Science-Watching: Proton-Coupled Energy Transfer/Omicron Spike Function

[from Science, First Release Notification for July 21]

Proton-Coupled Energy Transfer in Molecular Triads

Abstract

A photochemical mechanism was experimentally discovered and denoted proton-coupled energy transfer (PCEnT). A series of anthracenephenolpyridine triads formed the local excited anthracene state after light excitation at ca. 400 nm, which led to fluorescence around 550 nm from the phenolpyridine unit. Direct excitation of phenolpyridine would have required light around 330 nm, but the coupled proton transfer within the phenolpyridine unit lowered its excited state energy so that it could accept excitation energy from anthracene. Singlet-singlet energy transfer thus occurred despite the lack of spectral overlap between the anthracene fluorescence and the phenolpyridine absorption. Moreover, theoretical calculations indicated negligible charge transfer between the anthracene and phenolpyridine units. PCEnT was suggested as an elementary reaction of possible relevance to biological systems and future photonic devices.

Access the full paper [via institutional access or paid download].

Omicron Spike Function and Neutralizing Activity Elicited by a Comprehensive Panel of Vaccines

Abstract

The SARS-CoV-2 Omicron variant of concern comprises several sublineages with BA.2 and BA.2.12.1 having replaced the previously dominant BA.1, and BA.4 and BA.5 increasing in prevalence worldwide. We show that the large number of Omicron sublineage spike mutations lead to enhanced ACE2 binding, reduced fusogenicity, and severe dampening of plasma neutralizing activity elicited by infection or seven clinical vaccines relative to the ancestral virus. Administration of a homologous or heterologous booster based on the Wuhan-Hu-1 spike sequence markedly increased neutralizing antibody titers and breadth against BA.1, BA.2, BA.2.12.1, and BA.4/5 across all vaccines evaluated. Our data suggest that although Omicron sublineages evade polyclonal neutralizing antibody responses elicited by primary vaccine series, vaccine boosters may provide sufficient protection against Omicron-induced severe disease.

Read the full paper. [Archived PDF]

“2022 Monkeypox Outbreak: Situational Awareness” with Syra Madad [Zoom]

[from Harvard Kennedy School’s Belfer Center, part of Harvard University]

Thursday, July 21, 2:30-4:00 PM EDT

RSVP (Required)

The 2022 Monkeypox outbreak continues to expand with case counts mounting in many countries. This seminar will cover where we are in the global fight against monkeypox, where we may be headed as a nation, and what we need to do right now to mitigate the growing threat of monkeypox. Join Belfer Fellow Dr. Syra Madad in conversation with Kai Kupferschmidt, Dr. Krutika Kuppalli, Dr. Anne Rimoin, Dr. Boghuma Kabisen Titanji, and Dr. Jay K. Varma.

About the Speakers

Dr. Anne Rimoin is a Professor of Epidemiology at the UCLA Fielding School of Public Health. She is the Gordon-Levin Endowed Chair in Infectious Diseases and Public Health. Dr. Rimoin is the director of the Center for Global and Immigrant Health and is an internationally recognized expert on emerging infections, global health, surveillance systems, and vaccination.

Rimoin has been working in the DRC since 2002, where she founded the UCLA-DRC Health Research and Training Program to train U.S. and Congolese epidemiologists to conduct high-impact infectious disease research in low-resource, logistically-complex settings.

Dr. Rimoin’s research focuses on emerging and vaccine-preventable diseases. It has led to fundamental understandings of the epidemiology of human monkeypox in post-eradication of smallpox, long-term immunity to Ebola virus in survivors and durability of immune response to Ebola virus vaccine in health workers in DRC. Her current research portfolio includes studies of COVID-19, Ebola, Marburg, Monkeypox and vaccine-preventable diseases of childhood.

Boghuma Kabisen Titanji (MD, MSc., DTM&H, PhD) is a Cameroonian born physician-scientist and Assistant Professor of Medicine at Emory University in Atlanta. She obtained her MD from the University of Yaoundé I in Cameroon and worked for two years after graduation as a medical officer, before pursuing post-graduate research training in London, United Kingdom. As an awardee of the prestigious Commonwealth Scholarship program, she obtained a Masters Degree in Tropical Medicine and International Health from the London School of Hygiene and Tropical Medicine, a diploma in Tropical Medicine and Hygiene from the Royal College of Physicians and a Ph.D. in Virology from University College London. Dr. Titanji joined Emory University School of Medicine in 2016 where she completed a residency in Internal Medicine, on the ABIM research pathway and a fellowship Infectious Diseases. She has three parallel career interests: translational and clinical research in HIV and emerging virus infections, science communication, and global health. Her clinical focus is general infectious diseases and people with HIV. Her current research focuses on chronic inflammation as a mediator of cardiovascular disease in people with HIV. She is passionate about leveraging translational research to improve the care of people with HIV, global health equity and using science to influence health policy through science communication and advocacy.

