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Sunday, October 30, 2022

AAAS version of report on lab-leak theory of pandemic’s origin

 The mysterious origin of the COVID-19 pandemic, like so many aspects of the response to it, has created deep divides along party lines in the United States. Today, the Republican minority staff of a bipartisan Senate committee set up to probe the origin of SARS-CoV-2 issued an “interim report” arguing for the narrative that the virus entered humans because of a lab-related incident and not a natural jump from animals to humans. Many virologists and evolutionary biologists who have studied the origins of outbreaks dismiss the lab-leak hypothesis, but other scientists have complained that the possibility was too readily downplayed, and it has become increasingly popular among conservative media outlets and some Republican politicians.

“Based on the analysis of the publicly available information, it appears reasonable to conclude that the COVID-19 pandemic was, more likely than not, the result of a research-related incident,” the minority staff concludes in its 35-page report. That conclusion stands in sharp contrast to those of other panels, including from the World Health Organization and U.S. intelligence agencies, which have deemed a zoonotic jump more likely or remained neutral given the lack of direct evidence on the origin of the virus.

Senator Richard Burr (R–NC), the ranking member of the Senate’s Committee on Health, Education, Labor, and Pensions (HELP), wrote in a forward to the report that the minority oversight staff spent 15 months reviewing scientific studies and interviewing experts. The goal, Burr wrote, was “to provide a clearer picture of what we know, so far, about the origins of SARS-CoV-2 so that we can continue to work together to be better prepared to respond to future public health threats.”

Michael Worobey, an evolutionary biologist at the University of Arizona who has co-authored scientific reports examining data from the early days of the pandemic that provide some of the strongest support for a jump from animals to humans, speculates that the timing of the report’s release could be “a cynical effort to try to win Republican votes” in the upcoming midterm congressional and state elections.  Or, Worobey says, “it could just be a bunch of staffers with no ability to understand the science who stumbled across a bunch of misinformation and disinformation-filled tweets.” (“Senator Burr felt enough compelling, open-source information had been gathered during staff's comprehensive review of the facts that an interim report was appropriate,” a senior aide to the minority staff told Science.)

Worobey’s origin papers, which argue for a zoonotic jump at a market in Wuhan, China, come in for significant criticism in the report, to which he responded today in a Twitter thread to two reporters who sent him questions based on a draft of the report they apparently obtained in advance of its release. “These comments are either intentionally misleading or the result of honest misunderstandings, perhaps due to a failure to read our papers, which address these issues in great detail,” Worobey wrote. (Two of his most closely scrutinized papers were recently published by Science.)

The report recounts many details discussed at length in the media and the scientific literature since SARS-CoV-2 emerged in Wuhan in late December 2019. It focuses intense attention on the Wuhan Institute of Virology (WIV), which has a long record of studying bat coronaviruses, some of which have similarities to SARS-CoV-2. Those who argue for a lab-related release often suggest that WIV scientists either conducted experiments that created the virus or obtained it in the wild. They suspect it then escaped somehow, causing the first cluster of cases at the Wuhan market.

No direct evidence has surfaced that WIV had a version of SARS-CoV-2 in its lab or did such genetic engineering, but supporters of the lab leak scenario cite circumstantial evidence and suspicious patterns, which the report recounts in detail. It emphasizes the lack of transparency from the Chinese government and putative biosecurity lapses at the WIV labs with equipment such as air ducts.

As for the natural spillover theory, the report repeatedly emphasizes that no direct evidence exists that an animal sold at the Wuhan market or farmed in China was infected with a virus similar to SARS-CoV-2 prior to the pandemic. “While the absence of evidence is not itself evidence, the lack of corroborating evidence … three years into the pandemic, is highly problematic,” it reads.

One section of the minority staff report focuses on a detail that has not received much attention to date: that Chinese scientists tested the first experimental COVID-19 vaccines in humans a month earlier than similar candidates developed through the U.S. government’s crash program Operation Warp Speed. The Chinese vaccines used a different technology from the first U.S. vaccines, but all depended on the genetic sequence of SARS-CoV-2. The speed of the Chinese vaccine effort leads the report to ask whether Chinese researchers had access to that sequence prior to the rest of the world. The report, however, doesn’t address whether other factors could explain the rapid pace, such as the urgency of the outbreak in China or different regulatory environments.

Senator Patty Murray (D–WA), who chairs the Senate HELP committee, issued a statement today that did not comment on the report’s content or the timing of the release. “The HELP Committee is continuing bipartisan work on this oversight report,” Murray’s statement said.


