Herd Immunity: What the Flock Are You Talking About?

When it comes to blocking the spread of viral pathogens that cause human disease, epidemiologists—people who study disease outbreaks—like to talk about herd immunity. But what do they mean when discussing the herd and their immunity? Today, I will tackle this subject but with a side jaunt: I am going to co-opt the word “herd” and replace it with “flock” thus making chickens the center of attention rather than cattle for this analogy about immunity in a population. (Disclaimer: I am utterly biased toward chickens and enjoy talking about my flock of 24 hens and pullets).

Who is the Herd Flock They Keep Talking About?

By using a collective term for a number of individuals such as “herd” or “flock”, epidemiologists and public health experts are referring to a population or community. Doing some investigation, I learned herd immunity was a term first used in 1917 and referred to…cows. That makes sense, right? When we talk about groups of cattle, the term used is “herd”. Turns out there was an infection that caused spontaneous miscarriages in cattle and became epidemic in American herds. Farmers managed this threat by destroying or selling the infected cows. However, a livestock veterinarian had a different view, describing this pathogen as “…a fire, which, if new fuel is not constantly added, soon dies down. Herd immunity is developed, therefore, by retaining the immune cows, raising the calves, and avoiding the introduction of foreign cattle” (1). Essentially, this veterinarian was noting that keeping the infected cows who had immunity against the contagion meant the herd were less likely to be reinfected and, thus, put an end to the epidemic.

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Engineering a Safer SARS-CoV-2 for Use in the Research Laboratory

This illustration, created at the Centers for Disease Control and Prevention (CDC), reveals ultrastructural morphology exhibited by coronaviruses such as SARS-CoV-2. Photo Credit: Alissa Eckert, MS; Dan Higgins, MAM CDC
SARS-CoV-2 illustration from CDC; Photo Credit: Alissa Eckert, MS; Dan Higgins, MAM
E = envelope; M = membrane

A worldwide pandemic requires scientific research to understand the viral pathogen. The focused efforts of global scientists are even more necessary in the face of a novel coronavirus like SARS-CoV-2, the causative agent of COVID-19. However, because SARS-CoV-2 causes human disease, research efforts are restricted by the need for physical laboratories that are equipped to handle the required level of containment and personnel trained to handle pathogens in these facilities. But what if we could bypass the restrictive facility requirements by engineering a synthetic, replication-defective version of SARS-CoV-2 that more researchers could use to study the pandemic coronavirus, expanding the capacity to test and develop methods to attenuate its devastating effect on humans?

The challenge is to develop a derivative of SARS-CoV-2 that reflects how it behaves in the cell but is compromised such that it is unable to infect cells more than a single time. That is, the virus can get into a cell or be introduced into cells and replicate but is unable to produce infectious virus would offer a pathway to expand research capacity without the use of special laboratory facilities. This replication-defective SARS-CoV-2 could be created to encode as much or as little of the genome needed to examine its lifecycle without becoming a fully infectious virus. In fact, this replication-defective version of SARS-CoV-2 could include additional genetic elements that could be used to control its expression, track the virus in cells and measure the level of its replication. This task has been undertaken by Dr. Bill Sudgen’s group at the University of Wisconsin–Madison McArdle Laboratory for Cancer Research, explained by graduate student Rebecca Hutcheson during her presentation “Making the Virus Causing COVID-19 Safe for Research”.

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Finding Signs of Cancer in Dinosaur Fossils

Centrosaurus is a herbivorous Ceratopsian dinosaur that lived in Canada in the Cretaceous Period. A recent report describes the characterization of cancer in a Centrosaurus dinosaur fossil.
Centrosaurus is a herbivorous Ceratopsian dinosaur that lived in Canada in the Cretaceous Period.

Did dinosaurs get cancer? That isn’t an easy question to answer. Finding and diagnosing cancer in dinosaur fossils has proven difficult. Any soft tissue, the typical location of tumors, has degraded over the millennia. Fossilized bones millions of years old are subject to wear and tear, making it hard to distinguish bone damage from possible pathology. By using the knowledge and expertise gained from diagnosing cancer in humans, a team reported in The Lancet Oncology that they found the first known case of osteosarcoma in a lower leg bone from a horned dinosaur found in southern Alberta, Canada.

