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Category Archives: Transhuman News
Jordan Hogg: In 15 years, Ive never come across another disabled director – The Guardian
Posted: October 15, 2022 at 5:41 pm
Director Jordan Hogg, 39, was born in Scarborough and has cerebral palsy. He graduated in film studies from Hull University, trained through Channel 4s 4Talent scheme and won a Bafta breakthrough award in 2020. He has directed episodes of Shameless, Screw, Death in Paradise, Casualty, Coronation Street and Ackley Bridge. He is now the lead director on the new BBC One series Ralph & Katie, a spin-off from Peter Bowkers The A Word, and the first ever TV drama with two learning-disabled lead actors.
Whats Ralph & Katie about and how did you land the directing job?I was really jammy. I had a meeting with [creator] Peter Bowker to potentially direct The A Word episode with Ralph and Katies wedding but didnt get the gig. When I saw on Twitter that a spin-off about their first year of marriage had been green-lit, I emailed my agent and said it was my dream gig. Unbeknown to us, Peter had already remembered me and written it for me to direct.
Its the first time Ive helmed a whole series. My fingerprints are all over it, even the soundtrack. Im entirely unmusical but theres a scene in episode five where Ralphs marching along to the sound of me banging drums and blowing horns. John Williams will be shitting kittens.
Why was it such a dream project?Ive always wanted to make a show about people with disabilities where its about their everyday lives. Ralph and Katie face all the same obstacles that anyone does. If you have a disability, 99% of the time you dont even realise. Your disability isnt at the forefront of your mind, so it isnt in the drama either. Personally, I forget Im disabled until I approach some stairs or Ive walked too far and my knees kicking off. Sat here talking now, it doesnt even dawn on me.
Is the hope that viewers look beyond the labels?The idea is that you quickly forget theres disability in the show and it becomes about the characters. I want it to be judged as a relationship drama, not a disabled drama. Ralph and Katies disability is more of a thing for other people than them. Its how everybody else reacts to it and all the crossed wires. Ralphs mum, Louise, [played by Pooky Quesnel] panics because shes so protective. My mothers exactly the same. Whenever I have a medical issue, shes there like a whippet but certain things you dont want to share with your mum [laughs].
What adjustments were made for lead actors Leon Harrop and Sarah Gordy, who both live with Downs syndrome?Nobodys even attempted this before, so we were adapting on the hoof. We had a wonderful woman called Jess Mabel Jones who was our creative coach effectively an interpreter for Leon and Sarah to help us find emotions. Shed come up with images and smells that they could associate with each storyline, to get in the right headspace. She used a rehearsal technique called mirroring, where shed perform a scene, then theyd do it back to her. At the end of each day, we did de-roleing to come out of character and back into the real world.
And people with disabilities were represented behind the camera tooFive out of six of the writing team have disabilities, plus obviously me. And we sent out an edict that there must be a disabled trainee in every department. We wanted to pioneer a new way of working and change the world.
Didnt you also set new standards for inclusivity and accessibility on set?Rather than sweeping changes, we spoke to everyone individually about their needs, whether they identified as having a disability or not. Much of it was minimal things. People asked for easy-read scripts or bigger print on call sheets. This lad Turbold, who was the best boy, wanted us to put boy in inverted commas in the credits, to stress its not just a male role. We trialled an app to leave anonymous feedback at the end of each day. The TV industry is weirdly set in its ways but we wanted to buck the trend. What we put in place wasnt expensive at all. All it takes is the desire to do it.
Do you hope those working practices become widely adopted?One hundred percent. The whole idea was to demonstrate whats possible and how other productions can be more welcoming. It benefits everybody. You get a much more productive shoot if individual needs are considered and everyones happy.
How far can Sarah and Leon go as actors?A long way. Sarah gets immersed in her roles and feels it deeply. And, hand on heart, Leon is one of the top three actors Ive ever worked with. His timing, instincts and listening qualities are off the chart. Hes always wanted to be a leading man and is so proud. Hes got loads of ideas for season two, mostly involving me being the bad guy and him running me over in various large vehicles (laughs).
How would you respond to potential criticism of the show as politically correct box-ticking?Well, Im a Yorkshireman, so theyd better not cross me. Just watch the show. Youll see its very politically incorrect at times. Its not woke or PC, its representative of society. Everyone has their story to tell, so why cant we tell ours?
Is the TV and film industry improving in terms of disability representation?Its getting there but too slowly. Its the most underrepresented demographic by far on both sides of the camera. In 15 years, Ive never come across another disabled director. An LA charity told me the other day that in high-end US drama, they know of five disabled writers and one disabled director. Thats in the whole of America. Weve done it on one show.
What were your childhood ambitions?Ive wanted to be a director since I was 12. My parents were getting a messy divorce and I vividly remember them having a row in the next room when Lawrence of Arabia came on telly. David Lean transported me to the desert for three hours. It was proper magic. I thought, if I can do this for one person someday, it would be amazing. But I was a kid with cerebral palsy from Scarborough and this life seemed so far away.
When I left school in 1999, there was no internet. I had no idea what opportunities were available. Instead, I did what any disabled kid does and became a fitness instructor! After doing that for four years, I went back to university to study film, learned all I could and worked my way up. Ive been massively fortunate to blag it this far.
Youve moved back to your home town of Scarborough. What drew you back?I settled in Manchester when I got my first job on Shameless. Me, my wife and son moved back to be by the seaside and near family. Its a nice place for Teddy, our little boy, to grow up. His Yorkshire accent is even heavier than mine. When I speak to Americans, I say: Remember that pub at the start of An American Werewolf in London? Its like that around here. But its home. I can open my patio doors and hear nothing but the sea.
How do you unwind when youre not working?I follow Newcastle United and love wrestling. I think its the purest form of storytelling. I listen to Johnny Cash, Thin Lizzy and the Eagles, and Im a massive Disney geek.
Whats the next project in the pipeline?Im directing a Channel 5 miniseries called Blind Spot. A four-part drama, kind of Rear Window meets The Conversation, which were filming in Budapest over Christmas. After that, who knows? I just got a US agent and the dream is to take our Ralph & Katie model across the pond.
If the government let you make one policy change tomorrow, what would it be?There should be a minimum quota of disabled people working in every industry. Because 18% of the population has a disability, 18% of your staff should. Disabled people always find easier ways to do things because we have to. Employers are missing out. Our lived experience and ingenuity is an untapped goldmine.
