Everyday Erinyes #321

 Posted by at 5:21 am  Politics
Jun 052022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

My primary care physiocian once told me I deserved an honorary medical degree because I can spell all my prescription drugs (proprietary and generic), as well as all my OTC meds (proprietary and generic) correctly. He was joking, of course. I simply was born with the spelling gene, and I also do my best to pay attention. But his remark does illustrate how little attention so many people pay to matters of their own health. I am not a doctor nor a medical technician, and I certainly don’t play one on TV. But I do do “due diligence” when anythong new turns up in or near my own body (near meaning physically near, like a pandemic, or emotionally near, like in one or more people I care about.) And cancer is something none of us can really avoid being near at some point or other. So when something like this turns up, so does my gaze.
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‘Masked’ cancer drug stealthily trains immune system to kill tumors while sparing healthy tissues, reducing treatment side effects

Dendritic cells (green) produce cytokines like IL-12, which can train T cells (pink) to attack tumors.
Victor Segura Ibarra and Rita Serda/National Cancer Institute via Flickr, CC BY-NC

Aslan Mansurov, University of Chicago Pritzker School of Molecular Engineering

Many cancer treatments are notoriously savage on the body. Drugs often attack both healthy cells and tumor cells, causing a plethora of side effects. Immunotherapies that help the immune system recognize and attack cancer cells are no different. Though they have prolonged the lives of countless patients, they work in only a subset of patients. One study found that fewer than 30% of breast cancer patients respond to one of the most common forms of immunotherapy.

But what if drugs could be engineered to attack only tumor cells and spare the rest of the body? To that end, my colleagues and I at the University of Chicago’s Pritzker School of Molecular Engineering have designed a method to keep one promising cancer drug from wreaking havoc by “masking” it until it reaches a tumor.

Immunotherapies help the immune system recognize and target cancer cells.

The promise of IL-12

Cytokines are proteins that can modulate how the immune system responds to threats. One way they do this is by activating killer T cells, a type of white blood cells that can attack cancer cells. Because cytokines can train the immune system to kill tumors, this makes them very promising as cancer treatments.

One such cytokine is interleukin-12, or IL-12. Though it was discovered more than 30 years ago, IL-12 still isn’t an FDA-approved therapy for cancer patients because of its severe side effects, such as liver damage. This is in part because IL-12 instructs immune cells to produce a large amount of inflammatory molecules that can damage the body.

Scientists have since been working to reengineer IL-12 to be more tolerable while retaining its powerful cancer-killing effects.

Masking the killer

To create a safer version of IL-12, my colleagues and I took advantage of one of the main differences between healthy and cancerous tissue: an excess of growth-promoting enzymes in cancers. Because cancer cells proliferate very rapidly, they overproduce certain enzymes that help them invade the nearby healthy tissue and metastasize to other parts of the body. Healthy cells grow at a much slower pace and produce fewer of these enzymes.

With this in mind, we “masked” IL-12 with a cap that covers the part of the molecule that normally binds to immune cells to activate them. The cap is removed only when it comes into contact with enzymes found in the vicinity of tumors. When these enzymes chop off the cap, IL-12 is reactivated and spurs nearby killer T cells to attack the tumor.

Killer T cells surrounding a cancer cell
Killer T cells (green and red) can attach to cancer cells (blue, center) and kill them by releasing toxic chemicals (red), a move scientists have dubbed ‘the kiss of death.’
NIH/Flickr

When we applied these masked IL-12 molecules to both healthy and tumor tissue donated by melanoma and breast cancer patients, our results confirmed that only the tumor samples were able to remove the cap. This indicated that masked IL-12 could potentially drive a strong immune response against tumors without causing damage to healthy organs.

We then examined how safe masked IL-12 is by measuring liver damage biomarkers in mice. We found that immune-related side effects typically associated with IL-12 were notably absent in mice treated with masked IL-12 over a period of several weeks, indicating improved safety.

In breast cancer models, our masked IL-12 resulted in a 90% cure rate, while treatment with a commonly used immunotherapy called a checkpoint inhibitor resulted in only a 10% cure rate. In a model of colon cancer, masked IL-12 showed a 100% cure rate.

Our next step is to test the modified IL-12 in cancer patients. While it will take time to bring this encouraging development directly to patients, we believe a promising new treatment is on the horizon.The Conversation

Aslan Mansurov, Postdoctoral Researcher in Molecular Engineering, University of Chicago Pritzker School of Molecular Engineering

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, “training” certainly implies a lower level of intellectual involvement than “teaching” or “educating,” but even so, it sounds like pure science fiction to even think about “training”a non-sentient  particle such as a protein to act in a certain way – to stop working in some environments and start working in others. Even though it accomplishes this mission by reacting in a particular way to particular enzymes, it still sounds virtually miraculous. This solution is not ready to approve yet, but it is ready for testing in live cancer patients, and, though I know it will take time, I am looking forward to seeing resutlts from that testing. Please, Eumenides, keep an eye out (and help in any way you can.)

The Furies and I will be back.

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Everyday Erinyes #320

 Posted by at 5:56 pm  Plus, Politics
May 292022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

There are a lot of things I could be putting front and center this week. However, they are pretty well already front and center. This story got knocked off of all the front pages, and I thought, before it gets back on them, it might be good to have some common sense and facts So here it is.
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What is monkeypox? A microbiologist explains what’s known about this smallpox cousin

Monkeypox causes lesions that resemble pus-filled blisters, which eventually scab over.
CDC/Getty Images

Rodney E. Rohde, Texas State University

On May 18, 2022, Massachusetts health officials and the Centers for Disease Control and Prevention confirmed a single case of monkeypox in a patient who had recently traveled to Canada. Cases have also been reported in the United Kingdom and Europe.

Monkeypox isn’t a new disease. The first confirmed human case was in 1970, when the virus was isolated from a child suspected of having smallpox in the Democratic Republic of Congo (DRC). Monkeypox is unlikely to cause another pandemic, but with COVID-19 top of mind, fear of another major outbreak is understandable. Though rare and usually mild, monkeypox can still potentially cause severe illness. Health officials are concerned that more cases will arise with increased travel.

I’m a researcher who has worked in public health and medical laboratories for over three decades, especially in the realm of diseases with animal origins. What exactly is happening in the current outbreak, and what does history tell us about monkeypox?

A cousin of smallpox

Monkeypox is caused by the monkeypox virus, which belongs to a subset of the Poxviridae family of viruses called Orthopoxvirus. This subset includes the smallpox, vaccinia and cowpox viruses. While an animal reservoir for monkeypox virus is unknown, African rodents are suspected to play a part in transmission. The monkeypox virus has only been isolated twice from an animal in nature. Diagnostic testing for monkeypox is currently only available at Laboratory Response Network labs in the U.S. and globally.

The name “monkeypox” comes from the first documented cases of the illness in animals in 1958, when two outbreaks occurred in monkeys kept for research. However, the virus did not jump from monkeys to humans, nor are monkeys major carriers of the disease.