Jay K. Varma, MD is a Professor of Population Health Sciences and Director of the Cornell Center for Pandemic Prevention and Response at Weill Cornell Medicine. Dr. Varma is an expert on the prevention and control of diseases, having led epidemic responses, developed global and national policies, and led large-scale programs that have saved hundreds of thousands of lives in China, Southeast Asia, Africa, and the United States. After graduating magna cum laude with highest honors from Harvard, Dr. Varma completed medical school, internal medicine residency, and chief residency at the University of California, San Diego School of Medicine. From 2001-2021, he worked for the U.S. Centers for Disease Control and Prevention with postings in Atlanta, Thailand, China, Ethiopia, and New York City. From April 2020 – May 2021, he served as the principal scientific spokesperson and lead for New York City’s COVID-19 response. Dr. Varma has authored 143 scientific manuscripts, 13 essays, and one book.

Kai Kupferschmidt is a science journalist based in Berlin, Germany. He is a contributing correspondent for Science where he often covers infectious diseases. Kai received a diploma in molecular biomedicine from the University of Bonn, Germany and later visited the Berlin Journalism School. He has won several awards for his work, including the Journalism Prize of the German AIDS Foundation. Together with two colleagues he runs a podcast on global health called Pandemia [German]. He has also written two books, one about infectious diseases and one about the science of the color blue.

Krutika Kuppalli, MD, FIDSA is a Medical Officer for Emerging Zoonotic Diseases and Clinical Management in the Health Emergencies Program at the World Health Organization where she currently supports activities for the Monkeypox outbreak and COVID-19 pandemic. She completed her Internal Medicine residency and Infectious Diseases fellowship at Emory University, a Post-Doctoral Fellowship in Global Public Health at the University of California, San Diego and the Emerging Leader in Biosecurity Fellowship at the Johns Hopkins Center for Health Security. Dr. Kuppalli currently serves on the American Society of Tropical Medicine and Hygiene (ASTMH) Trainee Committee and is the Chair of the Infectious Diseases Society of America (IDSA) Global Health Committee.

Dr. Kuppalli was previously awarded the NIH Fogarty International Clinical Research Fellowship and conducted research in Southern India to understand barriers to care and how emerging infections impacted persons living with HIV/AIDS. She was the medical director of a large Ebola Treatment Unit in Sierra Leone during the 2014 West Africa Ebola outbreak, helped lead the development and implementation of pandemic response preparedness activities in resource limited settings, and has consulted on the development of therapeutics for emerging pathogens. Her clinical and research interests focus on health systems strengthening in resource limited settings, research and clinical care for emerging infections, outbreak preparedness and response, and policy. She has worked in numerous countries including Ethiopia, India, Sierra Leone, Uganda, and Haiti.

During the COVID-19 pandemic Dr. Kuppalli served as a consultant for the San Francisco Department of Health and helped develop and operationalize a field hospital. She served as an expert witness to the U.S. Congress, Financial Services Committee Task Force on Artificial Intelligence (AI) about how digital technologies may be leveraged for exposure notification and contact tracing to improve the pandemic response. She also collaborated with the Brennan Center for Justice to develop guidelines to inform “Healthy in-person Voting” in advance of the 2020 U.S. election and testified before the U.S. House Select Subcommittee regarding these recommendations. Prior to her position at WHO, she was the medical lead for COVID-19 vaccine rollout at the Medical University of South Carolina (MUSC) and helped coordinate vaccine education events for the staff and community and oversaw the reporting of adverse vaccine events.