'National Academy of Medicine rejects Republican allegations against member Peter Daszak'

 Republican members of Congress have failed to persuade the U.S. National  Academy of Medicine (NAM) to expel one of its members, conservation biologist Peter Daszak. In an email to its members, NAM concluded there “was no evidence” that Daszak had violated its code of conduct, as the representatives had alleged in a complaint to NAM.

The complaint suggests Daszak  is somehow linked to the mysterious origin of the COVID-19 pandemic. Daszak runs a research nonprofit, EcoHealth Alliance, that has collaborated with China’s Wuhan Institute of Virology (WIV). The Chinese institute has received intense scrutiny because the first cases of the pandemic surfaced where it is located. Although no direct evidence ties WIV to the emergence of SARS-CoV-2, some believe the virus leaked from the lab or may even have been engineered by scientists there.

NAM typically keeps its conduct probes confidential, but Science obtained an email—from someone who had no connection to the investigation—that explained the decision to members. And NAM’s code of conduct webpage was recently updated to note the decision. The email, sent from NAM’s leadership on 26 October, said the group convened a Conduct Review Committee to look into allegations against Daszak, and that the officials accepted the recommendation to exonerate him.

Daszak declined to comment on the details of the allegations or NAM’s probe and decision. "Because the NAM has conducted this review under strict confidentiality, I’m not in a position to share either the complaint or the NAM letter informing me of their decision," Daszak told Science.

But the complaint that kicked off the inquiry is a public document. On 30 November 2021, three members of the House Committee on Energy and Commerce—Representatives Cathy McMorris Rodgers (R–WA), the Republican chair, Brett Guthrie (KY) and Morgan Griffith (R—VA)—sent a 16-page  letter to NAM that focuses on a grant EcoHealth received from the National Institutes of Health, which included a subaward to WIV. The representatives asked NAM to investigate whether Daszak should be expelled from the prestigious institution, which elected him as a member in 2018.

The representatives offer a long list of allegations in their letter. Daszak, they contend, “repeatedly and willfully” refused to share data related to the grant, “acted in ways that are antithetical to responsible conduct of scientific research,”  refused to cooperate with congressional requests, and “made political arguments rather than measured scientific analysis.” They took him to task for promoting the hypothesis that the pandemic began because of a natural transmission of SARS-CoV-2 from animals to humans and aggressively dismissing the potential role of WIV and a possible laboratory-related incident. His actions, they assert, “effectively shut down all scientific discussion about the pandemic origins very early into the outbreak.”

Some of the issues raised in the letter are also heavily scrutinized in an interim “minority oversight staff” report issued this week by Senator Richard Burr (RNC), the lead Republican on a bipartisan committee that’s probing the origin of the pandemic. That report concludes that the pandemic most likely began when the virus somehow escaped from WIV—a position many scientists dismiss.

A NAM member who confirmed the validity of the exoneration email but asked not to be named says it was clear that the request for the probe was “frivolous and political” from the outset. This member also was outraged that Republicans who filed the complaint later revealed that NAM agreed to launch an investigation, violating the confidentiality of the process. “The rest of us were champing at the bit to speak out and maintained a silence about this,” this NAM member says.

Another NAM member who also asked not to be named said the complaint reflected a desire by some Republicans to blame China for the pandemic. “I  think it’s really bad for pandemic preparedness,” this member said. “We need international collaboration to confront pandemics effectively.”


Stem cell grafts and rehabilitation combined boost spinal cord injury results

 In recent years, researchers have made measurable progress, using animal models, to promote tissue regeneration in spinal cord injuries (SCI) through implanted neural stem cells or grafts. Other efforts have shown that intensive physical rehabilitation can improve function after SCI by promoting greater or new roles for undamaged or spared cells and neural circuits.

In a new paper, published August 22, 2022 in the journal JCI Insight, researchers at University of California San Diego School of Medicine address the question of whether  can augment functional outcomes when combined with pro-regenerative therapies, such as stem cell grafting.

Using a , researchers induced a cervical lesion that impaired the animals' ability to grasp with its forelimbs. There were four groups: animals who underwent the lesion alone; animals who received a subsequent grafting of neural stem cells designed to grow and connect with existing nerves; animals who received rehabilitation only; and animals who received both stem cell therapy and rehabilitation.

Rehabilitation therapy for some animals began one month after initial injury, a time point that approximates when most  are admitted to SCI rehabilitation centers. Rehabilitation consisted of  that rewarded them with food pellets if they performed grasping skills.

The researchers found that rehabilitation enhanced regeneration of injured corticospinal axons at the lesion site in rats, and that a combination of rehabilitation and grafting produced significant recovery in forelimb grasping when both treatments occurred one month after injury.