Electron microscope view of monkeypox, showing oval-shaped, mature virus particles and spherical, immature virions
Monkeypox belongs to the Poxviridae family of viruses, which includes smallpox.
CDC/ Cynthia S. Goldsmith

Epidemiology

Since the first reported human case, monkeypox has been found in several other central and western African countries, with the majority of infections in the DRC. Cases outside of Africa have been linked to international travel or imported animals, including in the U.S. and elsewhere.

The first reported cases of monkeypox in the U.S. was in 2003, from an outbreak in Texas linked to a shipment of animals from Ghana. There were also travel-associated cases in November and July 2021 in Maryland.

Because monkeypox is closely related to smallpox, the smallpox vaccine can provide protection against infection from both viruses. Since smallpox was officially eradicated, however, routine smallpox vaccinations for the U.S. general population were stopped in 1972. Because of this, monkeypox has been appearing increasingly in unvaccinated people.

Person getting temperature tested at airport
Indonesia began screening travelers after a monkeypox case was reported in Singapore in May 2019.
Jepayona Delita/Future Publishing via Getty Images

Transmission

The virus can be transmitted through contact with an infected person or animal or contaminated surfaces. Typically, the virus enters the body through broken skin, inhalation or the mucous membranes in the eyes, nose or mouth. Researchers believe that human-to-human transmission is mostly through inhalation of large respiratory droplets rather than direct contact with bodily fluids or indirect contact through clothes. Human-to-human transmission rates for monkeypox have been limited.

Health officials are worried the virus may currently be spreading undetected through community transmission, possibly through a new mechanism or route. Where and how infections are occurring are still under investigation.

Signs and symptoms

After the virus enters the body, it starts to replicate and spread through the body via the bloodstream. Symptoms usually don’t appear until one to two weeks after infection.

Monkeypox produces smallpox-like skin lesions, but symptoms are usually milder than those of smallpox. Flu-like symptoms are common initially, ranging from fever and headache to shortness of breath. One to 10 days later, a rash can appear on the extremities, head or torso that eventually turns into blisters filled with pus. Overall, symptoms usually last for two to four weeks, while skin lesions usually scab over in 14 to 21 days.

While monkeypox is rare and usually non-fatal, one version of the disease kills around 10% of infected people. The form of the virus currently circulating is thought to be milder, with a fatality rate of less than 1%.

Vaccines and treatments

Treatment for monkeypox is primarily focused on relieving symptoms. According to the CDC, no treatments are available to cure monkeypox infection.

Because smallpox is closely related to monkeypox, the smallpox vaccine can protect against both diseases.

Evidence suggests that the smallpox vaccine can help prevent monkeypox infections and decrease the severity of the symptoms. One vaccine known as Imvamune or Imvanex is licensed in the U.S. to prevent monkeypox and smallpox.

Vaccination after exposure to the virus may also help decrease chances of severe illness. The CDC currently recommends smallpox vaccination only in people who have been or are likely to be exposed to monkeypox. Immunocompromised people are at high risk.The Conversation

Rodney E. Rohde, Regents’ Professor of Clinical Laboratory Science, Texas State University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, it sounds to me as though health officials are paranoid over this – and I say that not in mockery, but in approval. Unfounded assumptions, particularly about transmission, are one of the ways pandemics start and get worse.There’s quite a bit we don’t know about monkey pox – but with the professionals watching it as they are, that will likely change soon. Hopefully we will learn enough.

The Furies and I will be back.

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Everyday Erinyes #319

 Posted by at 4:03 pm  Politics
May 222022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

It’s all very well to discuss how to deal with a tyrant or an autocrat when you actually have one – whether in your own country, or from the outside looking in at another country. But, you know, things change. It seems pretty clear that Texas, for instance, is a virtual autocracy right now. But it hasn’t always been so. Ann Richards was governor once – up until 1996. Between then and 2015, something happened. But what exactly? During those years, one assumes Texas was sliding into autocracy. How exactly?

NATO was formed to be an alliance of western democracies. Turkey is a member. Turkey is being described as “sliding into autocracy.” How far down that slippery slope is it really? Is it far enough to be expelled from NATO? Is there even any provision for a country to be expelled from NATO if it ceases to be a democracy? At one point does a nation cease to be a democracy?
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Why Turkey isn’t on board with Finland, Sweden joining NATO – and why that matters

Room for any more at NATO? Not according to Turkey’s president.
Kenzo Tribouillard/AFP via Getty Images

Ronald Suny, University of Michigan

After decades of neutrality, the two Nordic states that have to date remained out of the North Atlantic Treaty Organization have reacted to Russia’s invasion of Ukraine by declaring an intention to join the American-led alliance. But there is a major obstacle in their way: Turkey.

The increasingly autocratic and anti-democratic president of Turkey, Recep Tayyip Erdogan, has said he will not agree to the entry of these two countries. And as a member of NATO, Turkey’s approval is needed for Finland and Sweden to join.

Erdogan is alone among NATO leaders in publicly stating that he is against the two countries’ joining the alliance.

Harboring terrorists or grudges?

The Turkish president’s opposition is based on his view that Finland and Sweden support “terrorists.” What Erdogan means is that both countries have given protection and residence to members of the Kurdistan Workers’ Party, or PKK – the major armed group mounting resistance to Turkey’s harsh treatment of its millions of Kurdish citizens. The plight of the country’s Kurds, part of a large but stateless ethnic group in the region, has long been a bone of contention between Turkey and parts of the international community.

Despite the PKK’s being listed by the U.S. and EU as a terrorist group, Finland and Sweden have been reluctant to extradite members of the group to Turkey over human rights concerns. Erdogan has responded by calling Sweden a “hatchery” for terrorism and claiming neither country has “a clear, open attitude” toward terrorist organizations, adding: “How can we trust them?”

Erdoğan’s ire with Finland and Sweden has also been exacerbated by the country hosting followers of Turkish scholar and cleric Fethullah Gulen. These followers are part of an educational and political movement with which Erdogan had been allied, but with which he broke as it grew more powerful. The Turkish president accuses the Gulenists of staging a failed coup against his government in 2016.

All international politics is local

As if that were not enough, the neutral northern Europeans condemned Turkey’s 2019 incursion into Syria. In that operation, the Turks targeted Rojava – a socialist, feminist autonomous Kurdish enclave near the Turkish border. Complicating the matter, the Syrians of Rojava were – despite their links to the PKK – allies of the American forces. The Kurds of Rojava played a crucial role beating back the Islamic State group in Syria but were later abandoned by the Trump administration, which pulled U.S. troops back from the Turkish border, allowing its NATO ally to launch a military operation against the Kurds.

Foreign policy is almost always intimately tied to domestic concerns. In the case of Turkey’s government, a major fear is the threat to its grip on power posed by the Kurds – and international pressure over Turkey’s record of repressing the group.