Since joining WHO in August 2021, Dr. Kuppalli has been part of the WHO headquarters incident management team (IMST) for COVID-19, the clinical characterization and management working group for COVID-19, the COVID-19 therapeutics steering committee, and is the technical focal point for the post COVID-19 condition (Long COVID) steering committee. She is a member of the secretariat on the scientific advisory group on the origins of emerging and re-emerging infectious diseases (SAGO) which was convened by the Director General to understand and investigate the origins of SARS-CoV-2 and other novel pathogens. More recently since the development of the multi-country monkeypox outbreak she has been part of the IMST at WHO as one of the clinical management focal points. In this capacity she was part of the WHO core group that helped write the recently published Clinical Management and Infection Prevention and Control guidelines for Monkeypox and advising on the clinical endpoints for the global CORE therapeutics protocol.

Dr. Kuppalli is recognized as a scientific expert in global health, biosecurity and outbreak response. She was recognized by NPR Source of The Week early in the pandemic as an expert to follow and named to Elemental’s 50 Experts to Trust in a Pandemic. She has been a frequent contributor to numerous domestic and international media outlets including The New York Times, NPR, Reuters, The Washington Post, Vox, Stat News, San Francisco Chronicle, Forbes, NBC Bay Area, BBC News.

Coronavirus Update: Fall Boosters Could Have Bits of Omicron

[from ScienceNews Coronavirus Update, by Erin Garcia de Jesús]

For all the coronavirus variants that have thrown pandemic curve balls—including alpha, beta, gamma, deltaCOVID-19 vaccines have stayed the same. That could change this fall.

Yesterday, an advisory committee to the U.S. Food and Drug Administration met to discuss whether vaccine developers should update their jabs to include a portion of the omicron variant—the version of the coronavirus that currently dominates the globe. The verdict: The omicron variant is different enough that it’s time to change the vaccines. Exactly how is up in the air; the FDA still has to weigh in and decide what versions of the coronavirus will be in the shot.

“This doesn’t mean that we are saying that there will be boosters recommended for everyone in the fall,” Amanda Cohn, chief medical officer for vaccine policy at the U.S. Centers for Disease Control and Prevention said at the June 28 advisory meeting. “But my belief is that this gives us the right vaccine for preparation for boosters in the fall.”

The decision to update COVID-19 vaccines didn’t come out of nowhere. In the two-plus years that the coronavirus has been spreading around the world, it has had a few “updates” of its own—mutating some of its proteins that allow the virus to more effectively infect our cells or hide from our immune systems.

Vaccine developers had previously crafted vaccines to tackle the beta variant that was first identified in South Africa in late 2020. Those were scrapped after studies showed that current vaccines remained effective.

The current vaccines gave our immune systems the tools to recognize variants such as beta and alpha, which each had a handful of changes from the original SARS-CoV-2 virus that sparked the pandemic. But the omicron variant is a slipperier foe. Lots more viral mutations combined with our own waning immunity mean that omicron can gain a foothold in the body. And vaccine protection isn’t as good as it once was at fending off COVID-19 symptoms.

The shots still largely protect people from developing severe symptoms, but there has been an uptick in hospitalizations and deaths among older age groups, Heather Scobie, deputy team lead of the CDC’s Surveillance and Analytics Epidemiology Task Force said at the meeting. And while it’s impossible to predict the future, we could be in for a tough fall and winter, epidemiologist Justin Lessler of the University of North Carolina at Chapel Hill said at the meeting. From March 2022 to March 2023, simulations project that deaths from COVID-19 in the United States might number in the tens to hundreds of thousands.

A switch to omicron-containing jabs may give people an extra layer of protection for the upcoming winter. PfizerBioNTech presented data at the meeting showing that updated versions of its mRNA shot gave clinical trial participants a boost of antibodies that recognize omicron. One version included omicron alone, while the other is a twofer, or bivalent, jab that mixes the original formulation with omicron. Moderna’s bivalent shot boosted antibodies too. Novavax, which developed a protein-based vaccine that the FDA is still mulling whether to authorize for emergency use, doesn’t have an omicron-based vaccine yet, though the company said its original shot gives people broad protection, generating antibodies that probably will recognize omicron.

Pfizer and Moderna both updated their vaccines using a version of omicron called BA.1, which was the dominant variant in the United States in December and January. But BA.1 has siblings and has already been outcompeted by some of them.

Since omicron first appeared late last year, “we’ve seen a relatively troubling, rapid evolution of SARS-CoV-2,” Peter Marks, director of the FDA’s Center for Biologics Evaluation and Research in Silver Spring, Maryland, said at the advisory meeting.

