Tag: Viruses

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Public Health by Dr Alex Stockdale

In mid-2021 The Sciku Project teamed up with the Literature and Science Hub at the University of Liverpool to run the ‘Research in Verse Poetry Competition’, open to staff and postgraduate research students across the university to submit poems about their research subject. The competition saw poems addressing all sorts of topics, ranging from gravity to slavery to life in the lab.

Dr Alex Stockdale’s poem ‘Public Health’ was praised by the judges as a notable entry:

Public Health

In a long corridor wailing
Bite
The virus knuckles and grasps
Enters cells
At birth was I living with him
His genome nestling in mine

Now fluid fills the belly
Tumour fills my liver
Hope left this station
Staring out the window
At a blue calm sky on a roaring hot day in Malawi

Too late they said
Too hard
Nothing more to say
I don’t have much time left to live but I want you to know
It could have been prevented

Background

This poem is about my research into liver disease in Blantyre, Malawi. We found that over 70% of liver cancer is caused by hepatitis B. Infection can be prevented by vaccination starting at birth and by antiviral treatment for pregnant women. Currently, vaccination starts at 6 weeks of age and my research is exploring whether this is sufficient to prevent transmission. This poem draws attention to the many people who present with late stage liver cancer in Malawi, for whom median prognosis is only 6 weeks at diagnosis, and for whom hepatitis B infection remains a preventable disease. 

Dr Alexander Stockdale is a clinical researcher at the University of Liverpool with a focus on viral hepatitis and HIV in sub-Saharan Africa.

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Vaccines and Protection by B.R. Shenoy

Vaccines protect us
Trigger an immune response
Prevent infection

by B.R. Shenoy

Mechanism of Action of Vaccines

“A vaccine works by training the immune system to recognize and combat pathogens, either viruses or bacteria. To do this, certain molecules from the pathogen must be introduced into the body to trigger an immune response.

“These molecules are called antigens, and they are present on all viruses and bacteria. By injecting these antigens into the body, the immune system can safely learn to recognize them as hostile invaders, produce antibodies, and remember them for the future. If the bacteria or virus reappears, the immune system will recognize the antigens immediately and attack aggressively well before the pathogen can spread and cause sickness”

— PublicHealth, ‘How Vaccines Work’

B.R. Shenoy is a biochemistry and chemical toxicology, M.S. She is a contributing writer for The Good Men Project. Her work has also appeared in Scary Mommy, Positively Positive, and Idle Inks. She is a content creator on Medium. You can catch up with her on Twitter @Shenoy100.

This sciku was originally published on Medium: https://medium.com/illumination/vaccines-and-protection-a-sciku-ca1491e36b13

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The Core Correlate of COVID-19 Vaccine Acceptance by Dr Michael J. Leach

vaccine acceptance
correlates with a belief
in the greater good

by Dr Michael J. Leach

During 2020 and 2021, acceptance of coronavirus disease-19 (COVID-19) vaccines has been among the most topical areas of health science research. As COVID-19 vaccine availability continues to rise worldwide in a global effort to combat the ongoing coronavirus pandemic, more and more people are faced with the question of whether or not to get vaccinated. Even when an approved COVID-19 vaccine is readily available to a particular subgroup of the global population, a high level of vaccine uptake cannot be guaranteed. For one reason or another, individuals within the population may be hesitant to roll up their sleeves to receive the COVID-19 vaccine.

In a UK population-based study, Freeman et al. (2021) investigated factors related to vaccine hesitancy through an online survey completed by 5,114 adults over September-October 2020. The research team measured vaccine hesitancy within the study population using a specially developed tool—the Oxford COVID-19 vaccine hesitancy scale. While 71.7% of surveyed adults expressed willingness to accept the COVID-19 vaccine, 16.6% were very unsure about vaccination and 11.7% showed strong vaccine hesitancy.

Among the various beliefs, views, attitudes, and past experiences considered by the researchers in their analysis, the factor most strongly correlated with vaccine hesitancy was whether or not individuals believed in the collective importance of COVID-19 vaccination. An individual’s belief in the collective importance of COVID-19 vaccination is defined as the recognition that getting vaccinated protects the community and saves lives. This belief is consistent with the critically important field of public health and with the idea of doing something—in this case, getting vaccinated—for ‘the greater good’.

Based on the results of their study, Freeman et al. suggest that public health messages highlighting the societal benefits of vaccination could be broadcast in an effort to increase belief in the collective importance of COVID-19 vaccination and, thus, improve vaccine acceptance and uptake.