Ralph & Katie airs Wednesdays at 9pm on BBC One. The entire series is available as an iPlayer box set
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Jordan Hogg: In 15 years, Ive never come across another disabled director - The Guardian
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The phenomenon of ‘Hawa’ vs ‘Poran’ – Dhaka Tribune
Posted: at 5:41 pm
Eid Ul Azha 2022 saw the release of three Bangladeshi films- Ananta Jalils Din: The Day, Raihan Rafis Poran, and Anonno Mamuns Psycho. Despite having a stellar cast (Pujja Cherry, Shahiduzzaman Selim, Rosey Siddiqui etc), Psycho didnt fare well in the box office. As for Din: The Day, people regretted that it wasnt as comical as AJs previous films. Mejbaur Rahman Sumons Hawa entered the scene almost three weeks after Eid. Some people at the cineplexes were torn between watching Hawa or Poran, Chris Hemsworths chiseled body in Thor and Brad Pitts swag in Bullet Train escaping their notice entirely.
This may very well mark the beginning of a new era where the story, not the celebrities, is the star of the film. It was more about what, rather than who, they were there to watch. People had to wait for hours to get tickets for either of these films because of the houseful situation at the cineplexes that seat much fewer audiences than larger local halls (Usually a film doesnt have houseful shows this late into its release, but Poran did). I went to one such local hall, Sainik Club in the capital, to watch Poran on its fourth week and to Bashundhara City to watch Hawa on its debut week. The first had about 15 people in the theatre with no wait time, the latter kept me waiting for four hours in the afternoon on a weekday.
Both films are massive box office successes catering to audiences of conflicting tastes. Poran is on firmer grounds in this regard because its target audiences were oblivious to the glaring misogyny and overall unfortunate craftsmanship of the film. When I interviewed the audiences after the film ended, they all had good things to say including making bhalo chhilo (which was impossible to determine with the faulty projection on the ghola screen), just wow, and meyeta bodmaish (that just might be what the film had set out to prove in the first place. The men are killing each other, but please go ahead and blame the girl for dating two guys at once because that is worse than murder apparently).
Sadly, for Hawa, its audiences-cum-critics are the film buffs, people who spend a considerable portion of their lives watching/analyzing world films. This crowd is nearly impossible to please. So, while the mass is praising the politically incorrect Poran, the educated crowd is split in half about Hawa. All the festivals and film appreciation courses in world couldnt prepare us for acknowledging an artistic films mainstream success.
Hawas audiences are like its two promotional songs. Theres the mass (Shada Shada Kala Kala) and theres the contemplative connoisseurs (E Hawa). Whether we give it credit for setting a higher bar for local films, anyone can commend its effective marketing. Some may say its a tad too aggressive, especially when it is not a plot-heavy film, the kind the mass audience have grown accustomed to.
In the film, a snake charmer (Nazifa Tushi) is caught on the fish net of Chan Majhis (Chanchal Chowdhury) boat. The seamen lust over her as they meet their untimely demise one by one under mysterious circumstances. Thats about the extent of kahini in this film.
I cant responsibly point out how Hawa could be a bigger hit, without mentioning what scares me about Poran being such a massive blockbuster. The fact that its misogynistic sentiments are lost on our people is worrying. If it wasnt loosely based on a true story, I would conclude the writers never met a female specimen of their species in the entirety of their lives, prompting them to conjure up such characters.
Roman (Sariful Razz) is the go to mastan of a corrupt politician. His relationship with struggling college student Ananya (Bidya Sinha Mim) escalates from eve teasing to sexual abuse to a loving couple without a logical progression. One minute he attempts to break her jaw on a secluded street, the next he is her boyfriend (insert surprised GIF). Those of us who forgot to check our brains at the door will suffer throughout the 2hour 19mins, for the film is riddled with such contradictions. Ananya turns out to be a bully herself, using her brute of a boyfriend to threaten classmates and teachers to help her cheat on exams. He even helps her get close to her other love interest, Sifat (Yash Rohan), under the impression that Ananya needs the reluctant nerd to tutor her. Ananya, while still in a relationship with Roman, pressures Sifat to marry her. Although the two have zero chemistry, he caves (insert said GIF again). I can go on all day pointing out whats wrong with this film, but if you get it, you get it already.
However the films may be, Hawa and Poran pulled audiences into theatres, the way Marvel movies used to before they lost their sheen. If the Netflix top 10 movie list is any indication, then its safe to comment we have a preference towards films closer to our culture. Yet every Bangladeshi film last year suffered in the box office competing with Hollywood films. Shimu was released at the same time as Batman. Lal Moroger Jhuti, Nona Joler Kabbo, Chandraboti Kotha- all shared the same fate. What brought the audiences in large flocks this time around? The entertainment factor. Its like the crowd had been singing the chorus of Smells Like Teen Spirit all along, but we were busy collecting accolades, riding our high horses, reaching a grandiose technical finesse for our ever so ghola screens.
Sadia Khalid Reeti is a film critic/screenwriter and is the Showtime Editor of Dhaka Tribune
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SMOKERS’ CORNER: THE RESURGENCE OF THE FAR-RIGHT – Newspaper – DAWN.COM – DAWN.com
Posted: at 5:41 pm
Illustration by Abro
The 2010s witnessed a surge in the electoral fortunes of far-right parties in Europe. Most of these parties were once languishing on the fringes of mainstream politics. But in the past decade, many of them have greatly surpassed their previous electoral performance.
Recently, the far-right Brothers of Italy won a majority in general elections in Italy. The party is likely to form the new government. It will become the third far-right regime elected in Europe since 2010. The other two are in Hungary and Poland.
In April 2022, the presidential candidate of the far-right National Front in France bagged an impressive 41.45 percent of the total vote. In the September 2022 parliamentary elections in Sweden, the far-right Sweden Democrats won the second largest number of seats.
A change of tactics by far-right parties in Europe helped them break out from the fringes. Adopting populism was the tactic. Populism is often understood as a thin ideology. It borrows ideas from the more established ideologies of the left and the right to concoct alarming narratives. Such narratives portray a party as being the voice of the people.
The surge in far-right electoral fortunes in the 2010s was largely associated with the surge in the appeal of dedicated far-right parties. In some cases, however, its more moderate parties that have opportunistically veered towards far-right rhetoric
A populist poses as a warrior fighting against the corrupt, complacent and conniving elites. Populism enhances the threat of a crisis, warning of an impending breakdown.
European far-right groups increasingly began to style their politics in a populist manner. Their mission is to safeguard their regions Christian heritage, keep out immigrants and, of course, challenge the elites. They explain globalisation, multiculturalism and liberalism as attacks on the common (Caucasian) natives of Europe who, apparently, are being replaced by non-European races. But the surge in the electoral fortunes of far-right politics is not only associated with dedicated far-right parties.
In the US and, to a certain extent, in the UK, right-wing populist figures were able to infiltrate mainstream centre-right parties and push them further to the right. It is a curious case of entryism because the roots of entryism lie in the far-left tendencies of Marxism, such as Trotskyism.