This case of bone cancer discovered in a specimen of Centrosaurus apertus found in the Canadian Dinosaur Park Formation was confirmed by examining the bone surface along with radiographic and histological analysis. The 77–75.5-million-year-old case was compared to both a normal C. apertus fibula from the Oldman formation also in southern Alberta, Canada, as well as a human fibula with an osteosarcoma.

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Targeting Glioblastoma Cells by Packaging a Lentiviral Vector Inside a Zika Virus Coat

A recent article published in Cancers demonstrates a new method for targeting glial cells using a lentiviral packaging system that incorporated Zika virus envelope proteins. By using the reporter gene firefly luciferase, researchers demonstrated that a pseudotyped virus could infect cultured glioblastoma cells.

Introduction

Space-fill drawing of the outside of one Zika virus particle, and a cross-section through another as it interacts with a cell. The two main proteins of the viral envelope, the envelope proteins and membrane proteins, are shown in red and purple respectively. The lipid membrane of the envelope is shown in light lavender.The capsid proteins, in orange, are shown interacting with the RNA genome, in yellow, at the center of the virus. The cell-surface receptor proteins are in green, the cytoskeleton in blue, and blood plasma proteins in gold. Drawn by David Goodsell.
Space-fill drawing of the outside of one Zika virus particle, and a cross-section through another as it interacts with a cell. The two main proteins of the viral envelope, the envelope proteins and membrane proteins, are shown in red and purple respectively. The lipid membrane of the envelope is shown in light lavender. The capsid proteins, in orange, are shown interacting with the RNA genome, in yellow, at the center of the virus. The cell-surface receptor proteins are in green, the cytoskeleton in blue, and blood plasma proteins in gold. Drawn and copyright owned by David Goodsell.

Viruses enjoy a fearsome reputation. SARS-CoV-2 is only the latest infectious agent that has garnered attention by becoming a worldwide pandemic. Even the viral name suggests that SARS-CoV-2 was not the first of its type [SARS-CoV is the virus behind the severe acute respiratory syndrome (SARS) that spread worldwide in the early 2000s]. There are many different families of viruses (e.g., coronavirus for SARS-CoV-2 or lentiviruses for HIV-1) and each show a preference to the cell types they want to infect. By investigating the life cycle of viruses to better understand their mechanisms, researchers can discover new opportunities that may be exploited.

In 2015 and 2016, the virus that concerned health authorities was Zika virus (ZIKV). While this virus generally caused mild disease, the babies of women who were infected during pregnancy were at increased risk for microcephaly and other brain defects. These defects were traced back to Zika virus infecting nerve tissue, specifically, glial cells. This discovery provided an opportunity to explore how Zika virus might affect the brain tumor, glioblastoma multiforme (GMB), especially the glioblastoma stem cells (GSCs) that resist conventional treatment and contribute to the poor prognosis for GMB. Studies suggested that Zika virus infection prolonged survival in animal glioma models and selectively killed GSC with minimal effects on normal cells. In fact, the molecules used by ZIKV to enter cells were predominantly found on tumors, not normal cells. Knowing that the ZIKV envelope proteins prM and E provide the target specificity for glial cells, Kretchmer et al. wanted to explore if ZIKV envelope proteins substituted in lentivirus packaging systems would be able to enter glioblastoma cells.

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Identifying the Ancestor of a Domesticated Animal Using Whole-Genome Sequencing

What animal can be found around the globe that outnumbers humans three to one? Gallus gallus domesticus, the humble chicken. The human appetite for eggs and lean meat drive demand for this feathered bird, resulting in a poultry population of over 20 billion.

Controversy over the origin of the domestic chicken (when, where and which species) have lead some researchers to look for that information in the genomes of contemporary chicken breeds and wild jungle fowl, the candidates from which chickens were derived. By sequencing over 600 genomes from Asian domestic poultry as well as 160 genomes from all four wild jungle fowl species and the five red jungle fowl subspecies, Wang et al. wanted to understand and identify the relationships and relatedness among these species and derive where domesticated chickens first arose.