Turkey’s Kurdish populations are not allowed free elections in the eastern Anatolian region, where they are the majority. Meanwhile, education and cultural institutions in the Kurdish language face a de facto ban.

The path ahead for NATO

Finland and Sweden are neutral countries not beholden to the strategic compromises that the United States and NATO are forced to make to hold the alliance together. Both countries have to date been free to take a moral position on Turkey’s position on Kurdish rights and have officially protested the repressions of dissidents, academics, journalists and minority groups.

Meanwhile, NATO countries have equivocated before their fellow member, agreeing to label the PKK a terrorist organization.

So where does this all leave Finland and Sweden’s application for NATO membership?

The rules for entry into the strategic alliance require unanimity of the current NATO members.

As such, Turkey can effectively veto the entry of Finland and Sweden.

The standoff highlights an underlying problem the alliance is facing. NATO is supposed to be an alliance of democratic countries. Yet several of its members – notably Turkey and Hungary – have moved steadily away from liberal democracy toward ethnonational populist authoritarianism.

Finland and Sweden, on the other hand, fulfill the parameters of NATO membership more clearly than several of the alliance’s current members. As the United States proclaims that the war in Ukraine is a struggle between democracy and autocracy, Turkey’s opposition to the Nordics who have protested its drift to illiberalism are testing the unity and the ideological coherence of NATO.The Conversation

Ronald Suny, Professor of History and Political Science, University of Michigan

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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AMT, I have one word: “filibuster.”

The Furies and I will be back.

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Everyday Erinyes #318

 Posted by at 10:36 am  Politics
May 152022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

Yes, I realize I just wrote about rivers last week. But rivers – water – like butterflies but even more so – are foundational to our survivsl at any time, and in the face of climate change it really is not possib;e to overestimate their importance. And rivers depend on watersheds. And watersheds, apparently, are, to put it mildly, poorly understood.

New Mexico – and I include in that former New Mexicans who have taken their knowledge elsewhere – is on the cutting edge when it comes to stream gauges and other technology to understand water flow. This probably should not be a surprise. Nobody knows water flow like people who live in areas which are essentially deserts, and especially people who have grown up in those areas. I’ve lived in high desert, but I didn’t grow up in one, and I assure you the phrase “stream gauge placement bias” would never have occurred to me, let alone passed my lips until reading this.
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How much do we know about our watersheds? New study says gaps in knowledge exist because of ‘bias’ in stream gauge placement

Corey Krabbenhoft saw the ebbs and flows of New Mexico’s rivers growing up in Albuquerque. From that experience, she knew how many of the waterways in the state only flow at certain times of the year.

As a postdoctoral researcher at the University of Buffalo, she is the lead author on a new paper published in the journal Nature Sustainability that looks at stream gauges, particularly in what the authors call “bias” in placement.

Krabbenhoft explained that the study doesn’t focus on where the stream gauges are located, but rather what types of rivers are represented globally when it comes to monitoring with gauges. This paper documented that ephemeral waters, headwaters and waterways in protected areas like wilderness areas are less likely to have stream gauges on them, which can lead to a gap in knowledge about how the river systems work.

In contrast, larger rivers that often have dams on them regulating the flows and usually pass through more populated areas are more likely to have these gauges.

In the introduction, the study authors state that this “weakens our ability to understand critical hydrologic processes and make informed water-management and policy decisions.”

Hydrologist George Allen, an associate professor at Texas A&M University and an author of the paper, said the team of researchers used a system called the Global Reach-level A priori Discharge Estimates for Surface Water and Ocean Topography (GRADES) dataset, which gathers publicly-available data. He said this does have limitations. While the United States tends to provide its data, other countries are less transparent.

The study traces its roots to a meeting in 2019 in New Mexico. During the meeting, the team decided to look into topics like water gauges.

Allen explained that the National Science Foundation funded a research coordination network to focus on dry rivers. This team had a diverse set of backgrounds including hydrologists like Allen and ecologists like Krabbenhoft. The team spent a handful of days in New Mexico talking about science and came up with several research ideas, including the location of stream gauges.

Krabbenhoft said the southwest United States is arid and many of the rivers are underrepresented when it comes to gauges.

This means not as much is known about the smaller rivers in the arid southwest despite the fact that those rivers play an important role in the ecosystem health and hydrology.

Map of river basin areas throughout the United States

Krabbenhoft said if all the information is being gathered downstream rather than upstream in areas like headwaters, it limits the ability to predict what’s going to happen in the watershed and to respond to those changes.

How did we get here?

The study authors describe this bias as inadvertent and say that it arose from the installation of gauges being dictated by national and local planning.

New Mexico holds a special distinction in the United States when it comes to water management. In 1889, the U.S. Geological Survey installed its first gauge on the Rio Grande at the town of Embudo, between Española and Taos. The Embudo gauge was installed in part as a training initiative that allowed hydrographers to develop stream gauging techniques.

It has since become an important gauge to measure the flows of the Rio Grande.

As interstate compacts were signed to ensure distribution of water among states, stream gauges began to play a critical role in meeting those goals.

Chris Stageman with the New Mexico Interstate Stream Commission said New Mexico’s gauges have been used to collect measurements that ensure compliance with compacts like the Rio Grande Compact and for making sure that different projects are in compliance with environmental permits.

For example, gauges help water managers to track how much water in the Rio Grande is considered native, meaning it originated in the drainages that feed the river, and how much of it is non-native, meaning it was moved into the Rio Grande as part of the San Juan-Chama Project. This is important because the water from the San Juan River falls under the Colorado River Compact while native Rio Grande water is subject to the Rio Grande Compact. Downstream users like Texas are not entitled to the San Juan water.

The gauges also ensure that New Mexico is meeting its commitments to protecting endangered species and help with compliance in various permits.

What does the gauge network look like in New Mexico?

In New Mexico, various entities have steam gauges, which tend to be located along major rivers. The U.S. Geological Survey, the Elephant Butte Irrigation District, the New Mexico Office of the State Engineer and the U.S. Bureau of Reclamation all have installed gauges.

The majority of gauges in New Mexico are operated by the Water Science Center, which is based in Albuquerque.

Stageman said New Mexico, in his opinion, has a good network of steam gauges, however, he said “we can always do better.”

One area that he said could use additional monitors is irrigation return flows.

“We have fairly good gauging on the diversions from the river. But we don’t have a really good system of measuring the return flows to the river,” he said.

Stageman said the Office of the State Engineer also runs quite a few gauges measuring diversions off of the main river systems.

“That’s important especially in these times of water shortages,” he said. “It’s important for ensuring that people aren’t taking too much water.”

He said those gauges also help ensure the water is fairly distributed and reduce conflict.

He said, from a compact and environmental compliance perspective, New Mexico’s network of stream gauges provides adequate coverage of the state. There are gauges on the Rio Grande, the San Juan River, the Pecos River, the Gila River and the Canadian River as well as other waterways in the state. But, from other perspectives, such as environmental monitoring, he agreed with the authors of the paper.