In the early 1930s, the Marxist ideologue Leon Trotsky advised communists to dissolve their limited communist groups and infiltrate mainstream parties to change their ideological orientation. Entryism became a common communist tactic. But, as it became better known, many far-right groups started to practise it as well, infiltrating moderate right-wing parties in a bid to make them adopt far-right ideas.
For example, Donald Trump in the US was a political maverick who decided to contest Republican Party primaries for the 2016 presidential elections. To distinguish himself from the partys other hopefuls, Trump tapped into far-right emotions and narratives. This excited Republican Party supporters who had for long grumbled about the partys lukewarm stands on matters of race, religion and immigration. They saw in Trump a man who was willing to transcend the established conventions of old-style conservatism and blurt out populist takes on various issues, no matter how politically incorrect the takes were. He won.
Four years later, he failed to win a second term. But he was successful in radically refashioning the ideological orientation of the Republican Party, which now leans a lot more to the right. The same was the case with the UKs Conservative Party, when the eccentric populist Boris Johnson was able to push it towards becoming a more animated right-wing outfit.
In India, before Narendra Modi became prime minister, the mainstream Hindu nationalist Bharatiya Janata Party (BJP) had begun to distance itself from its far-right roots. Modi, a man who was still politically and emotionally attached to BJPs roots, has restored BJPs far-right/xenophobic demeanour.
Nevertheless, the surge in far-right electoral fortunes in the 2010s was largely associated with the surge in the appeal of dedicated far-right parties. Brazils Partido Social Liberal (PSL) is a non-European example and, to a certain extent, so is Pakistan Tehreek-i-Insaf (PTI). Yet, whereas PTI cannot be placed in the column of dedicated far-right parties, it can be compared with Hungarys ruling Fidesz party.
Fidesz emerged in 1988 as a centre-left outfit. It then began to move more to the centre. Unable to gain much electoral traction, it again shifted, but this time to the right. The party was able to somewhat increase its vote-bank in 1998. In the early 2000s, it was rocked by scandals, but the party decided to overcome this by forming an alliance with the right-wing Christian Democratic Peoples Party.
When issues such as immigration, globalisation, multiculturalism and the rise of Islamism surfaced across Europe, Fidesz found itself in an advantageous position to capitalise on these fears. The party took a populist turn by enhancing these fears and questioning liberalisms ability to safeguard Hungarys national identity and Christian heritage. It went on to win multiple elections between 2010 and 2022. It effectively turned Hungary into a conservative authoritarian state.
PTI was formed in 1995 as a centrist party. Some of its founders maintain that it was originally conceived as a left-wing outfit. They say, had this not been the case, the late Marxist Meraj Muhammad Khan would not have joined it in 1998. PTI remained on the fringes across the early 2000s, even though it began to shift to the right. This was mainly because of the influence of the mainstream Islamist party the Jamaat-i-Islami (JI), which PTIs chairman Imran Khan became an admirer of.
From 2007 onwards, Pakistans economy began to nosedive and Islamist violence grew manifold. Political turmoil saw the Musharraf dictatorship ousted in 2008 and the return of the countrys two main parties, the centre-right Pakistan Muslim League-Nawaz (PML-N) and the centre-left Pakistan Peoples Party (PPP). As Islamist violence escalated and the economy continued to decline, the military establishment aided PTI to fill what it claimed was a void.
The establishments reputation was scarred during Musharrafs later years when his double game of attacking one segment of extremists but nourishing others, began to trigger unprecedented Islamist violence. Khan and his PTI were propped to divert the attention away from the establishment towards the two mainstream parties. PTI turned populist and began to demonise PPP and PML-N. It then started to blame Islamist violence on the US.
By 2021, PTI (now as a ruling party) had increasingly adopted populism, bordering on the far-right. Despite being ousted in April 2022, PTIs slide into far-right territory has continued.
In Pakistans context, this means reinforcing Islamist points of view on various social issues, working towards gaining an electoral landslide so as to control all major centres of power in the country and establishing an authoritarian regime buttressed by engineered elections.
Published in Dawn, EOS, October 9th, 2022
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SMOKERS' CORNER: THE RESURGENCE OF THE FAR-RIGHT - Newspaper - DAWN.COM - DAWN.com
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Paddy Considine’s filmography: What were the House of the Dragon actor’s best works? – Bolavip
Posted: at 5:41 pm
The work Paddy Considine has been doing in his latest job has been making people talk. The 49-year-old actor is the one who gives life to Viserys Targaryen in the successful Game of Thrones spin-off, House of the Dragon. There are not many episodes left where his character is one of the main characters, due to the illness that the king possesses.
However, his work (along with that of Matt Smith) has been strongly praised by critics and audiences alike. It is rumored to be one of the favorites for upcoming awards shows, such as the Emmys. Episode 8 of HOTD has given a lot to talk about, especially for the heartbreaking moment played by Considine and Smith's characters.
With the actor's farewell with the cast, as has already happened with Milly Alcock and Emily Carey, it's time to review all the great performances of the figure. Here, check which were his best works and how to watch them on streaming.
1.Journeyman
After a decisive fight, boxer Matty Burton finds himself lying in the room. Weakened and struggling to remember things, he must give his all to recover and keep his family together.
Is not available to stream with a subscription service.
2.The Death of Stalin
On March 5, 1953, Iosif Stalin, General Secretary of the USSR, died in circumstances that have not yet been clarified. Over the course of two days, the power vacuum resulted in a fierce struggle for the succession. Among the contenders are Georgy Malenkov, the cunning Nikita Khrushchev and Lavrenti Beria, the sadistic head of the secret police.
Available on Amazon Prime Video.
3.The Girl with All the Gifts
In the future, a strange fungus has turned almost the entire population into insatiable zombies. A group of children immune to the effects of the virus are the only chance to save humanity. The children are sheltered in a military base located in a village in England, where they are studied in search of a cure. Melanie, one of the girls, stands out above the rest and causes the future of the human race to depend on her.
Available on Amazon Prime Video.
4.Macbeth
Protected by the deceitful prophecies of the Fateful Sisters, witches or goddesses of destiny, Macbeth decides to assassinate his king and take the crown. Aware of the horror to which he gives himself up, he forges his terrible destiny and allows himself to be possessed by the evil born of the lust for power, believing himself to be invincible and eternal.
Feature film adaptation of Shakespeares Scottish play about General Macbeth whose ambitious wife urges him to use wicked means in order to gain power of the throne over the sitting king, Duncan.
Available on HBO Max.
5.Miss You Already
Milly and Jess have been friends since they were little and have always shared everything. Although the two have grown up differently and have developed different lives, their friendship remains strong. However, this is put to the test when Milly is diagnosed with breast cancer. Milly needs her friend more than ever, but Jess must also face a drastic change in her life: she is pregnant.
Available onEPIX NOW.