"These new findings indicate that rehabilitation plays a critically important role in amplifying functional recovery when combined with a pro-regenerative therapy, such as a neural stem cell transplant," said first author Paul Lu, Ph.D., associate adjunct professor of neuroscience at UC San Diego School of Medicine and research health science specialist at the Veterans Administration San Diego Healthcare System.

"Indeed, we found a surprisingly potent benefit of intensive physical rehabilitation when administered as a daily regimen that substantially exceeds what humans are now provided after SCI."

Senior author Mark H. Tuszynski, MD, Ph.D., professor of neurosciences and director of the Translational Neuroscience Institute at UC San Diego School of Medicine, and colleagues have long worked to address the complex challenges of repairing SCIs and restoring function.

In 2020, for example, they reported on the observed benefits of neural stem cell grafts in mice and in 2019, described 3D-printed implantable scaffolding that would promote nerve cell growth.

Spinal cord injuries remain a largely unresolved medical challenge. Nearly 18,000 people in the United States suffer SCIs each year, with another 294,000 persons living with an SCI, usually involving some degree of permanent paralysis or diminished physical function, such as bladder control or difficulty breathing.

"There is a great unmet need to improve regenerative therapies after SCI," said Tuszynski. "We hope that our findings point the way to a new potential combination treatment consisting of neural stem cell grafts plus rehabilitation, a strategy that we hope to move to  over the next two years."


Explore further

Implanted neural stem cell grafts show functionality in spinal cord injuries

More information: Paul Lu et al, Rehabilitation combined with neural progenitor cell grafts enables functional recovery in chronic spinal cord injury, JCI Insight (2022). DOI: 10.1172/jci.insight.158000
https://medicalxpress.com/news/2022-10-stem-cell-grafts-combined-boost.html

New device for early diagnosis of degenerative eye disorders

 Researchers at an EPFL lab have developed an ophthalmological device that can be used to diagnose some degenerative eye disorders long before the onset of the first symptoms. In early clinical trials, the prototype was shown to produce images with a sufficient degree of precision in just five seconds.

Research into treatments to stop or limit the progression of degenerative eye disorders that can lead to blindness is moving ahead apace. But, at present, there is no device that can reliably diagnose these conditions before the first symptoms appear. These disorders, the best-known of which is age-related macular degeneration (AMD), involve changes to the eye's photoreceptors. And they all have the same root cause: the deterioration of the retinal pigmentary epithelium (RPE), a layer of cells that sits behind the photoreceptors.

The device developed at EPFL's Laboratory of Applied Photonics Devices (LAPD) observes changes in the RPE before the onset of symptoms, providing researchers with the first-ever in vivo images in which cells can be differentiated. Armed with this early detection capability, clinicians will be able to diagnose these disorders before irreversible symptoms occur. The results of the first clinical trial have been published in a paper in the journal Ophthalmology Science.

Observing changes in the cells behind the photoreceptors

In addition to causing AMD, the deterioration of the RPE is behind a number of other eye disorders, including retinitis pigmentosa and diabetic retinopathy. Located between the photoreceptors and the choroid (a thin layer of tissue containing the vessels that carry blood to the retina), the RPE plays an important role in maintaining visual function and preserving the health of the eye's rods and cones.

Several research groups have studied these cells under the microscope—in vitro—to determine their properties and to observe the morphological changes that occur with aging but also with the onset and progression of retinal disorders such as AMD and retinitis pigmentosa. Until now, however, there has been no simple and  for observing the RPE in a live patient—in vivo—for early detection and ongoing monitoring of these conditions.

Oblique light beams hold the key

Various attempts have been made to design a device that allows clinicians to examine the RPE. But each has so far failed on the grounds of inadequate resolution, patient safety concerns or excessively long exposure times. The team at EPFL developed a retinal camera that features two oblique beams, trained on the white of the eye, coupled with an adaptive optical system that corrects distortions in the light waves to produce a clear image. This technology, dubbed Transscleral Optical Imaging, is similar to existing retinal imaging systems in its use of infrared light beams.

But, according to Christophe Moser, who heads the LAPD at the School of Engineering, it has one key difference: "The beams focus obliquely through the white of the eye, which circumvents the problem of excess light caused by the highly reflective cone photoreceptor cells, located in the center of the eye, when you illuminate the retina via the pupil." The light waves are then captured by the camera as they exit the eye through the pupil. The team had something of a eureka moment when they saw the first clear image on screen, since it was the first time anyone had observed this part of the human body using a clinically compatible imaging camera.