Stacy Timmons, associate director of hydrogeology programs at the New Mexico Bureau of Geology, oversees the implementation of the state’s Water Data Act, which was passed in 2019.

Whether New Mexico has enough stream gauges comes down to the question of for what purpose, Stacy Timmons said. Timmons oversees the implementation of the state’s Water Data Act. In terms of basic water management, she said New Mexico’s network meets the needs.

But, if it comes to answering more in-depth questions like whether a river is gaining water or losing water at a specific point, Timmons said there isn’t enough data to answer that in many parts of the state.

She said the high population areas do tend to have good monitoring systems in place.

With drought becoming an increasingly more pressing reality in New Mexico, Timmons compared the water monitoring data to a fuel gauge in a car. She said if she’s driving along and her fuel gauge is showing the tank is close to empty, she will be checking it more frequently.

“I think as we face water scarcity, we need to have quick access to that data so we can make our decisions with that context and information,” she said.

The Water Data Act aims to make it easier for entities in New Mexico who monitor water data, such as stream gauges or reservoir levels, to share that information by aggregating it at a central location. This data will then be available to anyone who is interested in it.

“In New Mexico, we need to wake up to the reality of our water scarce future and do all we can to help the agencies that help us keep an eye on water resources and manage it carefully,” she said.

What are some limiting factors in stream gauge installation?

One of the biggest limiting factors in the number of gauges is costs. Stageman said the costs don’t end once the gauge is installed. Maintenance is required to keep them operational.

“We have to go out there and physically measure the water to make sure that the gauges are acting properly,” he said. “And our staff does that as well as the USGS staff. We kind of collaborate on all of that.”

The USGS has more than 8,000 streamgages nationwide and it can be expensive to keep those going. In recent years, the agency has retired gages. In the last 13 months, a lack of funding has led the USGS to shut down four streamgages, including one in New Mexico, according to a USGS website that tracks discontinued and endangered streamgages. This streamgage was located on the Rio Grande near White Rock above the Buckman Diversion. It operated for three years.

Timmons said another challenge with New Mexico’s ephemeral waters is the substrate. She said the streams tend to change course. The stream gauges would have to be moved if the waterway shifted location and that is not an easy task.

The sandy substrate that is common in New Mexico also limits where stream gauges can be placed, Stageman said.

He said if a gauge is placed below a wash that flows intermittently and carries a lot of sediment when it runs, that could wreak havoc on the equipment.

Why is this data important?

Allen said most rivers in the world are not large.

“They’re rivers that go dry, that are small,” he said. “And if we want to understand how climate change and land use are changing our freshwater resources, it’s important to have observations across all kinds of rivers, including the most common types of rivers, which are these small rivers.”

He said gauges can help track trends in river flows, including historical flows compared to current flows.

There are other methods that can be used to monitor rivers, Allen said. For example, he has looked at satellite data as a way of tracking changes in the rivers. But this doesn’t provide the same level of details as the river gauge. Allen said gauges provide a continuous stream of data while satellites might update every few days as the satellite passes over that location.

With climate change leading to aridification and drought, water management is becoming even more critical than ever before.

“Understanding how the drought is affecting water resources in New Mexico really depends on our ability to monitor the surface water resources,” Allen said.

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Alecto, Megaera, and Tisiphone, “enough for basic water management” now is good, but not good enough for basic water management tomorrow, and not good enough to predict potential future weak spots. There are seven states in the Colorado River Compact and three in the Rio Grande compact, and Colorado and New Mexico are in both compacts, which kind of makes us ground zero. If any of us is going to survive, we need to know about rivers and watersheds and water in general than we now do.

(If you want a soundtrack, here is one – a portrait in music of a river from little trickles at the mountain watershed all the way down to the mighty river that enters the ocean (and observing things and people along the way)

The Furies and I will be back.

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Everyday Erinyes #317

 Posted by at 4:20 pm  Politics
May 082022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

The sight of industrialists stealing resources from indigenous peoples, and of that theft essentially turning into genocide, is unfortunately nothing new. It is as famiiar at Standing Rock as it is in the Amazon basin. But there’s a new twist to this story – the potential use of satellite techno;ogy and data to provide proof of injury – and of agency when the guilty parties deny fault. See what you think.
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Satellites over the Amazon capture the choking of the ‘house of God’ by the Belo Monte Dam – they can help find solutions, too

NASA’s Landsat satellites have been monitoring changes on Earth’s landscape for 50 years.
NASA illustration

Pritam Das, University of Washington; Faisal Hossain, University of Washington; Hörður Bragi Helgason, University of Washington, and Shahzaib Khan, University of Washington

The Xingu River is revered as the “house of God” by the Indigenous people living along its Volte Grande, or Big Bend, in the Brazilian Amazon. The river is essential to their culture and religion, and a crucial source of fish, transportation and water for trees and plants.

Five years ago, the Big Bend was a broad river valley interwoven with river channels teaming with fish, turtles and other wildlife. Today, as much as 80% of the water flow is gone.

That’s because in late 2015, the massive Belo Monte Dam project began redirecting water from the Xingu River upstream from the Big Bend, channeling it through a canal to a giant new reservoir. The reservoir now powers one of the largest hydropower dams in the world, designed with enough capacity to power around 20 million households, though it has been producing far less.

A young person drops off baskets while people wait behind him in a narrow boat holding manioc, an edible root.
Indigenous communities living in the Big Bend region of the Xingu River and its Bacaja tributary rely on the river for food and to transport crops.
Taylor Weidman/LightRocket via Getty Images

Most of the river’s flow now bypasses the Big Bend, and the Indigenous peoples who live there are watching their livelihoods and way of life become endangered. Some of the most devastating effects are during the rainy season, when wildlife and trees rely heavily on having high water. The consortium of utilities and mining companies that runs the dam has pushed back on government orders to allow more water to reach the Big Bend, claiming it would cut their generation and profits. The group has argued in the past that there was no scientific proof that the change in water flow harmed fish or turtles.

There is proof of the Belo Monte Dam project’s impact on the Big Bend, though – from above. Satellite data shows how dramatically the dam has altered the hydrology of the river there.

The front satellite image shows the Big Bend of the Xingu River on May 26, 2000, before the Belo Monte Dam project began. Move the slider to the left to see the same region on July 20, 2017.

The same satellite data can also point to potential solutions and ways that operators of the Belo Monte Dam could revise the dam’s operations to keep both its renewable power and the Xingu River flowing at the most important times of the year.

As scientists who work with remote sensing, we believe satellite observations can empower populations around the world who face threats to their resources. The fact that satellite observations of surface water of the Xingu River can be clearly tied to the construction and operation of the Belo Monte Dam offers hope that this kind of knowledge can no longer be hidden.

50 years of Earth observation

Satellites have been monitoring changes in Earth’s landscapes for 50 years, ever since the U.S. launched the first Landsat satellite in July 1972. By piecing together data from the Landsat program and other satellites, scientists can reconstruct historical patterns of change in the landscape and predict current and future trends. They can monitor forest cover, drought, wildfire damage and desert expansion, as well as river flows and reservoir operations around the world.