6.Child 44
In 1953, Leo Demidov, an undercover Soviet police agent, loses his status, his power and his home when he refuses to denounce his own wife, Raisa, for treason. Exiled from Moscow to a shady provincial outpost, Leo and Raisa join forces with General Mikhail Nesterov in order to track down a serial child murderer.
Available on HBO Max.
7.The Suspicions of Mr Whicher: The Ties That Bind
A divorce case involving a landowner and his young wife spirals into something darker, drawing Whicher into the heart of the English countryside where he uncovers the most disturbing and destructive of secrets.
Available onBritBox via Amazon Prime Video.
8.The Suspicions of Mr Whicher: Beyond the Pale
Based on true events, The Suspicions of Mr Whicher tells the story of the Road Hill House murder, which took place in the summer of 1860 in the county of Wiltshire, United Kingdom. The Kent family home was the site of the abduction and murder of their youngest son, three-year-old Francis Saville Kent.
Available on Hoopla andBritBox via Amazon Prime Video.
9.Pride
Realizing that they have Margaret Thatcher, the police and the conservative press as their common enemies, London gays and lesbians band together to support striking coal miners in Wales in 1984.
Available on Amazon Prime Video.
10.The Double
Simon is a shy man who goes unnoticed at work, is despised by his mother and ignored by the woman of his dreams. The arrival of his new co-worker, James, will change his life radically. James, physically the same as him, but completely opposite in his way of being, will begin to supplant his identity.
Available on Amazon Prime Video.
11.The World's End
An immature 40-year-old man convinces his childhood friends to finish together a drinking marathon they started 20 years ago and never finished, but as they try to complete the feat, an unexpected threat emerges.
Available on HBO Max.
12.The Suspicions of Mr Whicher: Murder in Angel Lane
Whicher, a retired policeman meets Susan Spencer in a tavern. She is looking for her niece Mary, who has come all the way from London in search of her baby's father. But when Susan turns up dead and her baby is missing, Whicher offers his help in finding the killer.
Available on Hoopla and BritBox via Amazon Prime Video.
13.Now is Good
Tessa, a 17-year-old girl diagnosed with terminal cancer, makes it her mission to live her adolescence in fast motion. So, while her family faces fear and pain, she wants to enjoy every moment.
Available on Tubi.
14.Blitz
Blitz is a London serial killer who is killing police officers. Chief Inspector Roberts and Sergeant Brant, a tough, uncompromising and politically incorrect police detective, are tasked with trying to stop the psychopath.
Available on fuboTV.
15.The Suspicions of Mr Whicher
In 1860, Inspector Jack Whicher of Scotland Yard is sent to rural Wiltshire to investigate the murder of the three-year-old boy Saville Kent, who was snatched from his bed at night and murdered.
Available onHoopla and BritBox via Amazon Prime Video.
16.Submarine
A 15-year-old boy has two goals: to lose his virginity before his next birthday, and to keep his mother from leaving his father for a dance instructor.
Available on Tubi.
17.The Bourne Ultimatum
Jason Bourne continues his international quest to discover his true identity. From Russia to Europe, North Africa to the United States, Bourne must stay one step ahead of the people who want to capture or kill him before he has a chance to discover the truth.
Available on Peacock.
18.Cinderella Man
During the Great Depression, James J. Braddock, a retired boxer, decides to return to the ring in order to feed his family. He was not a talented boxer, but his courage, sacrifice and dignity took him to the top.
Available onSTARZ and Amazon Prime Video.
19.My Summer of Love
The affair of a rebellious young girlwith a worldly seductress affects her brother, a professing Christian.
Available on Amazon Prime Video.
20.24 Hour Party People
Manchester, 1976. The performance of the Sex Pistols in front of a capacity of 42 people changes the lives of Tony Wilson and his friends. From that night they formulate a plan that will change the face of pop music and bring notoriety to the whole city.
Available onFreevee,Kanopy, Tubi andHoopla.
21.In America
The Sullivans are an Irish family who emigrate to New York, where the father wants to pursue his dream of becoming an actor. The family lives in a ramshackle apartment in Manhattan, where they try to adapt to life in the new city. Despite the poor conditions in which they live, they all try to get by. However, the memory of Frankie, the son they lost, continues to haunt them.
Available onSTARZ and Amazon Prime Video.
1.House of the DragonAvailable on HBO Max.
2. The Outsider Available on HBO Max.
3. Peaky Blinders Available on Netflix.
4. Red Riding: In the Year of Our Lord 1980 Available on Amazon Prime Video.
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Word on the street: ‘Never heard of him’ – Aucklanders react to Brown mayoral win – Stuff
Posted: at 5:40 pm
Aucklanders were as glib and apathetic as their 30% voter turnout in reacting to Wayne Browns mayoral win on Sunday morning.
Brown won Aucklands mayoralty with 144,000 votes in the preliminary count, 55,000 ahead of main rival Efeso Collins. As of 3pm on Saturday, 355,000 votes were cast in a city of 1.1m eligible voters.
Auckland Transports (AT) chair has already resigned following Browns win, and the citys new boss wants to see more heads roll after calling for the entire AT board to go.
Browns strategy to victory was focusing on turning out the older than 50 homeowners with a simple message about fixing Auckland.
So, Stuff hit the streets of central Aucklands Karangahape Road, a Sunday market in the North Shores Takapuna, and high street in Onehunga to ask:
What do you think of Wayne Browns win?
Chris McKeen
Zena reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
I dont know, I havent heard anything, Im not sure. Im not sure who that is.
Chris McKeen
Amo reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
Hes a good man. Thats why I voted for him. He does well with the people.
Chris McKeen
Gregory reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
What party does he represent?
Chris McKeen
Jude reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
Someones got to win. Nothing I can do about it.
Chris McKeen
Fran reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
I was disappointed. I dont think we need old men. Weve got enough old men.
Chris McKeen
Bailey reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
I dont know. [Efeso Collins] was the only one I knew anything about.
Chris McKeen
Rusha reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
I would like to see public transport being looked at. I like the half prices for public transport at the moment theyre really, really good.
Chris McKeen
Rachel reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
Never heard of him... He doesnt represent me. Im a 40-year-old Mori woman. I dont think he represents me.
Chris McKeen
Steve reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
Its probably a politically incorrect thing to say, but the right person won.
Chris McKeen
Roimata reacted to the news that Wayne Brown had won the 2022 Tmaki Makaurau Auckland Mayoral election.
Im not too sure. I heard that he was also the mayor for the Far North.
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Word on the street: 'Never heard of him' - Aucklanders react to Brown mayoral win - Stuff
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Former Google CEO Issues Dire Warning About China – futurism.com
Posted: at 5:27 pm
A new report warns that China could soon be able to rule over the US economy and military using cutting edge tech a sign that the country is increasingly concerned about China's recent leaps in technological advancements.
