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Scientists solve genetic puzzle of the ‘Y’ chromosome



THE study provides the first complete view of a Y chromosome’s code, as per geneticist and co-author, Karen Miga.—Reuters

WASHINGTON: Scientists have taken an important step forward in understanding the human genome — our genetic blueprint — by fully deciphering the enigmatic Y chromosome present in males, an achievement that could help guide research on infertility in men.

Researchers on Wednesday unveiled the first complete sequence of the human Y chromosome, which is one of the two sex chromosomes — the X chromosome being the other — and is typically passed down from male parent to male offspring. It is the last of the 24 chromosomes — threadlike structures that carry genetic information from cell to cell — in the human genome to be sequenced.

People have a pair of sex chromosomes in each cell. Males possess one Y and one X chromosome while females have two X chromosomes, with some exceptions.

The Y chromosome’s genes help govern crucial reproductive functions including sperm production, formally called spermatogenesis, and are even involved in cancer risk and severity. But this chromosome had proven difficult to crack owing to its exceptionally complex structure.

Fuller understanding of the human genome will help guide research on infertility in men

“I would credit new sequencing technologies and computational methods for this,” said Arang Rhie, a staff scientist at the US National Human Genome Research Institute and lead author of a research paper detailing the achievement in the journal Nature.

“It finally provides the first complete view of a Y chromosome’s code, revealing more than 50 per cent of the chromosome’s length that was previously missing from our genome maps,” said University of California, Santa Cruz (UCSC) biomolecular engineering professor and study co-author Karen Miga, co-leader of the Telomere-to-Telomere consortium behind the research.

The complete X chromosome sequence was published in 2020. But until now, the Y chromosome part of the human genome had contained big gaps.

“This is especially important because the Y chromosome has been traditionally excluded from many studies of human diseases,” UCSC genomicist and study co-author Monika Cechova said.

“The Y chromosome is the smallest and the fastest-evolving chromosome in the human genome, and also the most repetitive, meaning that its DNA contains stretches of DNA repeated many times over,” Cechova added.

The work revealed features of medically relevant regions of the Y chromosome including a stretch of DNA — the molecule that carries genetic information for an organism’s development and functioning — containing several genes involved in sperm production. The new fuller understanding of the Y chromosome’s genes offers promise for practical applications including in fertility-related research, according to the researchers.

“Many of these genes are important for fertility and reproduction, and especially spermatogenesis, so being able to catalog normal variation as well the situations when, for example, azoospermia (an absence of sperm in semen) occurs, could be helpful for IVF (in vitro fertilization) clinics as well as further research into activity of these genes,” Cechova said.

In addition to identifying some additional Y chromosome genes, the researchers found that some DNA from the chromosome had been mistaken in previous studies as bacterial in nature.

Scientists continue to broaden the understanding of human genetics. A first accounting of the human genome was unveiled in 2003. The first complete human genome — albeit with the Y chromosome partial — was published last year. In May, researchers published a new version of the genome that improved on its predecessor by including a rich diversity of people to better reflect the global population of 8 billion.

Fully sequencing the Y chromosome adds to this.

“We now have a recipe on how to assemble the Y chromosome fully, which, while expensive at the moment, can translate into personalized genomics in the future,” Cechova said.

Published in Dawn, August 24th, 2023


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Imran’s life ‘in danger’, moved to lower class cell in Adiala Jail: lawyer



Former prime minister Imran Khan’s lawyer, Naeem Haider Panjutha, claimed on Tuesday that the PTI chief was moved to a lower class cell at the Adiala Jail last night and feared the ex-premier’s life was in danger.

Imran was shifted to Attock jail on August 5, 2023, after a court sentenced him to three years in prison in the Toshakhana case for concealing details of gifts he received as the prime minister of Pakistan.

After his sentence in the Toshakhana case was suspended by the Islamabad High Court, the government detained the ex-premier in the cipher case. He has since remained behind bars on judicial remand.

On September 26, Imran was shifted to Central Jail Adiala from District Jail Attock following IHC orders passed on a plea filed by the PTI.

Last night, the police ramped up security in the vicinity of the Adiala jail by deploying elite commandos and setting up additional security pickets to ensure foolproof measures. The decision was taken in light of recommendations by the Special Branch and relevant departments following a survey of Adiala Jail.

Talking to reporters in Islamabad today, Panjutha, spokesman to Imran on legal affairs, said Imran’s wife Bushra Bibi met the former prime minister in Adiala Jail today.