Now, omicron subvariants BA.2, BA.2.12.1, BA.4 and BA.5 are the dominant versions in the United States and other countries. The CDC estimates that roughly half of new U.S. infections the week ending June 25 were caused by either BA.4 or BA.5. By the time the fall rolls around, yet another new version of omicron—or a different variant entirely—may join their ranks. The big question is which of these subvariants to include in the vaccines to give people the best protection possible.

BA.1, the version already in the updated vaccines, may be the right choice, virologist Kanta Subbarao said at the FDA meeting. An advisory committee to the World Health Organization, which Subbarao chairs, recommended on June 17 that vaccines may need to be tweaked to include omicron, likely BA.1. “We’re not trying to match [what variants] may circulate,” Subbarao said. Instead, the goal is to make sure that the immune system is as prepared as possible to recognize a wide variety of variants, not just specific ones. The hope is that the broader the immune response, the better our bodies will be at fighting the virus off even as it evolves.

The variant that is farthest removed from the original virus is probably the best candidate to accomplish that goal, said Subbarao, who is director of the WHO’s Collaborating Center for Reference and Research on Influenza at the Doherty Institute in Melbourne, Australia. Computational analyses of how antibodies recognize different versions of the coronavirus suggest that BA.1 is probably the original coronavirus variant’s most distant sibling, she said.

Some members of the FDA advisory committee disagreed with choosing BA.1, instead saying that they’d prefer vaccines that include a portion of BA.4 or BA.5. With BA.1 largely gone, it may be better to follow the proverbial hockey puck where it’s going rather than where it’s been, said Bruce Gellin, chief of Global Public Health Strategy with the Rockefeller Foundation in Washington, D.C. Plus, BA.4 and BA.5 are also vastly different from the original variant. Both BA.4 and BA.5 have identical spike proteins, which the virus uses to break into cells and the vaccines use to teach our bodies to recognize an infection. So when it comes to making vaccines, the two are somewhat interchangeable.

There are some real-world data suggesting that current vaccines offer the least amount of protection from BA.4 and BA.5 compared with other omicron subvariants, Marks said. Pfizer also presented data showing results from a test in mice of a bivalent jab with the original coronavirus strain plus BA.4/BA.5. The shot sparked a broad immune response that boosted antibodies against four omicron subvariants. It’s unclear what that means for people.

Not everyone on the FDA advisory committee agreed that an update now is necessary—two members voted against it. Pediatrician Henry Bernstein of Zucker School of Medicine at Hofstra/Northwell in Uniondale, N.Y., noted that the current vaccines are still effective against severe disease and that there aren’t enough data to show that any changes would boost vaccine effectiveness. Pediatric infectious disease specialist Paul Offit of Children’s Hospital of Philadelphia said that he agrees that vaccines should help people broaden their immune responses, but he’s not yet convinced omicron is the right variant for it.

Plenty of other open questions remain too. The FDA could authorize either a vaccine that contains omicron alone or a bivalent shot, although some data hinted that a bivalent dose might spark immunity that could be more durable. Pfizer and Moderna tested their updated shots in adults. It’s unclear what the results mean for kids. Also unknown is whether people who have never been vaccinated against COVID-19 could eventually start with such an omicron-based vaccine instead of the original two doses.

Maybe researchers will get some answers before boosters start in the fall. But health agencies need to make decisions now so vaccine developers have a chance to make the shots in the first place. Unfortunately, we’re always lagging behind the virus, said pediatrician Hayley Gans of Stanford University. “We can’t always wait for the data to catch up.”

COVID-19 and “Naïve Probabilism”

[from the London Mathematical Laboratory]

In the early weeks of the 2020 U.S. COVID-19 outbreak, guidance from the scientific establishment and government agencies included a number of dubious claims—masks don’t work, there’s no evidence of human-to-human transmission, and the risk to the public is low. These statements were backed by health authorities, as well as public intellectuals, but were later disavowed or disproven, and the initial under-reaction was followed by an equal overreaction and imposition of draconian restrictions on human social activities.

In a recent paper, LML Fellow Harry Crane examines how these early mis-steps ultimately contributed to higher death tolls, prolonged lockdowns, and diminished trust in science and government leadership. Even so, the organizations and individuals most responsible for misleading the public suffered little or no consequences, or even benefited from their mistakes. As he discusses, this perverse outcome can be seen as the result of authorities applying a formulaic procedure of “naïve probabilism” in facing highly uncertain and complex problems, and largely assuming that decision-making under uncertainty boils down to probability calculations and statistical analysis.