The report was compiled,notably, by the think tank Special Competitive Studies Project (SCSP), which is chaired by former Google CEO Eric Schmidt.The report concluded that the US will have to catch up with China's advancements in tech or risk not only falling behind, but becoming subservient to China as well.
The tech titan's warnings are not falling on deaf ears. The White House is clearly taking the report's recommendations seriously.
"I dont need to tell you that advancements in science and technology are poised to define the geopolitical landscape of the 21st century," national security advisor Jake Sullivan said in prepared remarks, responding to the report's release. "They will generate game-changers in health and medicine, food security, and clean energy."
The report identifies three key "technology battlegrounds," including microelectronics, 5G connectivity, and artificial intelligence, which could "represent the next chapter of the industrial revolution."
China is already making major headway in expanding those technologies which could leave the US behind.
And that could have some disastrous consequences. In the worst case scenario, the report notes, China could take control over rare Earth minerals, which means that "Americas military is crippled, and the nation is plunged into a depression," and "Americans are forced to live in a world where China can turn off the technology tap."
As a result, "the United States and other democracies would become economically dependent, losing their engines of prosperity and freedom of action in the world," the report warns.
In short, the think tank argues that "there is ample reason for concern" about China winning the technology race.
But it's not game over for the US. The country can harness existing industries to build out "an advantage in critical technologies," the report concludes, while also investing to "bring technology hardware manufacturing back to the US."
According to the report, the US will have to act by the end of this decade to make sure China doesn't gain the upper hand a dire warning, representative of the emergence of a major power struggle between world powers.
What'll actually happen is anyone's guess. After all, China's already staring down the barrel of a precipitous population bomb that could wreak havoc on its economic ambitions. But the stakes,at least, are as clear as they've ever been.
READ MORE: Former Google CEO Eric Schmidt Warns China Could Cripple US Military, Economy [PCMag]
More on China: China is Leading the Next Revolution in Mobile Technology
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Researchers Say Microbes Assemble Into "Superorganisms" That Crawl Around Your Teeth – Futurism
Posted: at 5:27 pm
Image by Penn Dental Medicine
Researchers at the University of Pennsylvania School of Dental Medicine have accidentally discovered that bacteria and fungi can team up to form a mobile "superorganism" that will wreak havoc on your teeth, according to a new study published this month in the journal Proceedings of the National Academy of Sciences.
The researchers discovered these "interkingdom assemblages" while studying toddlers with severe tooth decay. A closer look revealed that the conjoined bacteria-fungi exhibited a greater resistance to antimicrobials, and in general were much more virulent.
What's worse is that these superorganisms are mobile and can "walk" something they couldn't do before joining forces in an assemblage.
"We noticed the bacteria and fungi forming these assemblages and developing motions we never thought they would possess: a 'walking-like' and 'leaping-like' mobility," said Hyun Koo, a co-corresponding author of the study and a professor at Penn Dental Medicine, in a press release.
"They have a lot of what we call 'emergent functions' that bring new benefits to this assemblage that they could not achieve on their own," he added. "It's almost like a new organism a superorganism with new functions."
According to the study, this emergent mobility is facilitated by small branches of fungal filaments called hyphae, that, as they extend and make contact with another surface, lift the whole assemblage up, carrying the bacteria with it.
The researchers posit that the assemblages gain their increased virulence, resilience, and mobility from their tight cohesion between cells and a strong,glue-like extracellular polymer formed as a result of the bacteria-fungi assembly.
Being both hard to kill and extremely mobile means that these superorganisms can quickly colonize your teeth and cause some pretty nasty tooth decay.
The researchers believe that studying how to target these assemblages could help prevent childhood tooth decay, which affects more than half of all six- to eight-year-old children in the United States, according to the Centers for Disease Control and Prevention.
"If you block this binding or disrupt the assemblage before it arrives on the tooth and causes damage, that could be a preventive strategy [against childhood cavities]," Koo suggested.
More on dental health: Lazy Flossers Rejoice! Tiny Robot Shapeshifters Will Brush and Floss for You
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Elon Musk Has Reportedly Been Telling Friends About Benefits of Shrooms and MDMA – Futurism
Posted: at 5:27 pm
Image by Getty Images/Futurism
It's no secret that Tesla CEO Elon Musk likes to let loose sometimes,in a respite between extremely long work days and an infamously packed schedule.
From lavish weekend-long parties to attending Burning Man, Musk has long been known to attend social gatherings of all kinds, as detailed in a recent New York Times feature.
And, perhaps unsurprisingly, recreational drug use is a topic that seems to come up a lot in his company.
According to the NYT, Musk likes to pass around a chartpurporting to explain why 3,4-Methylenedioxymethamphetamine (MDMA) and psilocybin mushrooms are healthier choices than alcohol.
As for taking these drugs himself, the richest man in the world seems to prefer playing it safe whatever that means in this context.
"I have been with him on mild exploratory journeys," David Marglin, a longtime friend of Musk's met him at Burning Man, told the NYT. "And he appreciates the value of those journeys."
"Nothing out of control or wild," he added, "but its all night, and theres dancing and revelry."
Then there was the time when musician Azealia Banks accused Musk of being on Twitter "while on acid" back in 2018, which Musk disputed.
However, Musk has long maintained that we should seriously consider the health benefits of these kinds of drugs.
"I think, generally, people should be open to psychedelics," Musk said during a 2021 interview. "A lot of people making laws are kind of from a different era, so I think, as the new generation gets into political power, I think we will see greater receptivity to the benefits of psychedelics."
Musk maintains that psychedelics may actually be better than commonly used drugs, such as selective serotonin reuptake inhibitors (SSRIs), which are often prescribed to treat depression.
In April, Musk tweeted that "Ive talked to many more people who were helped by psychedelicsand ketamine than SSRIsand amphetamines."
But that doesn't mean we should take him by his word after all, he's a business magnate, not a neuroscientist.
And it's worth noting that while psilocybin is generally seen as fairly safe by doctors, the same isn't necessarily true of MDMA, known for causing intense euphoria and sometimes brutal hangovers. It might not be a disaster to take it every once in a while, but it's widely established that abusing it frequently can lead to a wide range of neurological issues.
There certainly has been plenty of recent interest and a significant number of small studies by the scientific community to study the potential therapeutic use cases of psychedelic and other recreational drugs.
For instance, some studies have found that the psilocybin can improve the symptoms of depression. Scientists have also found that LSD-based drugs could also help with anxiety and depression.
The evidence, however, is still preliminary and many of these studies are still too small to draw any definitive conclusions.Methodologically, it's also impossible to establish a meaningful control group, because if someone starts tripping, it becomes pretty clear to them that they didn't take the placebo.