The researchers developed a clinical prototype in partnership with EarlySight, a spin-off from the same EPFL lab. With an exposure time of less than five seconds—a key speed advantage for potential diagnostic use—the camera is capable of capturing 100 raw images. Algorithms then align and aggregate the raw footage to produce a single, high-quality image on screen. The interface features five buttons, each corresponding to a predefined area of the eye, allowing the desired image to be selected. Users can also click anywhere on the diagram of the back of the eye to select the precise area they want to image.

The prototype device, known as Cellularis, was developed as part of the European Union's EIT Health ASSESS project, in partnership with Francine Behar-Cohen's research team at the French National Health and Medical Research Institute (INSERM) in Paris, and with the clinical research center at Jules-Gonin Eye Hospital in Lausanne. The camera was then assessed in a clinical trial—led by Irmela Mantel, a physician associate at the Medical Retina Unit of Jules-Gonin Eye Hospital—designed to evaluate the device's ability to produce clear RPE images in 29 healthy volunteers. In each case, the images generated by the camera were precise enough to quantify the morphological characteristics of the participants' RPE cells. They were stored in a database for future contribution to .

"The morphology of these cells, which play an essential role in retinal function, is a strong indicator of their health," says Laura Kowalczuk, a scientist at EPFL and at Jules-Gonin Eye Hospital, and the paper's lead author. "The ability to precisely detect RPE cells and observe morphological changes occurring in them is vital to the early detection of degenerative retinal disorders and to monitoring the efficacy of new treatments."


Explore further

Researchers decode retinal circuits for circadian rhythm, pupillary light response

More information: Laura Kowalczuk et al, in vivo Retinal Pigment Epithelium Imaging using Transscleral OPtical Imaging in healthy eyes, Ophthalmology Science (2022). DOI: 10.1016/j.xops.2022.100234
https://medicalxpress.com/news/2022-10-device-early-diagnosis-degenerative-eye.html

Novel mechanisms and therapeutic targets for acute myeloid leukemia

 Patients with acute myeloid leukemia, the most common type of adult blood cancer, show large-scale genomic mutations and altered DNA folding patterns that could help identify potential therapeutic targets, according to a Northwestern Medicine study published in Nature.

Feng Yue, Ph.D., the Duane and Susan Burnham Professor of Molecular Medicine, was senior author of the study.

More than 20,000 patients are diagnosed with  (AML) in the United States annually, according to the American Cancer Society and prognosis is grim, with a five-year survival rate of only 30 percent.

AML is caused when  in  interfere with the production of other blood-producing cells. AML can present as different combinations of genomic mutations in different patients. These mutations disrupt proper cell functioning, including the organization of chromatin 3D structures that regulate cell replication, differentiation transcription.

Different subtypes of AML are driven by these distinct genomic mutations, which creates a roadblock for treatment—patients with different subtypes can respond differently to the same therapy.

"Therefore, it is crucial to understand how those subtype-defining mutations give rise to the leukemia cell phenotype through changing the chromatin 3D structure," said Yue, who is also a professor of Biochemistry and Molecular Genetics, of Pathology and director of the Center for Cancer Genomics at the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.

In the current study, Yue and colleagues used deep sequencing and whole-genome sequencing techniques to analyze  from patients with and without AML, finding that patients with AML harbored large-scale genomic mutations. These mutations were associated with unique DNA folding patterns, or chromatin "loops" in AML cells. Additional genetic sequencing of these samples revealed thousands of novel loops that directly control key AML oncogenes.

To validate their findings, the investigators treated the AML cells with a DNA hypomethylating agent drug and used gene editing techniques to knock down the genes DNMT1, DNMT3A and DNMT3B, which are essential for DNA methylation and proper gene expression.

The team found that both the  and the gene knockdown changed genome folding patterns in the AML cells, suggesting that AML-specific DNA folding can in fact be reversed.

"All previous studies have been focused on 'enhancer' control units that can strengthen the gene expression. This is the first time that we've identified 'silencers' in leukemia or any cancer, which can shut down essential genes from long distance," Yue said.

Furthermore, these novel chromatin loops, gene activators and "silencers" could be used as potential therapeutic targets for AML, according to Yue.

"The restoration of pathogenic chromatin structure warrants further investigation into the targeted clinical usage of the existing drugs that could manipulate DNA methylation in  or leukemia," Yue added.