This attitude, he suggests, might be captured in a few simple “axioms of naïve probabilism”:

Axiom 1: more complex the problem, the more complicated the solution.

This idea is a hallmark of naïve decision making. The COVID-19 outbreak was highly complex, being a novel virus of uncertain origins, and spreading through the interconnected global society. But the potential usefulness of masks was not one of these complexities. The mask mistake was consequential not because masks were the antidote to COVID-19, but because they were a low cost measure the effect of which would be neutral at worst; wearing a mask can’t hurt in reducing the spread of a virus.

Yet the experts neglected common sense in favor of a more “scientific response” based on rigorous peer review and sufficient data. Two months after the initial U.S. outbreak, a study confirmed the obvious, and masks went from being strongly discouraged to being mandated by law. Precious time had been wasted, many lives lost, and the economy stalled.

Crane also considers another rule of naïve probabilism:

Axiom 2: Until proven otherwise, assume that the future will resemble the past.

In the COVID-19 pandemic, of course, there was at first no data that masks work, no data that travel restrictions work, no data of human-to-human transmission. How could there be? Yet some naïve experts took this as a reason to maintain the status quo. Indeed, many universities refused to do anything in preparation until a few cases had been detected on campus—at which point they had some data, as well as hundreds or thousands of other as yet undetected infections.

Crane touches on some of the more extreme examples of his kind of thinking, which assumes that whatever can’t be explained in terms of something that happened in the past is speculative, non-scientific and unjustifiable:

“This argument was put forward by John Ioannidis in mid-March 2020, as the pandemic outbreak was already spiralling out of control. Ioannidis wrote that COVID-19 wasn’t a ‘once-in-a-century pandemic,’ as many were saying, but rather a ‘once-in-a-century data-fiasco’. Ioannidis’s main argument was that we knew very little about the disease, its fatality rate, and the overall risks it poses to public health; and that in face of this uncertainty, we should seek data-driven policy decisions. Until the data was available, we should assume COVID-19 acts as a typical strain of the flu (a different disease entirely).”

Unfortunately, waiting for the data also means waiting too long, if it turns out that the virus turns out to be more serious. This is like waiting to hit the tree before accepting that the available data indeed supports wearing a seatbelt. Moreover, in the pandemic example, this “lack of evidence” argument ignores other evidence from before the virus entered the United States. China had locked down a city of 10 million; Italy had locked down its entire northern region, with the entire country soon to follow. There was worldwide consensus that the virus was novel, the virus was spreading fast and medical communities had no idea how to treat it. That’s data, and plenty of information to act on.

Crane goes on to consider a 3rd axiom of naïve probabilism, which aims to turn ignorance into a strength. Overall, he argues, these axioms, despite being widely used by many prominent authorities and academic experts, actually capture a set of dangerous fallacies for action in the real world.

In reality, complex problems call for simple, actionable solutions; the past doesn’t repeat indefinitely (i.e., COVID-19 was never the flu); and ignorance is not a form of wisdom. The Naïve Probabilist’s primary objective is to be accurate with high probability rather than to protect against high-consequence, low-probability outcomes. This goes against common sense principles of decision making in uncertain environments with potentially very severe consequences.

Importantly, Crane emphasizes, the hallmark of Naïve Probabilism is naïveté, not ignorance, stupidity, crudeness or other such base qualities. The typical Naïve Probabilist lacks not knowledge or refinement, but the experience and good judgment that comes from making real decisions with real consequences in the real world. The most prominent naïve probabilists are recognized (academic) experts in mathematical probability, or relatedly statistics, physics, psychology, economics, epistemology, medicine or so-called decision sciences. Moreover, and worryingly, the best known naïve probabilists are quite sophisticated, skilled in the art of influencing public policy decisions without suffering from the risks those policies impose on the rest of society.