“There is danger to Imran Khan’s life,” he claimed. “Imran can be slow food poisoned … he is being mentally tortured and his movement has been restricted.”

Panjutha alleged that he had received reports last night that the PTI chief was moved to a lower class cell. “Security personnel has been stationed outside the cell and mobile phones have been taken for them,” he said, claiming that these were new ways of “breaking” Imran.

The PTI lawyer added that a petition pertaining to Imran’s conditions in jail was filed in the IHC and the application was fixed for hearing on October 5.

“There were objection [by the court] earlier that the matter has already but decided but no directions have been passed on Imran Khan’s health, which is a basic fundamental right enshrined in the Constitution,” Panjutha added.


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LHC orders Punjab govt to ensure PTI leader Hassaan Niazi’s contact with father



The Lahore High Court on Tuesday directed the interim Punjab government to ensure that contact is established between incarcerated PTI leader Hassaan Niazi and his father within a fortnight.

The order comes on a petition filed by Hassaan’s father, Hafeezullah Niazi, who petitioned the court to recover and allow a meeting with his son, who is in military custody.

Hassaan, a barrister and nephew of PTI chairman Imran Khan, was in hiding after the May 9 riots. He was arrested from Abbottabad on August 13 and handed over to the military for trial over his alleged involvement in the attack on the Lahore corps commander’s house.

On August 15, Hassaan’s father, Hafeezullah, filed a petition in the LHC seeking recovery of his son.

Two days later, a military official wrote to the police, requesting it to hand over Hassaan’s custody to the military for “trial by the court martial”.

Before the LHC began hearing the father’s plea, the police submitted a report in the court on August 18, detailing the offences in which the former was found to be allegedly involved.

The report was submitted by Punjab Additional Advocate General (AAG) Ghulam Sarwar while Justice Sultan Tanveer presided over the hearing.

The AAG informed the LHC in the hearing, “Hassaan Niazi has been handed over to the military”. He added that Hassaan was “named in the Jinnah House attack case and was a main suspect”.

The interim Punjab government told LHC in the hearing on August 26 that visiting a suspect in military custody was not allowed under any law.

Additional Advocate General Ghulam Sarwar Nahang stated in the hearing that the SC had already taken note of the trials of the May 9 suspects in military court and the question of the suspects’ meeting with family members was also pending before it.

He said proceedings in the high court on the same question of law would complicate the matter.

On September 28, barrister Faiz Ullah Khan Niazi submitted that 45 days have passed and since then the petitioner has been unaware of the whereabouts of his son.

In today’s hearing, a single-member bench comprising Justice Sultan Tanvir Ahmad ordered the Punjab government to establish contact between Hassaan and his father within a fortnight.

According to the written order, a copy of which is available with, the petitioner’s lawyer told the court his client would be satisfied if he was allowed to establish contact with his son.

According to the order, the government officials maintained that since the matter is still pending adjudication before the apex court, it is “in the fitness of the circumstances to adjourn the case till the decision is passed by the Supreme Court”.


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Knee injury forces Arshad Nadeem out of Asian Games a day before javelin throw final



Pakistan’s star javelin thrower Arshad Nadeem was on Tuesday ruled out of the Asian Games, under way in the Chinese city of Hangzhou, due to a chronic knee injury, the athlete confirmed to

Nadeem, a trailblazer and beacon of hope for the future of athletics in the country, won silver at the World Athletics Championship in Budapest earlier this year.

However, in a big blow for his fans, the athlete dropped out of the Asian Games just a day before the tournament’s Men’s Javelin Throw final, scheduled for Wednesday.

According to a statement issued by Pakistan’s Chef de Mission at the Asian Games, Nadeem had complained of “persistent pain for several weeks” at the first training session in Hangzhou on Sept 27.

It said the concern had become particularly pressing in the aftermath of the World Athletics Championship.

“On Oct 2, he again complained of pain in the right knee and express a desire to undergo an evaluation to determine the impact on his ability to participate in the Javelin Throw event at the Asian Games,” the statement said.

Subsequently, the Pakistan contingent’s chief medical officer recommended a comprehensive check-up of Nadeem who then underwent a thorough examination, including a non-invasive test i.e. MRI at a local
hospital here in Hangzhou.

“After consulting the medical personnel, Nadeem has now decided not to participate in the Asian Games in order to prevent any untoward situation that may hinder his training program and participation in the Paris 2024 Olympic Games,” the statement concluded.


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