Explore further

3D genome structure influences cancer

More information: Jie Xu et al, Subtype-specific 3D genome alteration in acute myeloid leukaemia, Nature (2022). DOI: 10.1038/s41586-022-05365-x
https://medicalxpress.com/news/2022-10-exploring-mechanisms-therapeutic-acute-myeloid.html

Family of DNA damage–inducing microbial metabolites found in guts of people with IBS

 A team of researchers at Yale University has identified a group of genotoxins produced by a gut microbe that can damage DNA, leading to an increased risk of developing colorectal cancer. In their paper published in the journal Science, the group describes the screening process they developed. Jens Puschhof and Cynthia Sears, with the German Cancer Research Center and the Johns Hopkins University School of Medicine, respectively, have published a Perspectives piece in the same journal issue outlining the work done by the team on this effort.

Prior research has shown that some bacteria that exist in the human gut can produce chemicals that contribute to the likelihood of their host developing . Escherichia coli, for example, has been found to produce a substance called colibactin that has been linked to an increased chance of developing cancer. Such substances are known generically as genotoxins—they cause problems by damaging DNA. In this new effort, the researchers noted that very few genotoxins have been identified and sought to find more.

The work involved first collecting  from people with , which has also been associated with an increased risk of colorectal cancers. Each of the samples was then screened using a process the team developed to determine whether substances produced by a given type of bacteria cause DNA damage in the cells they infect.

They discovered an entire family of metabolites they named indolimines that are produced by a bacteria known as Morganella morganii. Prior research had found an association between M. morganii and an increased risk of colorectal cancer, but until now, their genotoxins had not been identified. The researchers also looked for a more direct link—they injected M. morganii into the bowels of healthy mice and found that doing so increased their rate of tumor growth.

The researchers suggest that their work highlights the impact that metabolites in the microbiome can have on cancer risk. And Puschhof and Sears note that the researchers showed that there is likely a broad range of genotoxins in the microbiome, suggesting much more work is required to find them.


Explore further

Study suggests that C. difficile drives some colorectal cancers

More information: Yiyun Cao et al, Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites, Science (2022). DOI: 10.1126/science.abm3233

Jens Puschhof et al, Microbial metabolites damage DNA, Science (2022). DOI: 10.1126/science.ade6952


https://medicalxpress.com/news/2022-10-family-dna-damageinducing-microbial-metabolites.html

Russia Floats Putin-Biden Talks At Moment Most in US Want Diplomatic Solution, But Not That Badly

On the same weekend that Russia angered the West by pulling out of the UN-brokered grain export deal, which allowed Ukraine to ship its wheat and food supplies to global markets via an internationally monitored safety corridor, the Kremlin has floated a potential basis for "high-level re-engagement", state media reported on Sunday.

Despite this big step back on what constituted the only diplomatic 'positive' of the past months between the warring sides, Putin office spokesman Dmitry Peskov said in an interview with Rossiya-1 TV channel that talks with the United States remain possible if Washington "pays heed to our concerns."

Such an opening in negotiations related to the war in Ukraine would ultimately be contingent on "the US desire to go back to the state of things as of December-January" Peskov described, and the US must ask, according to his words: "what the Russians are offering may not suit all of us, but maybe we should still sit down with them at the negotiating table?" 

The last time President Vladimir Putin weighed in on the possibility came in statements earlier this month, wherein he stated, "there is no platform for any negotiations yet."

Peskov's reference to the pre-invasion "state of things" in the December-January timeframe appears to be a reference to Russia's insistence on agreement on a formal declaration that Ukraine would never enter the NATO military alliance and other "security guarantees". This came in in the form of written proposals offered by the Russian side at the time, which both the Ukrainian government and West rebuffed. 

NATO's official line has remained that it would never allow Russia to in effect exercise any kind of veto power over who or who should not be considered for membership in the bloc. Complicating the possibility of any near-term reengagement on this issue is the fact that NATO countries have only greatly increased their support to Kiev, turning Ukraine into a de facto NATO partner. 

And yet recent polling shows most Americans want a diplomatic track between Washington and Moscow, particularly given growing fears of nuclear confrontation. As one poll from last month revealed

Nearly 60 percent of Americans would support the United States engaging in diplomatic efforts "as soon as possible" to end the war in Ukraine, even if that means Ukraine having to make concessions to Russia, according to a new poll. 

The survey, conducted by Data for Progress on behalf of the Quincy Institute for Responsible Statecraft, also found that a plurality (49 percent) said the Biden administration and Congress have not done enough diplomatically to help end the war (37 percent said they had). 

Further, as Responsible Statecraft pointed out, the Ukraine war is not even among the three top driving concerns among the American public...

"Just six percent said Russia’s war in Ukraine is among the top three most important issues facing the United States today, with the top three being inflation (46 percent), jobs and the economy (31 percent), and gun violence (26 percent)," the think tank commented

https://www.zerohedge.com/geopolitical/russia-floats-basis-putin-biden-talks-moment-most-americans-want-diplomatic-solution