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Spread & Containment

Distantly related viruses share self-assembly mechanism

How do the hundreds of individual pieces that make up viruses assemble into shapes capable of spreading disease from cell to cell? Credit: Brome mosaic…

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How do the hundreds of individual pieces that make up viruses assemble into shapes capable of spreading disease from cell to cell?

Credit: Brome mosaic virus capsid: Lucas, R.W., Larson, S.B., McPherson, A., (2002) J Mol Biol 317: 95-108 – https://www.rcsb.org/structure/1JS9; MS2 virus capsid: Rowsell, S., Stonehouse, N.J., Convery, M.A., Adams, C.J., Ellington, A.D., Hirao, I., Peabody, D.S., Stockley, P.G., Phillips, S.E., (1998) Nat Struct Biol 5: 970-975 – https://www.rcsb.org/structure/5MSF

How do the hundreds of individual pieces that make up viruses assemble into shapes capable of spreading disease from cell to cell?

Solving the mystery of self-assembly can pave the way for engineering advancements like molecules or robots that put themselves together. It could also contribute to more efficient packaging, automated delivery and targeted design of medicine in our fight against viruses that cause colds, diarrhea, liver cancer and polio.

“If we understand the physical rules of how viruses assemble, then we can try to make them form incorrect structures to hinder their spread,” said Rees Garmann, a chemist at San Diego State University and lead author of a new paper that fills in a piece of the puzzle.

Garmann, along with two SDSU graduate students and collaborators at Harvard and UCLA, concluded that two distantly related RNA viruses — one that infects bacteria and one that infects plants — perform this chemical choreography in strikingly similar ways.

In both, and potentially other, viruses, the protein components perfectly pattern into pentagons and hexagons that form a symmetrical icosahedral shell, one of the most prevalent shapes among all viruses, thanks to a scaffold provided by a looped and folded strand of RNA.

Similar to how a snowflake requires a couple of molecules of frigid water to surround a dust particle before crystallizing, a virus’s jungle-gym-like sphere of proteins coalesces quickly only after a few proteins loosely attach to the RNA.

“Without the interactions between the proteins and the RNA that my students, Fernando Vasquez and Daniel Villareal, were studying, it would take a very long time — weeks, months, maybe never — for this virus to assemble,” Garmann said.

Yet the whole assembly process, which Garmann and his collaborators captured in detailed videos using an innovative iSCAT (interferometric scattering) microscope that records individual viruses, takes mere minutes.

“The iSCAT technique opened a new window onto virus self-assembly,” said Vinothan N. Manoharan, a co-author on the study and the Wagner Family Professor of Chemical Engineering and Professor of Physics at Harvard’s John A. Paulson School of Engineering and Applied Sciences. “Only by seeing individual viruses form could we determine that they don’t all assemble at the same time. That was key to understanding the self-assembly mechanism that the two types of virus share.”

Garmann says their experiments point the way to answering the next big mystery of how viruses ensure accuracy and functionality at all steps along the assembly line.

Knowing more about how viruses assemble is related to the 1950s-era physics paradox of how proteins fold into their proper shapes much faster than if they relied solely on chance encounters — a process estimated to take longer than the billions of years the universe has existed.

One Case Closed, Others Opened

Although the viruses in this study and the virus that causes COVID-19 both have RNA, the researchers say that extending these findings to the bigger, oddball SARS-CoV-2 virus would be premature.

“The hope of our research is to learn about some physical, fundamental interaction that occurs in these model systems,” said Vasquez, a doctoral student in chemistry. “Maybe with more data and time, they can be applied to studying a new virus.”

“Self-assembly — designing components that know how to get together — is totally different from how we build ordinary things,” Garmann said. “As engineers, we have a lot to learn from viruses.”

 

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About San Diego State University 

San Diego State University is a major public research institution that provides transformative experiences for its more than 36,000 students. SDSU offers bachelor’s degrees in 96 areas, master’s degrees in 84 fields and doctorates in 23 areas, with additional certificates and programs at regional microsites. SDSU ranks as the number 1 California State University in federal research support, as one of the top public research universities in California. In addition to academic offerings at SDSU, SDSU Imperial Valley and SDSU Georgia, SDSU Global Campus offers online training, certificates and degrees in areas of study designed to meet the needs of students everywhere. Students participate in transformational research, international experiences, sustainability and entrepreneurship initiatives, internships and mentoring, and a broad range of student life and leadership opportunities. SDSU is committed to inclusive excellence and is known for its efforts in advancing diversity and inclusion. SDSU is nationally recognized for its study abroad initiatives, veterans’ programs and support of LGBTQA+ students, as well as its powerhouse Division I Athletics Program. About 50% of SDSU’s undergraduate and graduate students are students of color. The university resides on Kumeyaay land and was most recently recognized as an Asian American Native American Pacific Islander-Serving Institution (AANAPISI). SDSU is also a long-standing Hispanic-Serving Institution (HSI). The university’s rich campus life and location offers opportunities for students to lead and engage with the creative and performing arts, career and internship opportunities with SDSU’s more than 491,000 living alumni, and the vibrant cultural life of the greater San Diego and U.S.- Mexico region.