An example of how that data can be used to help threatened communities is the global Reservoir Assessment Tool, which was created by colleagues and one of us at the University of Washington. It monitors how much water is in about 1,600 reservoirs around the world.

Screenshot of the tool showing a map of Brazil and an example dam's chart of water outflow.
The Reservoir Assessment Tool allows communities to track river flow changes caused by nearby dams and locate proposed dams. It currently tracks dams built before 2000.
University of Washington

Dam operators already collect thorough on-site data about water flow, but their datasets are rarely shared with the public. Remote sensing doesn’t face the same restrictions. Making that data public can help hold operators to account for and protect local communities and their rivers.

How satellites could pressure Belo Monte to share

Satellite monitoring can provide unprecedented insight into the operations of dams like the Belo Monte and their impact on downstream populations.

Existing satellite data can be used to monitor recent historical behavior of a dam’s operations, track the state of the river and patterns of inflow and outflow at the dam, and even forecast the likely state of the reservoir. Much of that data is easily accessible and free. For example, a tool created for the regional governing body of the Mekong River Commission is empowering communities along the river in Southeast Asia by giving them access to satellite data about water flow at each dam – data that cannot be hidden or modified by those in power.

While estimates based on remote sensing have higher uncertainty than on-site measurements, unfettered access to such information can provide local populations with evidence to argue, in court if necessary, for more water releases.

Members of Indigenous groups living in the Big Bend region talk about changes they’ve seen since the dam was built.

Long-term observations of dams and hydroclimate records show it is possible to revise the standard operating procedures of dams so they allow more water to flow downstream when needed. A compromise with the Belo Monte Dam could ensure that enough water flows to the Xingu’s Big Bend region while also providing hydropower benefits.

By making the impact of the Belo Monte Dam and others like it public to the world, agencies and the general public can put pressure on the dam’s operators and its investors to release more water. Public pressure will become increasingly important, as water disputes in the Amazon are expected to worsen as the planet warms and deforestation continues. Climate change will affect river flow patterns in the Amazon and likely increase droughts, leaving less water during some periods.

A tool for social justice

The Amazonian native population has declined, and dams and nearby mining operations, like those threatening the Xingu’s Big Bend region, play a role. The current Brazilian government under president Jair Bolsonaro has generally sided with wealthy landowners and industry over Indigenous peoples, making access to independent data crucial for protecting these communities.

Monitoring dams is a powerful way satellites can make a difference. Nearly two-thirds of Brazil’s electricity comes from more than 200 large and 400-plus small hydropower plants, and more large dams are expected to be built in the Amazon this decade. Many are in areas with Indigenous populations.

Wide aerial view of Amazon rainforest and the dam under construction.
The Belo Monte Dam’s construction, shown here in 2012, flooded land and changed the river.
Mario Tama/Getty Images

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Remote sensing may not directly solve the problem of social injustice, but it offers the tools needed to recognize the problems and explore solutions. Being able to monitor changes in near-real time and compare them with historical operations can help maintain the checks and balances required for equitable growth.

Raaghul Senthilkumar, a former Master’s student at the University of Washington, contributed to this article.The Conversation

Pritam Das, Graduate Research Assistant, University of Washington; Faisal Hossain, Professor of Hydrology, University of Washington; Hörður Bragi Helgason, Graduate Research Assistant, University of Washington, and Shahzaib Khan, Graduate Research Assistant in Computational Hydrology, University of Washington

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, as the authors point out, satellite data is not a solution – it is only a tool – but it appears to me to be a darned good one. Put on your Eumenides hats, and stir up indigenous people and activists who care, and help them acquire and use this tool, with all other tools, to defend themselves. And, please – without delay. Our environmentsal losses, cultural losses, human losses have been so severe already, largely through delay, that we really cannot afford any more.

The Furies and I will be back.

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Everyday Erinyes #316

 Posted by at 4:29 pm  Politics
May 012022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

I can’t say that there’s much, if anything, new in this article. It does juxtapose two issues of which we are only too well aware, and demonstrates that the two are actually more or less the same. Hopefully we can learn something from that.
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Rising authoritarianism and worsening climate change share a fossil-fueled secret

Brazil’s Jair Bolsonaro and Donald Trump threw their weight behind industries that are driving climate change.
Jabin Botsford/The Washington Post via Getty Images

Eve Darian-Smith, University of California, Irvine

Around the world, many countries are becoming less democratic. This backsliding on democracy and “creeping authoritarianism,” as the U.S. State Department puts it, is often supported by the same industries that are escalating climate change.

In my new book, “Global Burning: Rising Antidemocracy and the Climate Crisis,” I lay out connections between these industries and the politicians who are both stalling action on climate change and diminishing democracy.

It’s a dangerous shift, both for representative government and for the future climate.

Corporate capture of environmental politics

In democratic systems, elected leaders are expected to protect the public’s interests, including from exploitation by corporations. They do this primarily through policies designed to secure public goods, such as clean air and unpolluted water, or to protect human welfare, such as good working conditions and minimum wages. But in recent decades, this core democratic principle that prioritizes citizens over corporate profits has been aggressively undermined.

Today, it’s easy to find political leaders – on both the political right and left – working on behalf of corporations in energy, finance, agribusiness, technology, military and pharmaceutical sectors, and not always in the public interest. These multinational companies help fund their political careers and election campaigns to keep them in office.

In the U.S., this relationship was cemented by the Supreme Court’s 2010 decision in Citizens United. The decision allowed almost unlimited spending by corporations and wealthy donors to support the political candidates who best serve their interests. Data shows that candidates with the most outside funding usually win. This has led to increasing corporate influence on politicians and party policies.

When it comes to the political parties, it’s easy to find examples of campaign finance fueling political agendas.

In 1988, when NASA scientist James Hansen testified before a U.S. Senate committee about the greenhouse effect, both the Republican and Democratic parties took climate change seriously. But this attitude quickly diverged. Since the 1990s, the energy sector has heavily financed conservative candidates who have pushed its interests and helped to reduce regulations on the fossil fuel industry. This has enabled the expansion of fossil fuel production and escalated CO2 emissions to dangerous levels.

The industry’s power in shaping policy plays out in examples like the coalition of 19 Republican state attorneys general and coal companies suing to block the Environmental Protection Agency from regulating greenhouse gas emissions from power plants.

At the same time that the energy sector has sought to influence policies on climate change, it has also worked to undermine the public’s understanding of climate science. For instance, records show ExxonMobil participated in a widespread climate-science denial campaign for years, spending more than US$30 million on lobbyists, think tanks and researchers to promote climate-science skepticism. These efforts continue today. A 2019 report found the five largest oil companies had spent over $1 billion on misleading climate-related lobbying and branding campaigns over the previous three years.

The energy industry has in effect captured the democratic political process and prevented enactment of effective climate policies.