The original research article described here is available open access online:
Freeman D et al. (2021). COVID-19 vaccine hesitancy in the UK: the Oxford coronavirus explanations, attitudes, and narratives survey (Oceans) II. Psychological Medicine 1–15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7804077/pdf/S0033291720005188a.pdf

Michael J. Leach (@m_jleach) is an Australian epidemiologist, biostatistician, and poet based at the Monash University School of Rural Health. His debut poetry collection is Chronicity (Melbourne Poets Union, 2020).

Check out more sciku by Michael, including ‘Drug-Induced Hip Fractures‘, ‘The Psychopharmacological Revolution‘, ‘Quality of Life at Seven Years Post-Stroke‘, ‘The Early Impacts of COVID-19 on Australian General Practice‘, ‘The Burden of Bushfire Smoke‘, and ‘Australian Science Poetry‘ with science communicator Rachel Rayner. Michael also has another Covid-19-related sciku published in Pulse which is well worth checking out: ‘flu shot announcement‘.

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Saba, the morning breeze by Dr Jolene Ramsey

We know you were small
Preying on Proteus too
Surprise, DNA!

by Dr Jolene Ramsey

Bacteriophages, or phages, are the viruses that infect bacteria. They come in different shapes and sizes, but are often icosahedral (spherical) and tailed. A tailed phage is structured like a filled lollipop, where the candy represents the phage head, the filling represents the nucleic acid genome, and the stick is like the tail. The overwhelming majority of phages scientists and students have discovered up to this point are tailed with a DNA genome, largely due to bias in our sampling methods. Recent investigations suggest many phages with RNA genomes remain to be isolated, and they were hypothesized to be small and round, similar to the ones that are already known. We want to find them.

In a very focused hunt, we looked for small RNA phages against the human opportunistic pathogen Proteus using a filtration selection method. After a few rounds of selection, there was a prime candidate that was definitely small, but it didn’t pass the other tests that define RNA phages. It was a puzzle. For clues, we looked at the phage shape in the electron microscope. To our astonishment the phage had a tail and a very small head! We immediately verified that it had a DNA genome as well. Though the search was a failure, we put phage Saba in the arsenal for use in other projects. To fully survey the diverse kinds of phage in the environment we will need to develop and refine targeted and general protocols for phage isolation. This will give us the most accurate picture of the phage universe.

Original research: https://doi.org/10.1128/MRA.01094-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘The Phriendly Phage‘.

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The Phriendly Phage by Dr Jolene Ramsey

Phage are phriends, not phood
Not Phriendly to host, but nice
Plaques phor lab hunters

By Jolene Ramsey

Vibrio natriegens is an environmental microbe that naturally resides in marine habitats, including brackish waters and salty marshes. If you Google this bacterial species, all the top hits will tout its ‘fast’ growth. Unusual among bacteria, but common with other vibrios, V. natriegens has a  >5 Megabase genome split across two chromosomes. It also has a high count of total ribosomes, the cellular machines that make protein. As a non-pathogenic environmental organism, researchers are exploring its use in various biotechnology applications, including as a protein production system. This is one reason some are hoping V. natriegens will become the next lab workhorse in molecular and industrial microbiology that could even rival E. coli.

With an interest in improving the resources available to use in this field of research, we decided to look for bacteriophages that target V. natriegens. Bacteriophages, or phage, are the viruses that infect bacteria. Because phage rely so heavily on their host cell to copy themselves, they turn out to be extremely useful tools for probing how the cell works. As a kind of natural predator, phages can be found everywhere the host lives. The phage this Sciku is about, named Phriendly, was found in a sample collected by a college student brand-new to research on a trip to the beach.

The phage hunt process involves layering spots of environmental samples on top of growing bacteria, then looking for clear spots where the bacteria did not grow (or died due to infection) called plaques. A few of the beach samples yielded these plaques. One was a hazy, weak plaque that was difficult to propagate. We nicknamed it ‘problem phage’. In contrast, another had large, clear plaques that appeared quickly and consistently. We dubbed it the ‘friendly phage’. Following our cute tradition, we replace all ‘f’ sounds with the ‘ph’ used in the word phage to come up with the name Phriendly. Along with others, Phriendly is in a collection of phages we hope can be tools to better harvest the great potential its host microbe has for advancing biotechnology.

Original research: https://doi.org/10.1128/MRA.01096-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘Saba, the morning breeze’.