Read the paper. [Archived PDF]

Pathogens-Watching

New Articles in PLOS Pathogens

Insertive Condom-Protected and Condomless Vaginal Sex Both Have a Profound Impact on the Penile Immune Correlates of HIV Susceptibility

by Avid Mohammadi, Sareh Bagherichimeh, Yoojin Choi, Azadeh Fazel, Elizabeth Tevlin, Sanja Huibner, Zhongtian Shao, David Zuanazzi, Jessica L. Prodger, Sara V. Good, Wangari Tharao & Rupert Kaul

Summary: In heterosexual men, the penis is the primary site of Human Immunodeficiency Virus (HIV) acquisition. Levels of inflammatory cytokines in the coronal sulcus are associated with an increased HIV risk, and we hypothesized that these may be altered after insertive penile sex. Therefore, we designed the Sex, Couples and Science Study (SECS study) to define the impact of penilevaginal sex on the penile immune correlates of HIV susceptibility. We found that multiple coronal sulcus cytokines increased dramatically and rapidly after sex, regardless of condom use, with a return to baseline levels by 72 hours. The changes observed after condomless sex were strongly predicted by cytokine concentrations in the vaginal secretions of the female partner, and were similar in circumcised and uncircumcised men. We believe that these findings have important implications for understanding the immunopathogenesis of penile HIV acquisition; in addition, they have important implications for the design of clinical studies of penile HIV acquisition and prevention.

[Archived PDF]

Engineering, Decoding and Systems-Level Characterization of Chimpanzee Cytomegalovirus

by Quang Vinh Phan, Boris Bogdanow, Emanuel Wyler, Markus Landthaler, Fan Liu, Christian Hagemeier & Lüder Wiebusch

Summary: Human cytomegalovirus (HCMV) infection is associated with systemic disease in immunocompromised individuals and congenitally infected neonates. Animal CMVs and their bacterial artificial chromosome (BAC) clones have been utilized as models for CMV infection and thereby contributed immensely to the understanding of pathogenesis, host immune response and underlying molecular mechanism of CMV infections. As the closest relative to HCMV, the chimpanzee CMV (CCMV) holds a great potential as a model system for HCMV infection but its application was limited due to the lack of tools and data for functional genomic analyses. Here, the cloning of the CCMV as a BAC vector made its viral genome available to gene targeting techniques that allow the efficient application of reverse genetic strategies. Furthermore, the multi-omic datasets created in this study provide an in-depth view of the viral gene repertoire and the host cell responses to infection, confirming the close phylogenetic relationship between HCMV and CCMV on a system level. Taken together, the newly established CCMVBAC system presents a framework for HCMV modeling and comparative studies to address key questions in evolutionary processes and infection mechanisms.

[Archived PDF]

RplI Interacts with 5′ UTR of exsA to Repress Its Translation and Type III Secretion System in Pseudomonas aeruginosa

by Dan Wang, Xinxin Zhang, Liwen Yin, Qi Liu, Zhaoli Yu, Congjuan Xu, Zhenzhen Ma, Yushan Xia, Jing Shi, Yuehua Gong, Fang Bai, Zhihui Cheng, Weihui Wu, Jinzhong Lin & Yongxin Jin

Summary: Ribosomes provide all living organisms the capacity to synthesize proteins. The production of many ribosomal proteins is often controlled by an autoregulatory feedback mechanism. Paeruginosa is an opportunistic human pathogen and its type III secretion system (T3SS) is a critical virulence determinant in host infections. In this study, by screening a Tn5 mutant library, we identified rplI, encoding ribosomal large subunit protein L9, as a novel repressor for the T3SS. Further exploring the regulatory mechanism, we found that the RplI protein interacts with the 5’ UTR (5’ untranslated region) of exsA, a gene coding for transcriptional activator of the T3SS. Such an interaction likely blocks ribosome loading on the exsA 5’ UTR, inhibiting the initiation of exsA translation. The significance of this work is in the identification of a novel repressor for the T3SS and elucidation of its molecular mechanism. Furthermore, this work provides evidence for individual ribosomal protein regulating mRNA translation beyond its autogenous feedback control.

