Sunday, January 8, 2023

Phage therapy

It never went out of fashion in Eastern Europe

A treatment first used more than a century ago, that uses bacteria-killing viruses, is making a comeback in Australia and doctors hope it will help counter a growing crisis of antibiotic-resistant superbugs.

The Alfred hospital in Melbourne has become the first health service in Victoria to begin using the pioneering phage therapy, which involves utilising harmless viruses – known as bacteriophages – to kill germs in cases where traditional antibiotics have failed.

Professor Anton Peleg, head of infectious diseases at The Alfred, said phage therapy was being used for an increasing number of patients battling potentially deadly superbugs, on compassionate grounds.

“They are patients with severe bacterial infections that are either life-threatening, or limb threatening, or function threatening, where they don’t have any other options left,” Peleg said. “It is a salvage treatment pathway.”

Discovered in 1917 by French-Canadian biologist Felix d’Herelle, bacteriophages are viruses that naturally evolved to prey on harmful bacteria. In the 1940s, the treatment largely disappeared, while the Western world shifted to antibiotics.

However, global interest in the therapy was reawakened recently by the rise of superbugs that have developed a resistance to antibiotics.

“We desperately need novel approaches to attack superbugs, approaches that are different to existing traditional antibiotics,” Peleg said.

Increasingly, phages are now being seen by some scientists as a potential complement or even an alternative to antibiotics, the overuse of which has contributed to increasing bacterial resistance and the advent of the superbug.

The Alfred’s phage therapy program began at the end of last year in partnership with Monash University’s Centre to Impact AMR (antimicrobial resistance), and has already been used to treat people who are severely ill with antibiotic-resistant infections, including patients with cystic fibrosis, who have endured years of chronic lung infections.

Others being referred to the program include those with drug-resistant prosthetic joint or limb infections and severe burn wounds.

“We recently received another referral for a woman with a recurrent urinary tract infection with terribly resistant bacteria,” Peleg said.

According to the World Health Organisation, antimicrobial resistance is a rising threat to global health, jeopardising decades of medical progress and transforming common infections into deadly ones. A UN report suggests yearly deaths from drug-resistant diseases could rise from 700,000 to 10 million in 30 years if no action is taken.

Phage therapy, which is most commonly provided intravenously, can be required for several months. Peleg said patients at The Alfred undergoing the treatment were monitored closely to evaluate the activity of the phage in their bodies.

Peleg said the treatment depended on accurate diagnosis of the bacterial strain causing infection and the phage required to fight it. With billions of different bacteria killing viruses in our natural environment – found in river systems, soil and sewage – sourcing the appropriate phage can be difficult.

To speed up this process, Peleg and his team spent the past four years collecting the most common bacteria that have caused infections at The Alfred. Among them is Staphylococcus aureus bacteria, also known as golden staph and pseudomonas.

The hospital also has an onsite translational phage lab, where staff scour environmental sources, identify phages, then test their activity with a combination of antibiotics. The phages are then produced and packaged into vials by an expert team at Monash University.

“We’ve been storing the most common bacteria causing infection at The Alfred and are looking for phage that have killing activity against those bacteria to develop a phage biobank,” Peleg said. “This allows us to have a cocktail of multiple phages, prepared to use for future patients with bacterial infections.”

University of Sydney microbiologist Professor Jon Iredell is on the front line of phage therapy in Australia and has used the treatment alongside other medications to treat dozens of patients in NSW since 2007. Among them are children, patients with golden staph or E. coli infections and people on life support.

He said phage therapy was gaining traction in Australia, with teams in Melbourne and Western Australia treating their first patients recently.

But Iredell said a lack of robust data and large-scale clinical studies had hindered advancements and understanding. In Australia, the treatment is still deemed experimental and is awaiting approval by the Therapeutics Goods Administration.

“It’s our job to be sceptical, and we have to make sure this is safe, but all the data suggests so far that it is safe when it is used properly and the phage is made properly,” Iredell said.

Australians wanting the treatment must fit strict eligibility criteria, including being referred to an infectious disease specialist, who can certify they are already using the appropriate treatment and more was needed.

Iredell and Peleg are part of a group of doctors working to develop a regulatory framework to use phage therapy nationally in the hope it will pave the way for big clinical studies in Australian hospitals.

