Capstone Project: Influenza

Influenza A, SUbtype H1n1

This post is intended to be an overview, but much more detailed information can be found from the links at the bottom of this page. Please feel free to leave a question or comment!

Influenza, or the flu, is a common and highly contagious viral infection. While severity of infection varies year-to-year, the CDC estimates that there are between 9 million and 45 million cases of influenza in the United States alone each year, leading to 12,000-61,000 deaths. Globally, the WHO estimates there are roughly 1 billion cases annually.

Reports of influenza-like illness date back to 410 B.C. The most notable historic influenza, though, is that of 1918 – an H1N1 influenza virus which killed roughly 50 million people – approximately 3% of the world population at the time, and greater than the death toll of the First World War.

If the timeline does not load properly, reload the page. Click here to view summary timeline (featured image).


Symptoms of mild influenza infection include:

    • Fever/Chills
    • Headache
    • Cough
    • Sore throat
    • Congestion
    • Fatigue 

Influenza infection can become much more serious in individuals with pre-existing health conditions or weakened immune systems. One of the most common complications of influenza infection is pneumonia, which can lead to acute respiratory distress, and often results in hospitalization.

What exactly is the flu?

Viruses are submicroscopic pathogens composed of genetic material and a protein/lipid coat. Our genetic material is made up of DNA, or deoxyribonucleic acid, but the influenza virus carries something slightly different, called RNA (ribonucleic acid). These structures serve the same purpose of encoding the information to build necessary proteins. However, unlike our cells, viruses don’t have the cellular machinery needed to build those proteins. Instead, they must infect a host cell and recruit its machinery to synthesize new copies.

There are three  types of influenza viruses which infect humans – A, B, and C – but influenza A is the most common. Influenza A viruses can be further classified into subtypes based on the proteins found on their surface, hemagglutinin (HA) and neuraminidase (NA), which are what the H#N# nomenclature refers to. For example, the 2009 influenza pandemic was Influenza type A, subtype H1N1, meaning that it had type 1 hemagglutinin and neuraminidase surface proteins.

A visual representation of different influenza subtypes

The virus gains access to the host cell, typically in the respiratory tract, with the hemagglutinin surface protein, which binds a chemical structure embedded in the host cell membrane called sialic acid. This binding allows the virus to enter the cell and release its RNA segments inside, which are transported to the nucleus for processing. RNA acts like a code that provides the cell with instructions for building proteins, but the RNA carried by the influenza virus is negative-sense. This means that it must be converted to the complementary positive-sense RNA (now called messenger RNA or mRNA) before the cell can interpret it. This conversion is facilitated by an RNA polymerase enzyme. The original, negative-sense RNA is also copied to become the genetic material of the newly synthesized viruses.

The influenza virus lifecycle. Hemagglutinin (HA); Neuraminidase (NA), messenger RNA (mRNA).

mRNA leaves the nucleus, and organelles called ribosomes convert it into functional proteins. These proteins are combined with the copies of the original RNA material to form new virus particles, which fuse with the cell membrane to exit the cell. The virus is released when the neuraminidase surface protein clips its linkage to a sialic acid on the host cell surface, and the freed virus can go on to infect other host cells.

This process takes a toll on the host cell, as the majority of resources are put towards viral production. Additionally, presence of the virus in the cell activates the immune system, preparing the body to fight the infection. Intracellular immune proteins recognize various unique viral components, such as its RNA, and produce signaling molecules, such as interferons and interleukins, designed to restrict viral replication. The effects of this signaling protect the body, but also lead to many of the symptoms typically associated with influenza, such as fever, inflammation, and irritation of the respiratory tract. 

Treatment and Prevention

While there are vaccines and antiviral treatments available, one of the most pharmacologically challenging characteristics of the influenza virus is its prominent ability to accrue mutations and recombine. Mutations occur frequently, and the segmented RNA can recombine if two different influenza subtypes infect the same cell. 

These events make it difficult to create effective vaccines because the antibodies an individual makes against a strain in the vaccine may not be effective if they are exposed to a mutated or recombinant strain later on, which is why the influenza vaccine is recommended annually. Despite this challenge, vaccination is still the best way to prevent and lessen the severity of influenza infection. These issues have prompted prominent interest in the possibility of a universal influenza vaccine, which would theoretically target a well conserved portion of the virus, though, this project has proven difficult. As the research progresses, though, this will hopefully become a reality in the future. 

For more information on current and future potentially universal influenza vaccines, check out this video from a lab at Mount Sinai.

You can learn more by exploring my Capstone Project Pages: 

  1. Clinical Characterization 
  2. Identification and Characterization of the Infectious Agent 
  3. Cellular & Molecular Basis of Infection 
  4. Host Immunity & Preserving the Healthy State 
  5. Treatment, Prevention, & Transmission 
  6. Examining Genetic Factors & Predispositions 

Or, click below to view my Capstone Project Landing Page. 


Main Text

  1. CDC. Disease Burden of Influenza. (Accessed April 21, 2020)
  2. WHO. Global Influenza Strategy 2019-2030. (Accessed April 21, 2020)
  3. History. Influenza. 2020 (Accessed April 22, 2020).
  4. CDC. Types of Influenza Viruses. (Accessed March 12, 2020)
  5. Eisenstein, M. Towards a universal flu vaccine. Nature Outlook. 2019
  6. Chen, X.; Liu, S.; Goraya, M.U.; Maarouf, M.; Huang, S.; and Chen, J. Host Immune Response to Influenza A Virus Infection. Front Immunol. 2018, 9: 320.
  7. Krammer, F.; Smith, G. J. D.; Fouchier, R. A. M.; Peiris, M.; Kedzierska, K.; Doherty, P. C.; Palese, P.; Shaw, M. L.; Treanor, J.; Webster, R. G.; et al. Influenza. Nat. Rev. Dis. Primer 2018, 4 (1), 1–21.
  8. Dou, D.; Revol, R.; Ostbye, H.; Wang, H.; and Daniels, R. Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement. Front Immunol. 2018, 9: 1581.