[Archived PDF]

Structure of a Bacterial Rhs Effector Exported by the Type VI Secretion System

by Patrick Günther, Dennis Quentin, Shehryar Ahmad, Kartik Sachar, Christos Gatsogiannis, John C. Whitney & Stefan Raunser

Summary: Bacteria have developed a variety of strategies to compete for nutrients and limited resources. One system widely used by Gram-negative bacteria is the T6 secretion system which delivers a plethora of effectors into competing bacterial cells. Known functions of effectors are degradation of the cell wall, the depletion of essential metabolites such as NAD+ or the cleavage of DNA. RhsA is an effector from the widespread plant-protecting bacteria Pseudomonas protegens. We found that RhsA forms a closed cocoon similar to that found in bacterial Tc toxins and metazoan teneurin proteins. The effector cleaves its polypeptide chain by itself in three pieces, namely the N-terminal domain including a seal, the cocoon and the actual toxic component which potentially cleaves DNA. The toxic component is encapsulated in the large cocoon, so that the effector producing bacterium is protected from the toxin. In order for the toxin to exit the cocoon, we propose that the seal, which closes the cocoon at one end, is removed by mechanical forces during injection of the effector by the T6 secretion system. We further hypothesize about different scenarios for the delivery of the toxin into the cytoplasm of the host cell. Together, our findings expand the knowledge of the mechanism of action of the T6 secretion system and its essential role in interbacterial competition.

[Archived PDF]

Non-Neutralizing Antibodies Targeting the Immunogenic Regions of HIV-1 Envelope Reduce Mucosal Infection and Virus Burden in Humanized Mice

by Catarina E. Hioe, Guangming Li, Xiaomei Liu, Ourania Tsahouridis, Xiuting He, Masaya Funaki, Jéromine Klingler, Alex F. Tang, Roya Feyznezhad, Daniel W. Heindel, Xiao-Hong Wang, David A. Spencer, Guangnan Hu, Namita Satija, Jérémie Prévost, Andrés Finzi, Ann J. Hessell, Shixia Wang, Shan Lu, Benjamin K. Chen, Susan Zolla-Pazner, Chitra Upadhyay, Raymond Alvarez & Lishan Su

Summary: In the past decade, HIV-1 has infected an estimated 1.5 to 2 million people every year, but vaccines needed to control this pandemic are unavailable. Among vaccines tested in the human efficacy trials, the RV144 vaccine regimen showed a modest efficacy and revealed non-neutralizing antibodies against the virus envelope glycoproteins as a correlate of reduced virus acquisition. To design more efficacious HIV-1 vaccines, a better understanding about antiviral mechanisms of these antibodies is needed. Here non-neutralizing monoclonal antibodies against two immunogenic sites on the virus envelope were evaluated for passive administration to humanized mice that were subsequently challenged with HIV-1. The antibodies did not block mucosal HIV-1 infection but reduced virus burden. The level of virus reduction correlated with the antibody binding potency and the effector functions mediated through their Fc fragments, which included antibody-dependent phagocytosis and complement activation, but not the commonly studied antibody-dependent cellular cytotoxicity. The importance of the Fc functions was further demonstrated by reduced virus control when mutations were introduced to decrease Fc activities. This study provides new evidence for the important contribution of multiple Fc-dependent antibody functions in immune control against HIV-1.

[Archived PDF]

Variability in an Effector Gene Promoter of a Necrotrophic Fungal Pathogen Dictates Epistasis and Effector-Triggered Susceptibility in Wheat

by Evan John, Silke Jacques, Huyen T. T. Phan, Lifang Liu, Danilo Pereira, Daniel Croll, Karam B. Singh, Richard P. Oliver & Kar-Chun Tan

Summary: Breeding for durable resistance to fungal diseases in crops is a continual challenge for crop breeders. Fungal pathogens evolve ways to overcome host resistance by masking themselves through effector evolution and evasion of broad-spectrum defense responses. Association studies on mapping populations infected by isolate mixtures are often used by researchers to seek out novel sources of genetic resistance. Disease resistance quantitative trait loci (QTL) are often minor or inconsistent across environments. This is a particular problem with septoria diseases of cereals such as septoria nodorum blotch (SNB) of wheat caused by Parastagonospora nodorum. The fungus uses a suite of necrotrophic effectors (NEs) to cause SNB. We characterized a genetic element, called PE401, in the promoter of the major NE gene Tox1, which is present in some Pnodorum isolates. PE401 functions as a transcriptional repressor of Tox1 and exerts epistatic control on another major SNB resistance QTL in the host. In the context of crop protection, constant surveillance of the pathogen population for the frequency of PE401 in conjunction with NE diversity will enable agronomists to provide the best advice to growers on which wheat varieties can be tailored to provide optimal SNB resistance to regional pathogen population genotypes.