Phage therapy has shown success in experimental cases overseas, including two patients in the US who recovered from intractable infections after being treated with genetically engineered bacteria-killing viruses.

In 2019, a teenager in the UK also made a remarkable recovery after being among the first patients in the world to be given a genetically engineered virus to treat a drug-resistant infection.

“All of us in the phage community often joke for every bacterial problem there is a phage solution because they’re the natural predators and since before humans evolved,” Iredell said. “Antibiotic resistant infections are one of the greatest risks to modern health infrastructure, and we need to act now.”

Tuesday, December 6, 2022

Geoffrey Chaucer was not a rapist

Geoffrey Chaucer is innocent! The fourteenth-century diplomat, customs collector and sometime poet has long been dogged by unsubstantiated sexual assault allegations. The suspicion arose, quite naturally, when a women testified that Chaucer had not raped her. After all, if he hadn’t raped her, why would she bother repudiating the claim? The only logical explanation (to a certain kind of mind) was that a voiceless, victimised woman had been paid to withdraw sexual harassment charges levelled against a prominent, powerful … poet?

As it turns out, the young Cecilia Chaumpaigne, a servant in the Chaucer household, had been the co-defendant with Chaucer in a charge of unlawful employment recruitment. In the wake of the Black Death (and the absence of a working holiday visa program), labour had become scarce in fourteenth-century London, and employers were hard-pressed to fill staffing needs. Chaumpaigne’s former employer, one Thomas Staundon, accused Chaucer of “raping” Chaumpaigne, alleging that Chaucer had poached her with an offer of better wages. Chaumpaigne countered that she had definitely left Staundon’s service before going to work for Chaucer. Case closed. The lady, it turned out, did protest too little.

Regular readers of this column will remember that the Latin word raptus, from which our word rape is derived, had its origins in the idea of carrying away, whether for worse or for better: “a raptor is a bird that carries away its prey; the rapture is the moment following the second coming of Christ when the saved will be carried away to heaven”. But memories are short, knowledge of etymology is limited, and accusations of sexual assault are pure feminist gold. And so the fourteenth-century court document in which a young woman certified that Chaucer had not raped her, first uncovered in 1873, was milked by feminist scholars for the next 149 years. Now that we know the full story, Chaucer can only be cancelled for his poetry.

The rehabilitation of the father of English poetry, however, is far from final. The two (male) historians who only this year uncovered the key documents clearing Chaucer emphasised that their findings “will not undo the countless advances feminist colleagues have made in our field”. Before publishing their work, they “invited three leading feminist Chaucerians to think through some of the implications of the new evidence for our field”. They concluded that (thank Gaia) “the new documents will not change the course charted by feminist scholarship to expose the shortcomings of the late medieval hegemonic order”. And they dutifully lamented the “often invisible fate of medieval servant women”.

Oh, and they reassured the BBC’s History Extra magazine that “we cannot rule anything out … there is a strong likelihood that this one case was not about rape, and that obviously doesn’t mean that Chaucer wasn’t a rapist”. Since, you know, he could still have been a rapist. Or a pedophile. Or a sodomite (though these days that would count in his favour). Yes, there’s still hope—more hope, at least, that Chaucer might have been a rapist than that he was a slave trader, an anti-vaxxer, or a climate change denier. Who knows what foul historical misdeeds may lurk unread in the Chaucer files? About the only thing we do know for certain is that two very nervous male medievalists are desperate to avoid being cancelled themselves.


Wednesday, October 26, 2022

Conserving the Axolotl

The waterways of Mexico are the only natural habitat of the axolotl — “water monster” in Nahuatl — although the amphibian is abundant in captivity and a popular pet in various corners of the world. But Zambrano says that differences between wild and captive-bred creatures are considerable because captive axolotls experience losses in physiological and behavioral capabilities.

While Zambrano’s original idea was for surviving axolotls to wiggle on their own into the restored canals or refuges, researchers are also looking into the possibility of introducing captive-bred creatures to these spaces themselves. Before that can be done, however, Zambrano said they need more information about the salamanders’ genetics and reproductive capabilities, among other things. It’s known that farmers sometimes release axolotls into canals after raising them in aquariums, but the researchers say this is generally frowned upon due to environmental regulations.