Corporate interests have also fueled a surge in well-financed antidemocratic leaders who are willing to stall and even dismantle existing climate policies and regulations. These political leaders’ tactics have escalated public health crises, and in some cases, human rights abuses.

Brazil, Australia and the US

Many deeply antidemocratic governments are tied to oil, gas and other extractive industries that are driving climate change, including Russia, Saudi Arabia, Iran, Iraq and China.

In “Global Burning,” I explore how three leaders of traditionally democratic countries – Jair Bolsonaro of Brazil, Scott Morrison of Australia and Donald Trump in the U.S. – came to power on anti-environment and nationalist platforms appealing to an extreme-right populist base and extractive corporations that are driving climate change. While the political landscape of each country is different, the three leaders have important commonalities.

Bolsonaro, Morrison and Trump all depend on extractive corporations to fund electoral campaigns and keep them in office or, in the case of Trump, get reelected.

Bolsonaro walks toward cameras with men behind him.
Polls show the Brazilian public has been deeply unhappy with President Jair Bolsonaro’s handling of the Amazon rainforest.
Sergio Lima/AFP via Getty Images

For instance, Bolsonaro’s power depends on support from a powerful right-wing association of landowners and farmers called the União Democrática Ruralista, or UDR. This association reflects the interests of foreign investors and specifically the multibillion-dollar mining and agribusiness sectors. Bolsonaro promised that if elected in 2019, he would dismantle environmental protections and open, in the name of economic progress, industrial-scale soybean production and cattle grazing in the Amazon rainforest. Both contribute to climate change and deforestation in a fragile region considered crucial for keeping carbon out of the atmosphere.

Bolsonaro, Morrison and Trump are all openly skeptical of climate science. Not surprisingly, all have ignored, weakened or dismantled environmental protection regulations. In Brazil, that led to accelerated deforestation and large swaths of Amazon rainforest burning.

In Australia, Morrison’s government ignored widespread public and scientific opposition and opened the controversial Adani Carmichael mine, one of the largest coal mines in the world. The mine will impact public health and the climate and threatens the Great Barrier Reef as temperatures rise and ports are expanded along the coast.

Morrison and his wife holds hands and smile on the left while a protester in a 'stop Adani' t-shirt is held back by security on the right.
Australian Prime Minister Scott Morrison (left) faced protests over his support for the Adani Carmichael mine, one of the largest coal mines in the world.
AP Photo/Rick Rycroft

Trump withdrew the U.S. from the Paris climate agreement – a move opposed by a majority of Americans – rolled back over 100 laws meant to protect the environment and opened national parks to fossil fuel drilling and mining.

Notably, all three leaders have worked, sometimes together, against international efforts to stop climate change. At the United Nations climate talks in Spain in 2019, Costa Rica’s minister for environment and energy at the time, Carlos Manuel Rodriguez, blamed Brazil, Australia and the U.S. for blocking efforts to tackle climate injustice linked to global warming.

Brazil, Australia and the U.S. are not unique in these responses to climate change. Around the world, there have been similar convergences of antidemocratic leaders who are financed by extractive corporations and who implement anti-environment laws and policies that defend corporate profits. New to the current moment is that these leaders openly use state power against their own citizens to secure corporate land grabs to build dams, lay pipelines, dig mines and log forests.

For example, Trump supported the deployment of the National Guard to disperse Native Americans and environmental activists protesting the Dakota Access Pipeline, a project that he had personally been invested in. His administration also proposed harsher penalties for pipeline protesters that echoed legislation promoted by the American Legislative Exchange Council, whose members include lawmakers and lobbyists for the oil industry. Several Republican-led states enacted similar anti-protest laws.

Under Bolsonaro, Brazil has changed laws in ways that embolden land grabbers to push small farmers and Indigenous people off their land in the rainforest.

What can people do about it?

Fortunately, there is a lot that people can do to protect democracy and the climate.

Replacing fossil fuels with renewable energy and reducing the destruction of forests can cut greenhouse gas emissions. The biggest obstacles, a recent U.N. climate report noted, are national leaders who are unwilling to regulate fossil fuel corporations, reduce greenhouse gas emissions or plan for renewable energy production.

The path forward, as I see it, involves voters pushing back on the global trend toward authoritarianism, as Slovenia did in April 2022, and pushing forward on replacing fossil fuels with renewable energy. People can reclaim their democratic rights and vote out anti-environment governments whose power depends on prioritizing extractive capitalism over the best interests of their citizens and our collective humanity.The Conversation

Eve Darian-Smith, Professor of Global and International Studies, University of California, Irvine

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, it really should not surprise anyone that climate change and authoritarianism are being backed by the same people – because, when your own greed is more impostant to you than other people’s lives – well, that is who you are. And, like any other problem, we won’t find solutions easily (or at all) if we are not honest and clear-sighted about what the issue is. For that reason, I would change the phrase “on both the political right and left” to something like “most generally on the political right, but with some notable and egregious examples on the left as well.” Not just my opinion – the graph a couple of paragraphs down shows the truth (and also that it is getting worse). But words should be accurate too.

The Furies and I will be back.

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Everyday Erinyes #315

 Posted by at 3:18 pm  Politics
Apr 242022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

Immunology is a relatively new field of medicine, and so it’s not surprising that there ia a lot we don’t know – and by them I mean there is a lot that immunologists don’t know. But even the stuff that immunologists know, there is w lot that regular people don’t know – and some of that would be helpful. One thing which would be really helpful (and likely is not completely grasped even by immunologists) would be how long each particular immunization can be expected to last. I know no one has ever suggested that I get a second shot of, for instance, gamma globulin. However, I have had three smallpox vaccinations over the course of my lifetime (only two of which I was old enough to remember getting.) And tetanus – I’ve been fortunate enough not to have been exposed, but Virgil has had several tetanus boosters since we’ve been married, each due to some mishap while doing custodial work.

This article is highly simplified for non=medical people, but it’s straigjhtfoward enough to give us a basic understanding some reasons behind boosting and not boosting, and even a feel for the directions in which immunologocal research are going.
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Why we can’t ‘boost’ our way out of the COVID-19 pandemic for the long term

Although the COVID-19 vaccines have saved millions of lives, they have been insufficient at preventing breakthrough infections.
Andriy Onufriyenko/Moment via Getty Images

Prakash Nagarkatti, University of South Carolina and Mitzi Nagarkatti, University of South Carolina

With yet another COVID-19 booster available for vulnerable populations in the U.S., many people find themselves wondering what the end game will be.

The mRNA vaccines currently used in the U.S. against COVID-19 have been highly successful at preventing hospitalization and death. The Commonwealth Fund recently reported that in the U.S. alone, the vaccines have prevented over 2 million people from dying and over 17 million from hospitalization.

However, the vaccines have failed to provide long-term protective immunity to prevent breakthrough infections – cases of COVID-19 infection that occur in people who are fully vaccinated.