[Archived PDF]

Mutational Analysis of Aedes aegypti Dicer 2 Provides Insights into the Biogenesis of Antiviral Exogenous Small Interfering RNAs

by Rommel J. Gestuveo, Rhys Parry, Laura B. Dickson, Sebastian Lequime, Vattipally B. Sreenu, Matthew J. Arnold, Alexander A. Khromykh, Esther Schnettler, Louis Lambrechts, Margus Varjak & Alain Kohl

Summary: Aedes aegypti mosquitoes that transmit human-pathogenic viruses rely on the exogenous small interfering RNA (exo-siRNA) pathway as part of antiviral responses. This pathway is triggered by virus-derived double-stranded RNA (dsRNA) produced during viral replication that is then cleaved by Dicer 2 (Dcr2) into virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs target viral RNA, leading to suppression of viral replication. The importance of Dcr2 in this pathway has been intensely studied in the Drosophila melanogaster model but is largely lacking in mosquitoes. Here, we have identified conserved and functionally relevant amino acids in the helicase and RNase III domains of Aeaegypti Dcr2 that are important in its silencing activity and antiviral responses against Semliki Forest virus (SFV). Small RNA sequencing of SFV-infected mosquito cells with functional or mutated Dcr2 gave new insights into the nature and origin of vsiRNAs. The findings of this study, together with the different molecular tools we have previously developed to investigate the exo-siRNA pathway of mosquito cells, have started to uncover important properties of Dcr2 that could be valuable in understanding mosquito-arbovirus interactions and potentially in developing or assisting vector control strategies.

[Archived PDF]

Probing the Structure and Function of the Protease Domain of Botulinum Neurotoxins Using Single-Domain Antibodies

by Kwok-ho Lam, Jacqueline M. Tremblay, Kay Perry, Konstantin Ichtchenko, Charles B. Shoemaker & Rongsheng Jin

Summary: Botulinum neurotoxins (BoNTs) are extremely toxic to humans by causing flaccid paralysis of botulism. The catalytic light chain (LC) of BoNTs is the warhead of the toxin, which is mainly responsible for BoNT’s neurotoxic effects. As an endopeptidase, LC is delivered by the toxin to inside neurons where it specifically cleaves neuronal SNARE proteins and causes muscle paralysis. While the currently available equine and human antitoxin sera can prevent further intoxication, they do not promote recovery from paralysis that has already occurred. We strike to develop single-domain variable heavy-chain (VHH) antibodies targeting the LC of BoNT/A (LC/A) and BoNT/B (LC/B) as antidotes to inhibit or eliminate the intraneuronal LC protease. Here, we report the identification and characterization of large panels of new and unique VHHs that bind to LC/A or LC/B. Using a combination of X-ray crystallography and biochemical assays, we reveal that VHHs exploit diverse mechanisms to interact with LC/A and LC/B and inhibit their protease activity, and such knowledge can be harnessed to predict their specificity towards different toxin subtypes within each serotype. We anticipate that the new VHHs and their characterization reported here will contribute to the development of improved botulism therapeutics having high potencies and broad specificities.

[Archived PDF]

B Cell Overexpression of FCRL5 and PD-1 Is Associated with Low Antibody Titers in HCV Infection

by Clinton O. Ogega, Nicole E. Skinner, Andrew I. Flyak, Kaitlyn E. Clark, Nathan L. Board, Pamela J. Bjorkman, James E. Crowe Jr., Andrea L. Cox, Stuart C. Ray & Justin R. Bailey

Summary: Antiviral immunity relies on production of protective immunoglobulin G (IgG) by B cells, but many hepatitis C virus (HCV)-infected individuals have very low levels of HCV-specific IgG in their serum. Elucidating mechanisms underlying this suboptimal IgG expression remains paramount in guiding therapeutic and vaccine strategies. In this study, we developed a highly specific method to capture HCV-specific B cells and characterized their surface protein expression. Two proteins analyzed were Fc receptor-like protein 5 (FCRL5), a cell surface receptor for IgG, and programmed cell death protein-1 (PD-1), a marker of lymphocyte activation and exhaustion. We measured serum levels of anti-HCV IgG in these subjects and demonstrated that overexpression of FCRL5 and PD-1 on memory B cells was associated with reduced anti-E2 IgG levels. This study uses HCV as a viral model, but the findings may be applicable to many viral infections, and they offer new potential targets to enhance antiviral IgG production.

[Archived PDF]