“The quality of the water is reduced a lot when you put in pesticides and fertilizers because they kill everything, including the axolotl.”  If the axolotl goes extinct in the wild, it would be a tremendous loss to Mexico and the world, he said.

“It’s not only one of the most researched species in terms of genetics, but it’s an animal that’s closely connected to our Mexican culture.”

As Mexico City’s population has grown, intensive water pumping has depleted much of the underground sources that are used to feed the maze of canals. They now get treated wastewater from nearby plants, which has contributed to the decay of waterways and chinampas.

Eslava was already involved in clean-up projects and restoration efforts with other Xochimilco residents when Carlos Sumano came calling in 2020. He relished the idea of the project because the university’s sponsorship would help provide funding and resources to assist chinamperos in reactivating dormant chinampa agriculture.

“All the fertilizer we need is down there in the water,” he said. “All the vegetation that disintegrates there is very rich material; it’s what our ancestors used. That’s why chinampa farming was so rich. There was an enormous diversity of crops, and everything was done using traditional methods like mud and native seeds.”

Those traditions had gradually succumbed to new agricultural practices that were ushered in starting in the 1940s with the promise of greater yields.

“The ‘green revolution’ was this vision of increasing agricultural productivity as fast as possible, as best as possible, and that’s when the use of pesticides and fertilizers started to grow,’” Zambrano said. “But the quality of the water is reduced a lot when you put in pesticides and fertilizers because they kill everything, including the axolotl.”

“I’ve been farming for a long time, and I want to keep doing it here, in Xochimilco,” he said in a recent interview. “I don’t want chinampas to disappear.”

Neither does Eslava, who spends much of his time improving plots. He and Sumano recently brought six very young axolotls bred in aquariums to a narrow, restored canal. The minuscule creatures, which resembled tadpoles, wiggled out of a bucket and into the water. Sumano explained that the axolotls were placed there to be monitored for a few days, after which Eslava took them back out.

Zambrano believes the project has already started to reap benefits, like healthy species in some canals and growing interest in reactivating abandoned chinampas, though he notes that ambitious restoration projects such as this one take time and effort.

Friday, October 7, 2022

Legends of 'Negrito' people living in Taiwan CONFIRMED: Skull of woman reveals 'short, dark-skinned people' lived on the island more than 6,000 years ago - before indigenous tribes - then suddenly disappeared

The ancient Taiwanese legend of 'short, dark skinned' people who lived in remote mountains and suddenly disappeared has been confirmed to be true following the discovery of a 'Negriot' woman's remains in a cave that dates back 6,000 years.

The nation's indigenous tribes have long shared stories about small stature hunter-gatherers who were already settled when they arrived 4,800 years ago - but a lack of evidence has shrouded this group in mystery for several hundred years.

A DNA analysis on the skull shows it is close to African samples and features of the cranium resemble Negritos of the Philippines and South Africa, who all are well known for their short stature and small body size.

Archaeologists also uncovered femur bones from the female, which suggest she stood about four feet, six inches tall.

It is still not known what happened to this ancient group, but researchers involved with the study suggest the arrival of the Austronesian peoples could have led to the decline and disappearance of the Negritos in Taiwan.

'The term 'Negrito', little black person, is a Spanish diminutive of negro, first used by the 16th-century Spanish missionaries to describe the hunter-gatherers in the Philippines,' reads the study published in World Archeology.

'As the Negrito groups are characterized by their short stature, dark skin, and frizzy hair, all groups of a similar phenotype in the neighboring region, including the Mani (Maniq) in southern Thailand, the Semang groups in Peninsular Malaysia, and the Andamanese in the Andaman Islands are often labeled together as the Negritos.'

There are 16 recognized Austronesian groups in Taiwan and all but one have similar legends about the Negrito people.

The legends about the apparent 'Negritos' of Taiwan were collected during three major cultural periods: the Chinese Qing Dynasty of 1683 to 1895, the Japanese Rule period of 1895 to 1945, and then the post-1945 era.

Several documents from the Quin Dynasty have mentioned the existence of 'small-statured and dark-skinned people' on the island, noting they spoke a different language and only intermarried among themselves.