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Using the Power of Technology for Viral Outbreaks

Artist’s rendition of a virus particle.

When the world is experiencing a viral pandemic, scientists and health officials quickly want data-driven answers to understand the situation and better formulate a public health response. Technology provides tools that researchers can use to develop a rapid sequencing protocol. With such a protocol, the data generated can help answer questions about disease epidemiology and understand the interaction between host and virus. Even better: If the protocol is freely available and based on cheap, mobile sequencing systems.

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Small Changes With Large Consequences: The Role of Genetic Variance in Disease Development

Structure of Human Ferrochelatase
Human Ferrochelatase 2 angstrom crystal structure. Generated from 1HRK (RCSB PDB) using Pymol. Copyright: Sarah Wilson / CC BY-SA

Understanding how disease states arise from genetic variants is important for understanding disease resistance and progression. What can complicate our understanding of disease development is when two people have the same genetic variant, but only one has the disease. To investigate what might be happening with ferrochelatase (FECH) variant alleles that result in erythropoietic protoporphyria (EPP), scientists used next-generation sequencing (NGS) along with RNA analysis and DNA methylation testing to assess the FECH locus in 72 individuals from 24 unrelated families with EPP.

What is FECH and its relationship to EPP?

FECH is the gene for ferrochelatase, the last enzyme in the pathway that synthesizes heme. The inherited metabolic disorder, EPP, is caused when the activity of FECH is reduced to less than a third of normal levels thus, increasing the levels of protoporphyrin (PPIX) without metal in erythrocytes. The consequences of the low-metal PPIX include severe phototoxic skin reactions and hepatic injury due to PPIX accumulation in the liver.

How does FECH expression affect EPP?

The EPP disease state is not simply the lack of two functional FECH genes. Disease occurs with a hypomorphic allele, mutations in FECH that reduce its function, in trans to a null FECH allele. Researchers focused on three common variants called the GTC haplotype that are associated with expression quantitative trait loci (eQTL) that reduce FECH activity. Interestingly, these three variants have been found in trans, but researchers wanted to learn if there were individuals who were homozygous for the GTC allele and how EPP manifested for them.

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Uncovering the Origins of the Commensal House Mouse

Figure of house mouse. Copyright George Shuklin.
📷: George Shuklin

When I encounter my cat fixated on specific locations in my kitchen, her behavior shows me that she has heard some mice in those areas. In fact, mice have been attributed as a reason that cats became companions to humans. Mice start gathering and reproducing so cats followed the food source and hunted the rodents, thus endearing themselves to humans, who were storing food for their own use. However, new evidence described in Scientific Reports has shown that mice have been associated with humans even before grain storage was widespread. In fact, by making our dwellings comfortable, we also created an inviting place for mice to live.

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Celebrating the 100th Cartoon with a Few Words from the Promega Cartoonist

Heading into 2020, we realized that our Cartoon Lab was reaching a milestone: the 100th cartoon! We asked the “official” Promega Cartoonist Ed Himelblau to list his Top Five Cartoons and what inspired them. See what he has chosen in his own words:

This was the first of my cartoons that Promega published and it’s still one of my favorites. The file on my computer is dated February, 1999. I have been an undergraduate in a lab. I’ve mentored undergraduates in lab. Today I have lots of undergraduates working in my plant genetics lab at Cal Poly in San Luis Obispo. For the record, I enjoy having undergraduates in the lab and I never make them dress like robots. In this cartoon, I particularly like the centrifuge and stir plate on the right. I’ve always tried to put something in each cartoon (a tube rack, an enzyme shipping box, a desiccator) that make molecular biologists say, “I know that!”

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NanoLuc® Luciferase Powers More than Reporter Assays

Bright NanoLuc® Luciferase

NanoLuc® luciferase has been discussed many times on this blog and our web site because the enzyme is integral to studying genetic responses and protein dynamics. While NanoLuc® luciferase was first introduced as a reporter enzyme to assess promoter activity, its capabilities have expanded far beyond a genetic reporter, creating tools used to study endogeneous protein interactions, target engagement, protein degradation and more. So where did the NanoLuc® luciferase come from and how does a one enzyme power several technologies?

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