But Musk, for one, is a firm believer in their potential and he's willing to go out of his way to prove it to you.
READ MORE: Elon Musk Has the Worlds Strangest Social Calendar [The New York Times]
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Elon Musk Says He Has Not Been Talking to Putin, Thank You Very Much – Futurism
Posted: at 5:27 pm
Who's telling the truth here?He Said, He Said
After reports emerged that Elon Musk had allegedly been in contact with Russian president Vladimir Putin, the SpaceX and Tesla CEO smacked them down in classically Muskian fashion.
"I have spoken to Putin only once and that was about 18 months ago," Musk tweeted in response to the claims. "The subject matter was space."
This response runs counter to reports from analyst Ian Bremmer, the founder of the Eurasia Group political risk consultancy, who in a note to subscribers claimed that Musk had been speaking with the Russian president regarding the invasion of Ukraine, and that Putin was "prepared to negotiate" if Ukraine accepted the Russia's annexation demands.
Bremmer went on to say in the note, which was viewed byVice,Bloomberg, and other news outlets, that he'd discussed the purported peace talks with Musk a few weeks prior and that the Russian demands were mirrored by the billionaire's now-infamous Twitter poll in which he asked his followers whether Ukraine should give in to specific Russian demands.
That poll, while wildly unpopular in the West, was apparently viewed favorably by the Kremlin, with officials cracking jokes that seemed to denote a sort of backhanded affection for Musk.
"I wasnt planning on writing about this," Bremmer wrote in the subscriber note, adding that "it feels important to write about whats happening."
In response to yet another tweet in the thread, Musk went on to say that it would be "pointless" for him to speak with Putin, given that "there is currently no overlap between Russian and Ukrainian demands."
While it's now unclear which figure is lying, it should be noted that Musk has heretofore seemed pretty supportive of Ukraine amid its invasion from its large and powerful neighbor, and even was reported to have spoken with Ukrainian president Volodymyr Zelensky in March of this year.
More Elon-ism:Professor of Engineering Issues Brutal Dig at Elon Musk, Sparking Backlash
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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians – Nature.com
Posted: at 5:22 pm
Subject recruitment
Subjects for this cross-sectional study were recruited based on recall from a community-based multi-ethnic prospective cohort27 that is part of the Singapore Population Health Studies project (SPHS -formerly Singapore Consortium of Cohort Studies). This subset included 109 subjects who were 48 to 76 years old with 65 males and 44 females (Supplementary Data1). Subjects in SPHS were recruited to participate in the National Health Survey, where subjects were selected at random using age- and gender- stratified sampling to obtain a representative sample set of residents in the country. During the period of recruitment from April 16th, 2008 to September 20th, 2018, subjects did not have any pre-existing major health conditions (cardiovascular disease, mental illness, diabetes, stroke, renal failure, hypertension and cancer) based on self-reporting27. The ethnicity of each subject was confirmed verbally so that all four grandparents of the subject belonged to the same ethnic group. As such, we do not anticipate that any self-selection bias was introduced. A separate comparison of baseline clinical measurements was performed, including age-adjusted BMI and HbA1c, against the rest of the subjects in the larger ethnicity-specific cohorts within Singapore Population Health Studies to ensure that the sampling for the initial cohort conformed to population norms. Informed consent was obtained from all participants. Each subject was given 60 Singapore Dollars for their participation in this study. All associated protocols for this study were approved by the National University of Singapore Institutional Review Board (IRB reference number H-17-026) on May 9th, 2017 and renewed until May 31st, 2021.
Fecal samples were collected from healthy subjects using the BioCollectorTM kit (The BioCollective, Colorado, USA). Samples were double-bagged and transferred to a polystyrene box, together with a pre-chilled ice-pack (20C). The polystyrene box was transferred to a cardboard box and later collected from the participants home within the same day. Samples brought to the Temasek Life Sciences laboratory were stored into an anaerobic chamber (atmosphere of N2 (75%), CO2 (20%), and H2 (5%)). Fecal samples were homogenized and subsamples transferred into sterile 2mL centrifuge tubes.
Genomic DNA was extracted from fecal material (0.25g wet weight) using the QIAamp Power Fecal Pro DNA kit (QIAGEN GmbH, Cat. No. 51804) and was quantified using Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific, Cat. No. Q32853). Integrity of the extracted DNA was verified using 0.5% agarose gel electrophoresis.
Metagenomic libraries were prepared with a standard DNA input of 50ng across all samples, using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, Cat. No. E7805), according to the manufacturers instructions. The reaction volumes were, however, scaled to a quarter of the recommended volumes for cost effectiveness. Barcoding and enrichment of libraries was carried out using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs; New England Biolabs, Cat. No. E6440). Paired-end sequencing (2151bp reads) was carried out on the Illumina HiSeq4K platform with a minimum and average depth per sample of 2.4Gb and 9.4Gb respectively.
Purity and integrity of DNA was assessed and ensured to fall within recommended ranges before library preparation. To preserve the integrity of DNA, the shearing step was omitted and DNA was used directly for DNA repair and end-prep. Single-plex libraries were prepared using 1D sequencing kit (Oxford Nanopore Technologies, SQK-LSK108 or SQK-LSK109) according to the 1D Genomic DNA by ligation protocol. For samples that were multiplexed (12-plex), the native barcoding kit (Oxford Nanopore Technologies, EXP-NBD103 or EXP-NBD104 and EXP-NBD114) was used and libraries were prepared according to the Native barcoding genomic DNA protocol. Both native barcode ligation and adapter ligation steps were extended to 30min instead of 10min. Single-plex samples were sequenced on either the MinION or GridION machine with either FLO-MIN106D or MIN106 revD flowcells. Multiplex samples were sequenced on the PromethION machine with FLO-PRO002 flowcells. Raw reads were basecalled with the latest version of the basecaller available at the point of sequencing (Guppy v3.0.4 to v3.2.6). Basecalled nanopore reads were demultiplexed and filtered for adapters with qcat (v1.1.0 https://github.com/nanoporetech/qcat). The minimum and average sample depth was 1.2 and 4.7Gb respectively. Number of reads ranged from 300,000 to 3.4 million (average=1.4 million).
Hi-C libraries were generated using Phase Genomics ProxiMeta kit (version 3.0), based on the standard protocol. Briefly, 500mg fecal material was crosslinked for 15min at room temperature with end-over-end mixing in 1mL of ProxiMeta crosslinking solution. Once crosslinking reaction was terminated, quenched fecal material was rinsed. Sample was resuspended and a low-speed spin was used to clear large debris. Chromatin was bound to SPRI beads and incubated for 1h with 150L of ProxiMeta fragmentation buffer and 11L of ProxiMeta fragmentation enzyme. Once washed, beads were resuspended with 100L of ProxiMeta Ligation Buffer supplemented with 5L of Proximity ligation enzyme and incubated for 4h. After reversing crosslinks, the free DNA was purified with SPRI beads and Hi-C junctions were bound to streptavidin beads and washed to remove unbound DNA. Washed beads were used to prepare paired-end deep sequencing libraries using ProxiMeta Library preparation reagents. Paired-end sequencing (2151bp reads) was carried out on the Illumina HiSeq4K platform. The minimum and average sample depth was 2.3 and 24.5Gb respectively.