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Spread & Containment

Mish’s Daily: Step Back to the Monthly Chart on Transportation

Last Friday, I spoke on Women of Wall Street Twitter Spaces and Fox Business’s Making Money with Charles Payne to talk about a key monthly moving average.What…

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Last Friday, I spoke on Women of Wall Street Twitter Spaces and Fox Business's Making Money with Charles Payne to talk about a key monthly moving average.

What makes this moving average so important right now is that three of the Economic Modern Family members are testing it. The three members, Granddad Russell 2000 (IWM), Grandma Retail (XRT) and Transportation (IYT), well deserve their status as what Stanley Druckenmiller calls the "inside" of the U.S. economy. In fact, the components of the modern family were put together before we heard Druckenmiller's viewpoint. We have observed how predictive they all are in helping us see in advance the next big market direction. Hence, these "inside" indicators -- right now -- are all sitting just above a 6–7-year business cycle low.

For the purposes of this daily and because we have featured this sector a lot lately, the chart of IYT is a perfect example of this moving average and what to watch for. Except for the brief blip in 2011 when the government shut down, and then again during the pandemic, IYT has sat above the dark blue line for 11 years. Currently, that line sits at the 195 area. The same is true with IWM and XRT, both marginally holding their monthly MAs.

So, watch IYT to either hold, and begin a rally possibly back closer to 220, or for IYT to fail 195, in which case we see the whole market selling off further.

To note, the other family members, such as Sister Semiconductors (SMH) and Prodigal Son Regional Banks (KRE) are still sitting well above the monthly MA. Big Brother Biotechnology (IBB), however, is now trading below it. And not in the family, but still notable, is the REIT sector (IYR), also sitting below it. SPY has the same MA, only that one sits at 310 (a long way off).

Incidentally, junk bonds broke down under this moving average in November 2021. The market has been slow to take junk bond's hint.

For more information on how to invest profitably in sectors like biotech, please reach out to Rob Quinn, our Chief Strategy Consultant, by clicking here.

Mish's Upcoming Seminars

ChartCon 2022: October 7-8th, Seattle (FULLY VIRTUAL EVENT). Join me and 16 other elite market experts for live trading rooms, fireside chats, and panel discussions. Learn more here.

The Money Show: Join me and many wonderful speakers at the Money Show in Orlando, beginning October 30th running thru November 1st; spend Halloween with us!

Get your copy of Plant Your Money Tree: A Guide to Growing Your Wealth and a special bonus here.


Follow Mish on Twitter @marketminute for stock picks and more. Follow Mish on Instagram (mishschneider) for daily morning videos. To see updated media clips, click here.

Mish in the Media

A business cycle is about 6-7 years - where are the indices now and what should you watch for? Mish discusses this question in this appearance on Fox's Making Money with Charles Payne.


ETF Summary

  • S&P 500 (SPY): Testing the previous low; 362 support, 370 resistance.
  • Russell 2000 (IWM): Broke the June low of 165.18; 162 support, 170 resistance.
  • Dow (DIA): Broke June low -289 support, 298 resistance.
  • Nasdaq (QQQ): Testing the June low;269 support, 280 resistance.
  • KRE (Regional Banks): Relative outperformer; 57 support, 61 resistance.
  • SMH (Semiconductors): 187 support, 194 resistance.
  • IYT (Transportation): 196 support, 200 resistance.
  • IBB (Biotechnology): 112 support, 118 resistance.
  • XRT (Retail): 55 support, 60 resistance.


Mish Schneider

MarketGauge.com

Director of Trading Research and Education

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We can turn to popular culture for lessons about how to live with COVID-19 as endemic

As COVID-19 transitions from a pandemic to an endemic, apocalyptic science-fiction and zombie movies contain examples of how to adjust to the new norm…

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An endemic means that COVID-19 is still around, but it no longer disrupts everyday life. (Shutterstock)

In 2021, conversations began on whether the COVID-19 pandemic will, or even can, end. As a literary and cultural theorist, I started looking for shifts in stories about pandemics and contagion. It turns out that several stories also question how and when a pandemic becomes endemic.