During the Japanese period, scholars collected and interpreted the tales about Negrito people through field research among the Austronesian tribes - a total of 25 of these legends in Taiwan were collected.

After 1945, this topic had attracted more attention, and the number of collected stories increased to 258 through linguistic and ethnological field research.

The Austronesian groups, however, varied on opinions about Negritos.

Some of the indigenous tribes viewed them as their ancestors, while others saw them as 'aliens and enemies,' the study describes.

One tribe, the Saisiyat, claim they learned medicine, singing, dancing and other rituals from the who they called, Ta'ai.

More than 1,000 years ago, the Saisiyat killed what they believe to be the last village of Negritos in a battle over women - and the tribe still feels the guilt of their ancestors' actions.

The Saisiyat forced a battle, cornering so many people on a bridge that the entire tribe drowned when warriors tipped it into a fast-flowing mountain river Chu Fung-lu, master of ceremonies for the memorial held in Wufeng Village deep in the mountains of central Taiwan, told Reuters.

The woman's remains were found buried inside one of the largest Xiaoma caves that sits on the eastern coastline of the island.

Also in the layers of dirt were deposits of Neolithic pottery-bearing and Iron Age findings that date back between 2,000 and 6,200 years ago.

The position of the woman's remains suggest she was laid to rest in a squatting position, which matches other methods of hunter-gatherer graves in southern China and Southeast Asia from late Paleolithic (50,000 to 12,000 years ago) through Mesolithic (10,000 to 20,000 years ago) and Preceramic, which began 4,000 years ago.

Archaeologists determined the sex through the skull, as the pelvis was not available to analyze.

'The individual was ascertained to be female because of the gracile cranium, small mastoid processes, smooth occipital muscle attachment area, perpendicular and elevated frontal bone, and the smooth contour of the mandibular base,' according to the study.

The Negrito population is believed to be tied to the 'first layer' of anatomically modern humans who show a closer resemblance to Africans than present-day Eurasians who represent the 'second-layer.'


Wednesday, September 14, 2022

Vanished arm of Nile helped ancient Egyptians transport pyramids materials

When the ancient Egyptians built the pyramids of Giza around 4,500 years ago, the Nile River had an arm — one that has long since vanished — with high water levels that helped laborers ship materials to their construction site, a new study finds.

The discovery builds on previous archaeological and historical findings that the Nile had an extra arm flowing by the pyramids. But now, by analyzing ancient pollen samples taken from earthen cores, it's clear that "the former waterscapes and higher river levels" gave the Giza Pyramid's builders a leg up, a team of researchers wrote in a paper published Aug. 29 in the journal the Proceedings of the National Academy of Sciences(opens in new tab).

The research sheds light on how the pyramids — royal tombs for the pharaohs Khufu, Khafre and Menkaure — rose to monumental heights. Their towering stature was achieved, in large part, thanks to the Nile's now-defunct Khufu branch, which "remained at a high-water level during the reigns of Khufu, Khafre, and Menkaure, facilitating the transportation of construction materials to the Giza Pyramid Complex," the team wrote in their paper.

Researchers have known for decades that the long-gone Khufu branch extended up to the Giza plateau in ancient times, but the new project aimed to find exactly how the water levels had changed over the past 8,000 years.

To reconstruct the Nile's past, in May 2019 the team drilled five cores into the Giza floodplain. The researchers measured the amount of pollen found in different parts of the cores to determine how pollen levels had changed over time. Time periods when water was plentiful should have more pollen than periods that were arid, the study authors wrote.

The pollen analysis revealed that at the time the ancient Egyptians built the Giza pyramids, water was plentiful enough that the Khufu branch would have flowed near the Giza pyramids. "It was a natural canal in the time of the fourth dynasty [when the pyramids were built]," study lead author Hader Sheisha, a physical geographer at Aix-Marseille University in France, told Live Science in an email.

Sheisha noted that the water level was important for pyramid construction. "It would be very difficult if not impossible to build the pyramids without the Khufu branch and without it having a good level, which provides enough accommodation space for the boats carrying such heavy blocks of stone," she said. When exactly the branch went extinct is not certain, but the research shows that by 2,400 years ago the water level of the branch was very low.