Because of this, the Centers for Disease Control and Prevention recently endorsed a second booster shot for individuals 50 years of age and older and people who are immunocompromised. Other countries including Israel, the U.K. and South Korea have also approved a second booster.

However, it has become increasingly clear that the second booster does not provide long-lasting protection against breakthrough infections. As a result, it will be necessary to retool the existing vaccines to increase the duration of protection in order to help bring the pandemic to an end.

As immunologists studying immune response to infections and other threats, we are trying to better understand the vaccine booster-induced immunity against COVID-19.

Activating longer-term immunity

It’s a bit of a medical mystery: Why are mRNA vaccines so successful in preventing the serious form of COVID-19 but not so great at protecting against breakthrough infections? Understanding this concept is critical for stopping new infections and controlling the pandemic.

COVID-19 infection is unique in that the majority of people who get it recover with mild to moderate symptoms, while a small percentage get the severe disease that can lead to hospitalization and death.

Understanding how our immune system works during the mild versus severe forms of COVID-19 is also important to the process of developing more targeted vaccines.

When people are first exposed to SARS-CoV-2 – the virus that causes COVID-19 – or to a vaccine against COVID-19, the immune system activates two key types of immune cells, called B and T cells. The B cells produce Y-shaped protein molecules called antibodies. The antibodies bind to the protruding spike protein on the surface of the virus. This blocks the virus from entering a cell and ultimately prevents it from causing an infection.

However, if not enough antibodies are produced, the virus can escape and infect the host cells. When this happens, the immune system activates what are known as killer T cells. These cells can recognize virus-infected cells immediately after infection and destroy them, thereby preventing the virus from replicating and causing widespread infection.

Thus, there is increasing evidence that antibodies may help prevent breakthrough infections while the killer T cells provide protection against the severe form of the disease.

Why booster shots?

The B cells and T cells are unique in that after they mount an initial immune response, they get converted into memory cells. Unlike antibodies, memory cells can stay in a person’s body for several decades and can mount a rapid response when they encounter the same infectious agent. It is because of such memory cells that some vaccines against diseases such as smallpox provide protection for decades.

But with certain vaccines, such as hepatitis, it is necessary to give multiple doses of a vaccine to boost the immune response. This is because the first or second dose is not sufficient to induce robust antibodies or to sustain the memory B and T cell response.

This boosting, or amplifying of the immune response, helps to increase the number of B cells and T cells that can respond to the infectious agent. Boosting also triggers the memory response, thereby providing prolonged immunity against reinfection.

T-cell activation explained.

COVID vaccine boosters

While the third dose – or first booster – of COVID-19 vaccines was highly effective in preventing the severe form of COVID-19, the protection afforded against infection lasted for less than four to six months.

That diminished protection even after the third dose is what led the CDC to endorse the fourth shot of COVID-19 vaccine – called the second booster – for people who are immunocompromised and those aged 50 and older.

However, a recent preliminary study from Israel that has not yet been peer-reviewed showed that the second booster did not further boost the immune response but merely restored the waning immune response seen during the third dose. Also, the second booster provided little extra protection against COVID-19 when compared to the initial three doses.

So while the second booster certainly provides a small benefit to the most vulnerable people by extending immune protection by a few months, there has been considerable confusion over what the availability of the fourth shot means for the general population.

Frequent boosting and immune exhaustion

In addition to the inability of the current COVID-19 vaccines to provide long-term immunity, some researchers believe that frequent or constant exposure to foreign molecules found in an infectious agent may cause immune “exhaustion.”

Such a phenomenon has been widely reported with HIV infection and cancer. In those cases, because the T cells “see” the foreign molecules all the time, they can get worn down and fail to rid the body of the cancer or HIV.

Evidence also suggests that in severe cases of COVID-19, the killer T cells may be exhibiting immune exhaustion and therefore be unable to mount a strong immune response. Whether repeated COVID-19 vaccine boosters can cause similar T cell exhaustion is a possibility that needs further study.

Role of adjuvants to boost vaccine-induced immunity

Another reason why the mRNA vaccines have failed to induce sustained antibody and memory response may be related to ingredients called adjuvants. Traditional vaccines such as those for diphtheria and tetanus use adjuvants to boost the immune response. These are compounds that activate the innate immunity that consists of cells known as macrophages. These are specialized cells that help the T cells and B cells, ultimately inducing a stronger antibody response.

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Because mRNA-based vaccines are a relatively new class of vaccines, they do not include the traditional adjuvants. The current mRNA vaccines used in the U.S. rely on small balls of fat called lipid nanoparticles to deliver the mRNA. These lipid molecules can act as adjuvants, but how precisely these molecules affect the long-term immune response remains to be seen. And whether the current COVID-19 vaccines’ failure to trigger strong long-lived antibody response is related to the adjuvants in the existing formulations remains to be explored.

While the current vaccines are highly effective in preventing severe disease, the next phase of vaccine development will need to focus on how to trigger a long-lived antibody response that would last for at least a year, making it likely that COVID-19 vaccines will become an annual shot.The Conversation

Prakash Nagarkatti, Professor of Pathology, Microbiology and Immunology, University of South Carolina and Mitzi Nagarkatti, Professor of Pathology, Microbiology and Immunology, University of South Carolina

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, being vaguely aware of this (though I didn’t know the technical term or anything close to this much) is why I hvae been so scrupulous in waiting the full recommended time between shots, and maybe a little more, just to be on the safe side. I won’t get my fourth (and probably last, unless something new comes up) shot before at least the third week in MAy. And will be hanging on to those masks (and mask extenders).

The Furies and I will be back.

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Everyday Erinyes #314

 Posted by at 2:21 pm  Politics
Apr 172022
 

Experts in autocracies have pointed out that it is, unfortunately, easy to slip into normalizing the tyrant, hence it is important to hang on to outrage. These incidents which seem to call for the efforts of the Greek Furies (Erinyes) to come and deal with them will, I hope, help with that. As a reminder, though no one really knows how many there were supposed to be, the three names we have are Alecto, Megaera, and Tisiphone. These roughly translate as “unceasing,” “grudging,” and “vengeful destruction.”

I don’t know whether the Erinyes are science geeks – but I suppose there’s no reason they might not be. Certainly it’s not unreasonable to suspect any person or group which is dedicated to truth and justice would be dedicated to science as well. But I know some of us are also interested in sceince as well as justice and truth, and this news, thoug it sounds small compared with what was previously accomplished, is still a big deal.
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The Human Genome Project pieced together only 92% of the DNA – now scientists have finally filled in the remaining 8%

Over half of the human genome contains repetitive DNA sequences whose functions are still not fully understood.
Malte Mueller/fStop via Getty Images

Gabrielle Hartley, University of Connecticut

When the Human Genome Project announced that they had completed the first human genome in 2003, it was a momentous accomplishment – for the first time, the DNA blueprint of human life was unlocked. But it came with a catch – they weren’t actually able to put together all the genetic information in the genome. There were gaps: unfilled, often repetitive regions that were too confusing to piece together.

