they are following up appropriately for roles they have applied.

Arda Atalay, head of Mena private sector at LinkedIn Talent Solutions, Rudy Bier, managing partner of Kinetic Business Solutions and Ben Kinerman Daltrey, co-founder of KinFitz

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