Read more: COVID will likely shift from pandemic to endemic — but what does that mean?


The 2020 film Peninsula, a sequel to the Korean zombie film, Train to Busan, ends with a group of survivors rescued and transported to a zombie-free Hong Kong. In it, Jooni (played by Re Lee) spent her formative years living through the zombie epidemic. When she is rescued, she responds to being informed that she’s “going to a better place” by admitting that “this place wasn’t bad either.”

Jooni’s response points toward the shift in contagion narratives that has emerged since the spread of COVID-19. This shift marks a rejection of the push-for-survival narratives in favour of something more indicative of an endemic.

Found within

Contagion follows a general cycle: outbreak, epidemic, pandemic and endemic. The determinants of each stage rely upon the rate of spread within a specified geographic region.

Etymologically, the word “endemic” has its origins with the Greek words én and dēmos, meaning “in the people.” Thus, it refers to something that is regularly found within a population.

Infectious disease physician Stephen Parodi asserts that an endemic just means that a disease, while still prevalent within a population, no longer disrupts our daily lives.

Similarly, genomics and viral evolution researcher Aris Katzourakis argues that endemics occur when infection rates are static — neither rising nor falling. Because this stasis occurs differently with each situation, there is no set threshold at which a pandemic becomes endemic.

Not all diseases reach endemic status. And, if endemic status is reached, it does not mean the virus is gone, but rather that things have become “normal.”

Survival narratives

We’re most likely familiar with contagion narratives. After all, Steven Soderbergh’s 2011 film Contagion, was the most watched film on Canadian Netflix in March 2020. Conveniently, this was when most Canadian provinces went into lockdown during the early stages of the COVID-19 pandemic.

A clip from the film Contagion showing the disease spreading throughout the world.

In survival-based contagion narratives, characters often discuss methods for survival and generally refer to themselves as survivors. Contagion chronicles the transmission of a deadly virus that is brought from Hong Kong to the United States. In response, the U.S. Centers for Disease Control is tasked with tracing its origins and finding a cure. The film follows Mitch Emhoff (Matt Damon), who is immune, as he tries to keep his daughter safe in a crumbling Minneapolis.

Ultimately, a vaccine is successfully synthesized, but only after millions have succumbed to the virus.

Like many science fiction and horror films that envision some sort of apocalyptic end, Contagion focuses on the basic requirements for survival: shelter, food, water and medicine.

However, it also deals with the breakdown of government systems and the violence that accompanies it.

A “new” normal

In contrast, contagion narratives that have turned endemic take place many years after the initial outbreak. In these stories, the infected population is regularly present, but the remaining uninfected population isn’t regularly infected.

A spin-off to the zombie series The Walking Dead takes place a decade after the initial outbreak. In the two seasons of The Walking Dead: World Beyond (2020-2021) four young protagonists — Hope (Alexa Mansour), Iris (Aliyah Royale), Silas (Hal Cumpston) and Elton (Nicolas Cantu) — represent the first generation to come of age within the zombie-infested world.

The four youth spent their formative years in an infected world — similar to Jooni in Peninsula. For these characters, zombies are part of their daily lives, and their constant presence is normalized.

The trailer for the second season of AMC’s The Walking Dead: World Beyond.

The setting in World Beyond has electricity, helicopters and modern medicine. Characters in endemic narratives have regular access to shelter, food, water and medicine, so they don’t need to resort to violence over limited resources. And notably, they also don’t often refer to themselves as survivors.

Endemic narratives acknowledge that existing within an infected space alongside a virus is not necessarily a bad thing, and that not all inhabitants within infected spaces desire to leave. It is rare in endemic narratives for a character to become infected.

Instead of going out on zombie-killing expeditions in the manner that occurs frequently in the other Walking Dead stories, the characters in World Beyond generally leave the zombies alone. They mark the zombies with different colours of spray-paint to chronicle what they call “migration patterns.”

The zombies have therefore just become another species for the characters to live alongside — something more endemic.

The Walking Dead, Fear the Walking Dead (2015-), Z Nation (2014-18), and many other survival-based stories seem to return to the past. In contrast, endemic narratives maintain a present and sometimes even future-looking approach.

Learning from stories

According to film producer and media professor Mick Broderick, survival stories maintain a status quo. They seek a “nostalgically yearned-for less-complex existence.” It provides solace to imagine an earlier, simpler time when living through a pandemic.