With advancements in technology that could handle these repetitive sequences, scientists finally filled those gaps in May 2021, and the first end-to-end human genome was officially published on Mar. 31, 2022.

I am a genome biologist who studies repetitive DNA sequences and how they shape genomes throughout evolutionary history. I was part of the team that helped characterize the repeat sequences missing from the genome. And now, with a truly complete human genome, these uncovered repetitive regions are finally being explored in full for the first time.

The missing puzzle pieces

German botanist Hans Winkler coined the word “genome” in 1920, combining the word “gene” with the suffix “-ome,” meaning “complete set,” to describe the full DNA sequence contained within each cell. Researchers still use this word a century later to refer to the genetic material that makes up an organism.

One way to describe what a genome looks like is to compare it to a reference book. In this analogy, a genome is an anthology containing the DNA instructions for life. It’s composed of a vast array of nucleotides (letters) that are packaged into chromosomes (chapters). Each chromosome contains genes (paragraphs) that are regions of DNA which code for the specific proteins that allow an organism to function.

Diagram of chromosome unraveling to coiled DNA, genes and component nucleotides
Genetic material is made of DNA tightly packaged into chromosomes. Only select regions of the DNA in a genome contain genes coding for proteins.
VectorMine/iStock via Getty Images Plus

While every living organism has a genome, the size of that genome varies from species to species. An elephant uses the same form of genetic information as the grass it eats and the bacteria in its gut. But no two genomes look exactly alike. Some are short, like the genome of the insect-dwelling bacteria Nasuia deltocephalinicola with just 137 genes across 112,000 nucleotides. Some, like the 149 billion nucleotides of the flowering plant Paris japonica, are so long that it’s difficult to get a sense of how many genes are contained within.

But genes as they’ve traditionally been understood – as stretches of DNA that code for proteins – are just a small part of an organism’s genome. In fact, they make up less than 2% of human DNA.

The human genome contains roughly 3 billion nucleotides and just under 20,000 protein-coding genes – an estimated 1% of the genome’s total length. The remaining 99% is non-coding DNA sequences that don’t produce proteins. Some are regulatory components that work as a switchboard to control how other genes work. Others are pseudogenes, or genomic relics that have lost their ability to function.

And over half of the human genome is repetitive, with multiple copies of near-identical sequences.

What is repetitive DNA?

The simplest form of repetitive DNA are blocks of DNA repeated over and over in tandem called satellites. While how much satellite DNA a given genome has varies from person to person, they often cluster toward the ends of chromosomes in regions called telomeres. These regions protect chromosomes from degrading during DNA replication. They’re also found in the centromeres of chromosomes, a region that helps keep genetic information intact when cells divide.

Researchers still lack a clear understanding of all the functions of satellite DNA. But because satellite DNA forms unique patterns in each person, forensic biologists and genealogists use this genomic “fingerprint” to match crime scene samples and track ancestry. Over 50 genetic disorders are linked to variations in satellite DNA, including Huntington’s disease.

46 human chromosomes colored blue with white telomeres against a black screen
Satellite DNA tends to cluster toward the ends of chromosomes in their telomeres. Here, 46 human chromosomes are colored blue, with white telomeres.
NIH Image Gallery/flickr, CC BY-NC

Another abundant type of repetitive DNA are transposable elements, or sequences that can move around the genome.

Some scientists have described them as selfish DNA because they can insert themselves anywhere in the genome, regardless of the consequences. As the human genome evolved, many transposable sequences collected mutations repressing their ability to move to avoid harmful interruptions. But some can likely still move about. For example, transposable element insertions are linked to a number of cases of hemophilia A, a genetic bleeding disorder.

Transposable DNA may be the reason why humans have a tailbone but no tail.

But transposable elements aren’t just disruptive. They can have regulatory functions that help control the expression of other DNA sequences. When they’re concentrated in centromeres, they may also help maintain the integrity of the genes fundamental to cell survival.

They can also contribute to evolution. Researchers recently found that the insertion of a transposable element into a gene important to development might be why some primates, including humans, no longer have tails. Chromosome rearrangements due to transposable elements are even linked to the genesis of new species like the gibbons of southeast Asia and the wallabies of Australia.

Completing the genomic puzzle

Until recently, many of these complex regions could be compared to the far side of the moon: known to exist, but unseen.

When the Human Genome Project first launched in 1990, technological limitations made it impossible to fully uncover repetitive regions in the genome. Available sequencing technology could only read about 500 nucleotides at a time, and these short fragments had to overlap one another in order to recreate the full sequence. Researchers used these overlapping segments to identify the next nucleotides in the sequence, incrementally extending the genome assembly one fragment at a time.

These repetitive gap regions were like putting together a 1,000-piece puzzle of an overcast sky: When every piece looks the same, how do you know where one cloud starts and another ends? With near-identical overlapping stretches in many spots, fully sequencing the genome by piecemeal became unfeasible. Millions of nucleotides remained hidden in the the first iteration of the human genome.

Since then, sequence patches have gradually filled in gaps of the human genome bit by bit. And in 2021, the Telomere-to-Telomere (T2T) Consortium, an international consortium of scientists working to complete a human genome assembly from end to end, announced that all remaining gaps were finally filled.

With the completion of the first human genome, researchers are now looking toward capturing the full diversity of humanity.

This was made possible by improved sequencing technology capable of reading longer sequences thousands of nucleotides in length. With more information to situate repetitive sequences within a larger picture, it became easier to identify their proper place in the genome. Like simplifying a 1,000-piece puzzle to a 100-piece puzzle, long-read sequences made it possible to assemble large repetitive regions for the first time.

With the increasing power of long-read DNA sequencing technology, geneticists are positioned to explore a new era of genomics, untangling complex repetitive sequences across populations and species for the first time. And a complete, gap-free human genome provides an invaluable resource for researchers to investigate repetitive regions that shape genetic structure and variation, species evolution and human health.

But one complete genome doesn’t capture it all. Efforts continue to create diverse genomic references that fully represent the human population and life on Earth. With more complete, “telomere-to-telomere” genome references, scientists’ understanding of the repetitive dark matter of DNA will become more clear.

[Get fascinating science, health and technology news. Sign up for The Conversation’s weekly science newsletter.]The Conversation

Gabrielle Hartley, PhD Candidate in Molecular and Cell Biology, University of Connecticut

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Alecto, Megaera, and Tisiphone, as technical as this information is, the article is jam-packed with analogies which make it much clearer. We have seen quantities of science which have increasingly demonstrated that we are more alike than we are different – and by “we,” science increasingly means not just humans and other humans, but humans and animals, even humans, animals, and plants. I am inclined to hope for more of the same, But I am even more inclined to hope that humans (and animals and plants as appropriate) can increasingly embrace our similarities and stop fretting so much about our differences, but instead, embracing them too. I’m sure that won’t happen spontaneously. And maybe that’s where you, ladies, can help us.

The Furies and I will be back.

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