The finds fit well with previous archaeological finds, which revealed a harbor close to the pyramids, as well as ancient papyri records that detailed workers bringing limestone to Giza via boat, the team noted in their paper.

Live Science contacted several experts not involved with the research to get their thoughts. Most were unable to comment at press time, but one who did, Judith Bunbury, a geo-archaeologist at the University of Cambridge in the United Kingdom, praised the research.

"The paper is an exciting contribution to our understanding of the dialogue between humans and their environment in Egypt within the context of changing climate," Bunbury told Live Science in an email.

Tuesday, September 13, 2022

Did Nero really fiddle while Rome burned?

The Roman emperor Nero ranks among the most infamous rulers of the Roman Empire for supposedly fiddling while Rome burned. But did that really happen? And does Nero really deserve his bad reputation?

As with all stories, we have to consider the source.

Born on Dec. 15, A.D. 37, Nero became the fifth emperor of Rome and the last of the Julio-Claudians, the dynasty that founded the empire, according to archaeologist Francesca Bologna, who curated the Nero Project at the British Museum(opens in new tab) in London.

Nero was only 2 years old when his mother, Agrippina the Younger — whose great-grandfather was Augustus, the empire's first emperor — was exiled by Emperor Caligula. At age 3, Nero's father, Gnaeus Domitius Ahenobarbus, died, leaving him in the care of his aunt. When Caligula was murdered in A.D. 41 and succeeded by Emperor Claudius, Nero was reunited with Agrippina, who later married her uncle Claudius, Bologna noted.

Despite having a biological son, Claudius designated Nero, his great nephew and stepson, as his heir, and Nero ascended to power in A.D. 54 at the age of 16. But his reign was short: Nero died in A.D. 68 at age 30 after taking his own life.

Roman historians have contended that Nero killed Agrippina and two of his wives, only cared about his art, and had very little interest in ruling the empire, Bologna said. However, "our sources for Nero are people that hated him," Harold Drake, a research professor emeritus of history at the University of California, Santa Barbara, told Live Science. One always has to keep in mind that much of his reputation "was written for us by his adversaries," he said. Bologna agreed, noting in her post for the British Museum that accounts of Nero "were keen on representing him in the worst possible light."

In July A.D. 64, Nero was vacationing in Antium (what is now the seaside town of Anzio, Italy) when he learned about what later became known as the Great Fire of Rome, Drake said. Before the conflagration burned itself out a week later, 10 of Rome's 14 districts had burned to the ground and thousands in a city of 500,000 to 1 million people had lost everything.

Nero raced back to Rome. He arranged emergency shelter and supplies of food and drink for the public, and opened his own palace and gardens for shelter, Drake noted(opens in new tab).

So, if Nero wasn't in Rome when the conflagration started, what's the origin of the rumor that "he fiddled" while the empire's capital burned?

Nero fancied himself a musician. At some point during the relief efforts, a rumor said he consoled himself by singing about another great fire — the fall of Troy, the Homeric tale that's the focus of the Roman poet Virgil's epic poem "The Aeneid," Drake said.

"He had done everything he could to deal with the fire, and he was exhausted," Drake said. "Being of an artistic bent, he consoled himself by comparing this disaster to the fall of Troy, which Romans liked to think they descended from, via the mythical ancestor Aeneas."

But even if Nero did play music while Rome was burning, he would not have used a fiddle, as bowed instruments would not become popular for another 1,000 years, Drake said. Instead, to accompany himself, Nero probably would have used a cithara, a portable harp-like instrument with seven strings, he explained.

There was precedent for Romans acting in such a manner. For example, the historian Polybius wrote that as the Roman general Scipio Aemelianus watched Carthage being destroyed, he quoted Homer's "The Iliad," saying, "'And a time will come when holy Ilium shall fall, and Priam, and Priam's folk of the good ashen spear,'" Drake said. "He was not thinking of Carthage but expressing fear that a like fate awaited the Romans."

In the aftermath of the Great Fire of Rome, Nero offered financial incentives to landlords to clear their property of debris and begin rebuilding, insisted that developers use stone instead of wood, straightened and widened streets, and ensured an adequate water supply for the city, Drake said. "Does that seem like the activity of a madman?" he asked.