Sequencing costs can vary substantially across sequencing centers and countries. Here we provide an estimate based on costs at the Genome Institute of Singapore in November 2021. Based on prices for library preparation kits as described in this manuscript, we estimate that Illumina library preparation costs ~US$50/sample and an Illumina HiSeq sequencing lane costs ~US$1000 with approximate throughput of >350 million paired-end reads (2151bp; >100Gbp). Considering that the average Illumina sequencing depth per sample in this study is ~10Gb, 10 samples can be multiplexed in a single lane, leading to the overall cost per sample of ~US$150. For ONT sequencing, we estimate that with an approximate flow-cell price of US$500 producing ~30Gbp of sequencing data, 5 samples can be multiplexed to obtain the average throughput in this study (~6Gbp). With ONT multiplexed library preparation costs of ~US$50/sample, we estimate that overall ONT costs are also ~US$150/sample. Metagenomic assembly of Illumina and Hybrid datasets with MEGAHIT and OPERA-MS, respectively, typically took less than 3h on an AWS C5 instance with 8 CPUs. Using as reference an AWS C5 instance price of 30 cents an hour for 8 CPUs, this translated to a computational cost of Illumina and ONT read statistics were generated with Fastq-Scan (v0.4.1, https://github.com/rpetit3/fastq-scan) and NanoStat53 (v1.4.0), respectively. To assess taxonomic concordance, Illumina and ONT reads were classified with Kraken254 (v2.1.1, UHGG database13) and relative abundances were estimated with Bracken55 (v2.6.1) at the species level (option -l R7) to compute Pearson correlation coefficients per sample. Illumina reads were assembled using MEGAHIT8 (v1.04, default parameters) and hybrid metagenomic assemblies were generated with Illumina and ONT data using OPERA-MS25 (v0.9.0, --polish). Contigs were binned with MetaBAT210 (v2.12.1, default parameters). Hi-C binning was provided by Phase Genomics using its internal pipeline with MetaBAT results for hybrid assemblies as a starting point. Assembly bins were evaluated based on MIMAG standards28, with contamination, completeness and N50 values determined with CheckM56 (v1.04), and non-coding RNA annotations from barrnap (https://github.com/tseemann/barrnap) (v0.9) and tRNAscan-SE57 (v2.0.5, default parameters). Assembly bins with contamination <10% and completeness >50% were designated as medium quality MAGs, those with contamination <5% and completeness >90% as near complete MAGs, and additionally near complete MAGs with complete 5S, 16S, and 23S rRNA genes and at least 18 unique tRNA genes were classified as high quality MAGs. All other bins were classified as low quality and were removed from further analyses. In total, 4497 medium quality, near complete and high quality MAGs were designated as being part of the SPMP database. Hybrid and short-reads assembly based MAGs were further assessed for chimerism with GUNC58 (v1.0.4, detailed output). Coding sequence lengths obtained from Prodigal59 (v2.6.3) calls were compared between the two datasets to assess the potential impact of long read indel errors on gene annotation. Concordant with prior work showing that hybrid metagenomic assemblies can have high base-pair accuracy25, we also noted that SPMP MAGs independently assembled from distinct individual gut metagenomes could exhibit high average nucleotide identity (>99.99%, consistent with Q40 quality). Representative MAGs for SLCs were used to create a custom Kraken60 (v2.1.1) database (https://github.com/DerrickWood/kraken2/wiki/Manual#custom-databases) and relative abundances for SLCs were estimated for each sample using Bracken55 (v2.6.0, default parameters). Rarefaction analysis for estimating overall species diversity was done using the R package iNext61 (v2.1.7, q=0, datatype=incidence_raw and endpoint=300), based on converting SLC relative abundance values from Bracken into presence-absence values at a threshold of 0.05%. Genus-level abundances for each sample were provided as input for R package MaasLin236 (v1.4.0) along with sample metadata (age, sex and ethnicity), and significant associations were determined by combining 3 MaasLin2 runs with a compound Poisson linear model. Metagenomic reads were mapped (--secondary=no) against reference databases indexed with minimap262 (v2.24-r1122, -I 24G; SPMP strain-level genomes and UHGG species-level representatives). Alignments were filtered at the strain-level with bamtools (v2.5.2, -tag NM:<2 -length >99) and unique reads were extracted based on samtools (v1.15.1) view results. To further evaluate the utility of SPMP genomes relative to the UHGG database for read mapping at the strain-level, we created databases with similar number of strains from both collections. Reference indexing and mapping were done in a similar fashion as described before. Alignments were filtered with pysam (v0.19.1) (read coverage 90%, identity 99%), and reads were classified at the species-level with Kraken (v2.1.1, RefSeq bacteria database). Specifically, we identified 21 species with many strain genomes in UHGG or SPMP (20) and having enough reads (>10 coverage) in at least 3 samples in an independent study of Singaporean gut metagenomes35. Illumina reads were mapped (minimap2, default parameters) independently to strain genomes for each species. Kraken2 classification (standard database) was used to assess if mapped reads came from the right species, and to calculate precision, sensitivity and F1 scores. We noted that median F1 scores were better using SPMP compared to UHGG for 17 out of 21 species. Overall, SPMP provided significantly better mapping performance (F1 score) relative to UHGG for 12 species (Wilcoxon p<0.05). The converse, i.e., significant improvements with UHGG relative to SPMP, were not observed for any species. Improvements in F1 scores were driven by better sensitivity in SPMP vs UHGG for abundant gut bacterial species such Prevotella copri and Alistipes onderdonkii. While median precision scores using SPMP and UHGG were similar (0.98 vs 0.99 for P. copri; 0.98 vs 0.97 for A. onderdonkii), sensitivity was notably higher in SPMP vs UHGG (0.96 vs 0.90 for P. copri; 0.99 vs 0.90 for A. onderdonkii). The SPMP database was compared to the GTDB database2 (release 95) using GTDBtks63 (v1.4.1) ani_rep command with default arguments, which leverages Mash64 (v2.3) to provide pairwise genome-wide similarity values between all query MAGs and GTDB sequences. Only pairs with Mash distance 0.05 were retained and used to define the best match for each SPMP MAG based on minimum Mash distance. GTDB matches were classified based on their metadata as being uncultivated (derived from environmental sample or derived from metagenome) or based on isolate strains. Both N50 values and MIMAG classifications were extracted from GTDB metadata. MAGs were placed into a phylogenetic tree using GTDB_TK (v1.4.1) with classify_wf (default options), based on pplacer_taxonomy values. To assess novelty in light of the latest human gut metagenome database, we further