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Click click go! by Dr Jolene Ramsey

Galaxy applied
Eyes scan Apollo data
To annotate phage

By Jolene Ramsey

Studying the genetic makeup of an organism helps us understand how they tick. Scientists often make precise notes about the position and function of important features within a genome, called annotation, akin to marking and reviewing the restaurants on a city map. Viruses tend to have smaller genomes, but they are packed with information. We annotate the genomes of bacteriophages, the viruses that infect and kill bacteria, to reveal their genetic secrets. While there are automated annotation programs, manual review by human eyeballs is necessary to ensure high quality outcomes. With the number of interesting new phage genomes rising daily, the need for user-friendly tools to analyze their genomes has grown as well.

Using our curated toolbox in an open-source, online bioinformatic portal called Galaxy (https://cpt.tamu.edu/galaxy-pub), features common to bacterial and phage genomes can be spotted and cataloged by novices and experts. There are many feature types, each one detected by a different tool. Instead of manually passing the genome through each tool, we are able to speed up and standardize the process using automatic pipelines that run a prescribed list of analyses. We can visualize the results in context using another linked platform called Apollo, and also compare to known genomes. The coupled Center for Phage Technology Galaxy and Apollo suite have allowed us to annotate >130 bacteriophage genomes, and train many students and researchers along the way.

Original research: https://doi.org/10.1371/journal.pcbi.1008214

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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Privateer, the phage by Dr. Jolene Ramsey

What’s in the EM?
A crayon? A tailocin?
No, that’s Privateer!

By Jolene Ramsey

Proteus mirabilis is an opportunistic human pathogen, causing a large proportion of urinary tract infections. These infections are particularly severe in the elderly, and their treatment is recalcitrant to many antibiotics. There is great interest in using the natural predators of Proteus, their viruses (bacteriophages), to mitigate this issue. However, not many Proteus bacteriophage have been identified or characterized yet.

In our recent study (Corban & Ramsey, 2021), we describe a new phage called Privateer that infects and kills Proteus mirabilis. We first saw this phage in the electron microscope (EM) and noticed its unusual elongated head shape. Privateer has some interesting genes that seem to be common only among the closest related phages. Studies like these are the foundation for future applications combating multi-drug resistant bacterial problems.

Original research: https://doi.org/10.7717/peerj.10645  

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She focuses on their explosive escape from the host cell after a successful infection. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her other sciku ‘Click click go!’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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TF gets in on the bud by Jolene Ramsey

Fat tags the protein

To the surface it transits

Wrapped in the virus

Living cells are like microscopic cities. The proteins, which are the workhorses of a cell, must accurately navigate to the place where they will perform their assigned tasks. Sometimes we equate the way that proteins get to their final destination to adding an address to a letter.

When a virus infects a cell, its proteins must conform to the cell norm or rewire the system. It is of interest to understand how viruses approach this problem. In the case of a small accessory protein called TF that is found in the virions of Sindbis virus, adding lipids to the protein serves as its ‘address’ to get it to the location where new virions are released from an infected cell.

Original research: https://dx.doi.org/10.1128%2FJVI.02000-16

During graduate school, Jolene Ramsey studied the molecular mechanisms governing enveloped eukaryotic virus assembly. She has a long-term interest in understanding how viruses exploit host cells to build more virions.  You can follow her on Twitter under the handle @jrrmicro

Enjoyed Jolene’s sciku? Check out her other sciku ‘Click click go!’, ‘Privateer, the phage’, ‘The Phriendly Phage’ and Saba, the morning breeze.

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Packaging signals by Maria White

Packaging signals:

Limiters of gene exchange

in influenza.

 

Influenza viruses, which have segmented genomes, can exchange genes through a process called reassortment, which can lead to the formation of novel influenza viruses. At the termini of each gene segment are regions called packaging signals, which direct the incorporation of each gene segment into virus particles during assembly.

A recent study by White et al (2017) demonstrated that heterologous packaging signals limit the efficiency of reassortment, but that this phenotype is dependent on the influenza virus gene segment being examined.

Of note, 85% of the reassortant viruses studied packaged a hemagglutinin (HA) segment carrying matched packaging signals relative to the background of the virus. The HA segment is of particular interest from a public health perspective due to its antigenic properties, and these data suggest that HA packaging signals could be an important factor in determining the likelihood that two influenza virus strains will undergo reassortment.

Original research: https://dx.doi.org/10.1128%2FJVI.00195-17

Maria White is a PhD candidate in the Immunology and Molecular Pathogenesis program at Emory University.