However, the shift from survival to endemic in contagion narratives provides us with many important possibilities. The one I think is quite relevant right now is that it presents us with a way of living with contagion. After all, watching these characters survive a pandemic helps us imagine that we can too.

Krista Collier-Jarvis does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

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Has the pandemic changed our personalities? New research suggests we’re less open, agreeable and conscientious

COVID-related changes in our personalities could go some way to explaining the widespread decrease in wellbeing.

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Lightspring/Shutterstock

For many of us, some personality traits stay the same throughout our lives while others change only gradually. However, evidence shows that significant events in our personal lives which induce severe stress or trauma can be associated with more rapid changes in our personalities.

A new study, published in PLOS ONE, suggests the COVID pandemic has triggered much greater shifts in personality than we would expect to have seen naturally over this period. In particular, the researchers found that people were less extroverted, less open, less agreeable and less conscientious in 2021 and 2022 compared with before the pandemic.


Read more: How we discovered that VR can profile your personality


This study included more than 7,000 participants from the US, aged between 18 and 109, who were assessed before the pandemic (from 2014 onwards), early in the pandemic in 2020, and then later in the pandemic in 2021 or 2022.

At each time point, participants completed the “Big Five Inventory”. This assessment tool measures personality on a scale across five dimensions: extroversion versus introversion, agreeableness versus antagonism, conscientiousness versus lack of direction, neuroticism versus emotional stability, and openness versus closedness to experience.

There weren’t many changes between pre-pandemic and 2020 personality traits. However, the researchers found significant declines in extroversion, openness, agreeableness and conscientiousness in 2021/2022 compared with before the pandemic. These changes were akin to a decade of normal variation, suggesting the trauma of the COVID pandemic had accelerated the natural process of personality change.


Read more: Languishing: what to do if you're feeling restless, apathetic or empty


Interestingly, younger adults’ personalities changed the most in the study. They showed marked declines in agreeableness and conscientiousness, and a significant increase in neuroticism in 2021/2022 compared with pre-pandemic. This may be due in part to social anxiety when emerging back into society, having missed out on two years of normality.

Personality and wellbeing

Many of us became more health-conscious during the pandemic, for example by eating better and doing more exercise. A lot of us sought whatever social connections we could find virtually, and tried to refocus our attention on psychological, emotional and intellectual growth – for example, by practising mindfulness or picking up new hobbies.

Nonetheless, mental health and wellbeing decreased significantly. This makes sense given the drastic changes we went through.

Notably, personality significantly impacts our wellbeing. For example, people who report high levels of conscientiousness, agreeableness or extroversion are more likely to experience the highest level of wellbeing.

So the personality changes detected in this study may go some way to explaining the decrease in wellbeing we’ve seen during the pandemic.

A young woman looks out the window.
Personality changed the most for younger people. fizkes/Shutterstock

If we look more closely, the pandemic appears to have negatively affected the following areas:

  • our ability to express sympathy and kindness towards others (agreeableness);

  • our capacity to be open to new concepts and willing to engage in novel situations (openness);

  • our tendency to seek out and enjoy other people’s company (extraversion);

  • our desire to strive towards our goals, do tasks well or take responsibilities towards others seriously (conscientiousness).

All of these traits influence our interaction with the environment around us, and as such, may have played a role in our wellbeing decline. For example, working from home may have left us feeling demotivated and as though our career was going nowhere (lower conscientiousness). This in turn may have affected our wellbeing by making us feel more irritable, depressed or anxious.

What next?

Over time, our personalities usually change in a way that helps us adapt to ageing and cope more effectively with life events. In other words, we learn from our life experiences and this subsequently impacts our personality. As we age, we generally see increases in self-confidence, self-control and emotional stability.

However, participants in this study recorded changes in the opposite direction to the usual trajectory of personality change. This is understandable given that we faced an extended period of difficulties, including constraints on our freedoms, lost income and illness. All these experiences have evidently changed us – and our personalities.


Read more: Personality can predict who's a rule-follower and who flouts COVID-19 social distancing guidelines


This study provides us with some very useful insights into the impacts of the pandemic on our psyche. These impacts may subsequently influence many aspects of our lives, such as wellbeing.

Knowledge allows us to make choices. So you might like to take the time to reflect on your experiences over the past few years, and how these personality changes may have affected you.

Any changes may well have protected you during the height of the pandemic. However, it’s worth asking yourself how useful these changes are now that the acute phase of the pandemic is behind us. Do they still serve you well, or could you try to rethink your perspective?

Jolanta Burke does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

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