So why might history remember Nero as a bad ruler? Almost everything the modern world knows about Nero comes from two sources: Roman senators and Christians. To both, Nero was an enemy.

"In general, senators loved to indulge their fantasy of a restored republic, sometimes by engaging in assassination plots, and then being outraged when the emperor reacted with hostility," Drake said.

As for the Christians, Roman senator and historian Tacitus suggested that because a rumor began circulating that Nero was responsible for the fire, he looked for a scapegoat in the Christians. The result was that many died from crucifixions, fires and other means. This often led Christians to blame Nero for the persecution they would endure from the Roman Empire, Drake said.

All that said, "I don't want to fall into the trap of justifying everything Nero did just because he has suffered from bad press," Drake said. "Nero was unquestionably pampered and overindulged by his tutors and, like other tyrants at other times, became much more arbitrary in his actions."

In the end, although Nero might not have been a madman, "there's little reason to doubt that he became increasingly unstable" over the course of his reign, Drake said. After the Great Fire of Rome, a group of nobles tried to assassinate him, and Nero grew increasingly paranoid, according to Hareth Al Bustani, author of "Nero and the Art of Tyranny(opens in new tab)" (Independently published, 2021).

Perhaps, given all that happened to Nero, any instability late in his life "should come as no surprise," Drake said.

Monday, July 25, 2022

The old person's lament

The poem below is about Ulysses -- more accuratey rendered as Odysseus -- Homer's hero in ancient Greece and king of Ithaca. Its line "I cannot rest from travel" summarizes a lot of old people today

It little profits that an idle king,
By this still hearth, among these barren crags,
Match'd with an aged wife, I mete and dole
Unequal laws unto a savage race,
That hoard, and sleep, and feed, and know not me.
I cannot rest from travel: I will drink
Life to the lees: All times I have enjoy'd
Greatly, have suffer'd greatly, both with those
That loved me, and alone, on shore, and when
Thro' scudding drifts the rainy Hyades
Vext the dim sea: I am become a name;
For always roaming with a hungry heart
Much have I seen and known; cities of men
And manners, climates, councils, governments,
Myself not least, but honour'd of them all;
And drunk delight of battle with my peers,
Far on the ringing plains of windy Troy.
I am a part of all that I have met;
Yet all experience is an arch wherethro'
Gleams that untravell'd world whose margin fades
For ever and forever when I move.
How dull it is to pause, to make an end,
To rust unburnish'd, not to shine in use!
As tho' to breathe were life! Life piled on life
Were all too little, and of one to me
Little remains: but every hour is saved
From that eternal silence, something more,
A bringer of new things; and vile it were
For some three suns to store and hoard myself,
And this gray spirit yearning in desire
To follow knowledge like a sinking star,
Beyond the utmost bound of human thought.

This is my son, mine own Telemachus,
To whom I leave the sceptre and the isle,—
Well-loved of me, discerning to fulfil
This labour, by slow prudence to make mild
A rugged people, and thro' soft degrees
Subdue them to the useful and the good.
Most blameless is he, centred in the sphere
Of common duties, decent not to fail
In offices of tenderness, and pay
Meet adoration to my household gods,
When I am gone. He works his work, I mine.

There lies the port; the vessel puffs her sail:
There gloom the dark, broad seas. My mariners,
Souls that have toil'd, and wrought, and thought with me—
That ever with a frolic welcome took
The thunder and the sunshine, and opposed
Free hearts, free foreheads—you and I are old;
Old age hath yet his honour and his toil;
Death closes all: but something ere the end,
Some work of noble note, may yet be done,
Not unbecoming men that strove with Gods.
The lights begin to twinkle from the rocks:
The long day wanes: the slow moon climbs: the deep
Moans round with many voices. Come, my friends,
'T is not too late to seek a newer world.
Push off, and sitting well in order smite
The sounding furrows; for my purpose holds
To sail beyond the sunset, and the baths
Of all the western stars, until I die.
It may be that the gulfs will wash us down:
It may be we shall touch the Happy Isles,
And see the great Achilles, whom we knew.
Tho' much is taken, much abides; and tho'
We are not now that strength which in old days
Moved earth and heaven, that which we are, we are;
One equal temper of heroic hearts,
Made weak by time and fate, but strong in will
To strive, to seek, to find, and not to yield.