compared our MAGs to the 5414 representative genomes from the Human Reference Gut Microbiome catalog (HRGM)22 with a similar Mash analysis (Supplementary Data6). MAGs were clustered at the species (95%) and strain-level (99%) based on average nucleotide identity estimates (ANI; using Mash with sketch size of 10k and k-mer size of 21bp) with agglomerative clustering (sklearn v0.23.2, AgglomerativeClustering function, options: linkage=single, n_clusters=None, compute_full_tree=True, affinity=precomputed). For each cluster, representative MAGs were defined using the highest eigen centrality value based on a weighted network graph produced by networkx (v2.5; eigenvector_centrality function). Strain-level clustering was done jointly with all species-level matches from the UHGG database (v1.0, ANI threshold of 95%). Phylogenetic analysis at the strain-level was conducted using the biopython Phylo package65, based on pairwise distances generated with FastANI66 (v1.32). Phylogenetic trees were visualized using FigTree (tree.bio.ed.ac.uk/software/figtree). SLCs were assigned putative species name and types based on comparisons with multiple databases, including GTDB, Pasolli et al.67 (SGB) and Almeida et al.13 (UHGG). SLCs types were defined as, (i) isolate: if GTDB match to an isolate was found (Mash distance 0.05), (ii) uncultivated: if a match to any database was found, but no isolates, (iii) novel: if no matches were found. SLCs were assigned putative species names based on a majority rule for MAGs in the cluster, with preference for GTDB ids (Supplementary Fig.9). Biosynthetic gene clusters (BGCs) in the SPMP database were identified using antiSMASH68 (v5.1.2, --genefinding-tool prodigal-m --cb-general --cb-knownclusters --cb-subclusters --asf --pfam2go --smcog-trees) and DeepBGC38 (v0.1.18, prodigal-meta-mode). BGCs with only one identified gene and with length <2kbp were removed for both sets of results. For antiSMASH this provided a set of 3,909 BGCs. DeepBGC results which overlapped with antiSMASH were removed if the genomic coordinates of both BGCs overlapped by 30% in either direction. DeepBGC candidates were further filtered for (i) being categorized with a known product class and (ii) containing at least one known biosynthetic pfam or TIGRFAM protein domain as defined by Cimermancic et al.69, providing an additional set of 23,175 BGCs. All 27,084 BGCs (3909 from antiSMASH + 23,175 from DeepBGC) were first categorized into different product classes: ribosomally synthesized and post-translationally modified peptides (RiPPs), nonribosomal peptide synthetases (NRPs), polyketide synthases (PKS), saccharides and others based on the labels reported by each algorithm. We further unified the antiSMASH and DeepBGC product class labels to integrate both datasets (Supplementary Table1). A fraction of mined BGCs were labeled as hybrids because antiSMASH or DeepBGC associated them with two different product classes e.g., bacteriocin;T1PKS. The BGCs in each product class were grouped into gene cluster families (GCFs) by sequence similarity using BiG-SCAPE39 (v1.01, --include_singletons --mix --no_classify --cutoffs 0.3). A total of 16,055 GCFs were defined by this approach and for each GCF we took the smallest BGC member as a representative of the family. Gene cluster diagrams of BGCs were created using Clinker70. BGCs in SPMP were classified as novel via a two-step approach. Firstly, BGC sequences were required to have <80% similarity to any existing sequence in the antiSMASH and MIBiG 2.071 databases using the clusterblast results from antiSMASH. Secondly, BGC annotations were compared to antiSMASH annotations from a comprehensive gut microbial genome collection (HRGM) using the standalone clusterblast software72 (v 1.1.0), to identify SPMP matches based on a 80% similarity threshold, similar to the approach described in Gallagher et al73. Besides bacteriocins, BGC mining in the SPMP database also identified other classes of ribosomally synthesized and post-translationally modified peptides (RiPPs) such as lanthipeptides and lassopeptides (Supplementary Fig.15A), which can also possess antimicrobial properties. Antimicrobial activities of putative peptides encoded by novel RiPP BGCs in SPMP were predicted using an ensemble voting approach (Supplementary Fig.15B) with four different AMP prediction models: AMPscanner74 (v2, convolutional neural network), AmpGram75 (random forest model), AMPDiscover76 (based on quantitative sequence activity models) and ABPDiscover (https://biocom-ampdiscover.cicese.mx/). Peptides predicted by antiSMASH in these RiPP BGCs were translated and all amino acid sequences with a length greater than 10 but lesser than 200 were used as inputs into these four models. Peptides were classified as AMPs if they received votes from both AMPscanner and AmpGram, and at least one vote from either AMPDiscover or ABPDiscover, and if the corresponding RiPP BGCs contained a transporter protein. The performance of this ensemble approach was evaluated using 78 known AMP sequences and 78 scrambled non-AMP sequences taken from the AmpGram benchmark dataset75. For our evaluation dataset, we identified and removed all sequences that were found in the training sets of AMPscanner, AmpGram, AMPDiscover and ABPDiscover using seqkit77 (v0.11.0) and samtools faidx (v1.9). The percentage hydrophobicity and overall charge of selected peptide sequences was determined using the AMP calculator in the AMP database 3 (APD3; https://aps.unmc.edu/prediction). Out of 107 RiPP BGCs that were not bacteriocins, 54 of them were predicted to also be AMPs. One of these was found to be a lanthipeptide (GCF459) in Dorea longicatena B (Supplementary Fig.15C), with no significant blastp matches to the NCBI nr database. This peptide sequence has a 32% hydrophobic amino acid composition and a net positive charge of +5, which could favor its insertion into the cell walls and membranes of its targets. Another novel AMP is a lassopeptide (GCF26) found in a Ruminococcus species (Supplementary Fig.15D), with similarly high proportion of hydrophobic amino acids (35%) and a slight net positive charge. To associate BGC presence/absence patterns with microbial community structure, correlation analysis (Fastspar78 v1.0.0, parameters: --iterations 100 --exclude_iterations 20, p-values from 1000 bootstrap replicates and permutation testing) was done based on SLC abundance profiles across samples (species with medium abundance 0.1% filtered out). Correlations in the network were kept if they had an associated p-value <0.05. No statistical method was used to predetermine sample size. No data were excluded from the analyses. The experiments were not randomized. The Investigators were not blinded to allocation during experiments and outcome assessment. Further information on research design is available in theNature Research Reporting Summary linked to this article. See original here:
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians - Nature.com
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