Note: Images in main text are not linked to direct sources because they are original content.

Timeline & Timeline Images

  1. CDC. Influenza (Flu) (Accessed Apr 14, 2020)
  2. CDC. 1918 Commemoration Historical Images [Image] (Accessed Apr 21, 2020).
  3. Wikipedia. Richard Pfeiffer [Image] (Accessed Apr 21, 2020).
  4. Machemer, T. How a few sick tobacco plants led scientists to unravel the truth about viruses. Smithsonian, 2020. (Accessed Apr 21, 2020).
  5. Huston History: The flu pandemic Huston faced 100 years ago [Image] (Accessed Apr 21, 2020).
  6. Science Photo. Influenza A Virus, TEM [Image]. (Accessed Apr 21, 2020).
  7. Virology Blog. The neuraminidase of the influenza virus [Image]. 2013. (Accessed Apr 21, 2020).
  8. Amantadine Syrup [Image] (Accessed Apr 21, 2020).
  9. Tao, Y.J.; and Zheng, W. Visualizing the Influenza Genome (Figure 1) [Image]. Science. 2012, 338(6114): 1545-1546.
  10. Moisse, K. Young Swine Flu Survivor Gets Kidney from Mom. ABC News. 2013 (Accessed Apr 21, 2020).

Antimicrobial host lysozyme has ironic interference with β-lactam antibiotic function


β-lactams are a prominent class of antibiotics including Penicillin which inhibit peptidoglycan cell wall synthesis in bacteria, leading to cell death. Paradoxically, macrophage lysozyme supports emergence of a β-lactam resistant L-form morphology which can survive and proliferate without a cell wall.

Antibiotics have undoubtedly altered the course of modern medicine, but the powerful compounds often praised as miraculous are not as infallible as some like to believe.2 The recent prominence of antibiotic resistance has led to a greater focus on the shortcomings and misuse of antibiotics.2 Understanding why and when antibiotic treatment will fail is of significant clinical importance, as antibiotics are still some of the most frequently prescribed and valuable medications today.

Bacterial cell walls contain the carbohydrate and amino acid polymer peptidoglycan (PG).1,3 Peptidoglycan synthesis is a multistep process occurring both inside and outside of the cell. As discussed in lecture, it begins with synthesis of a PG precursor, Lipid II, by Mur A, B, C, D, E, and F enzymes in the cytoplasm to generate a peptide-conjugated UDP-MurNAc molecule, which is then conjugated to an undecaprenyl unit in the membrane by MraY. MurG then attaches a GlcNAc, forming Lipid II. Lipid II is then flipped to reside on the surface of the cell, where transpeptidases build the peptidoglycan network through a series of nucleophilic acyl substitutions, forming long carbohydrate polymers linked by short peptides.1,3

Figure 1. The structure of penicillin.4 β-lactams are named for the central amide ring. The R group is variable.

Many antibiotics inhibit enzymatic steps involved in Lipid II synthesis, ultimately interfering with the cell wall and resulting in cell death.1,3 Perhaps even more common, though, are antibiotics which interfere with the processes occurring on the outside of the cell, including β-lactams.1 β-lactams, including Penicillin (Fig. 1), interfere with peptidoglycan synthesis by covalently modifying the pencillin binding protein transpeptidases (PBPs) essential for polymer formation, typically resulting cell death.

Kawai et al.1 identified an interesting connection between such antibiotics and a peculiar bacterial morphology known as the L-form. L-form bacteria lack the typically essential and characteristic cell wall, and undergo an odd heterogenous proliferation driven by changes in membrane growth.6 More specifically, L-form progeny “bleb” off from the rod-structured (walled) parent cell (Fig. 2) when membrane growth excessively surpasses that of the cytoplasm (the L-form is associated with increased fatty acid synthesis),6 but certain conditions are required for these cells to escape their cell walls in the first place – often referred to as the L-form switch.

Figure 2. A movie displaying the L-Form switch in B. subtilis. Images obtained every 5 minutes. Movie S1 from Kawai et al.1.

These authors previously demonstrated that upregulation of autolytic activity in the cell wall (via WalR) promotes this L-form escape from the walled morphology.5 L-form bacteria can continue to proliferate without a cell wall.6 Thus, they confer resistance to many common antibiotics because they do not require peptidoglycan synthesis.1

Antibiotics which inhibit Lipid II synthesis are known to induce L-form switch in many bacteria. β-lactam treatment had the opposite effect, inhibiting transition to the L-form state.1 The authors investigate the apparent difference in efficacy of Lipid II synthesis inhibitors versus PG assembly inhibitors in conferring the L-form switch, and find that antibiotics which interfere with class A PBPs appear to additionally block autolytic enzyme activity necessary L-form release. Experiments using time-lapse microscopy allow the authors to visualize the L-form switch under a variety of experimental conditions (i.e. Fig. 2), and they demonstrate that while L-form growth is typically prevented in the presence of PenG (a penicillin/β-lactam), it can be recovered with the addition of exogenous lytic enzyme.

The authors then put these initial findings in conversation with physiological systems by showing that host lytic enzymes can promote the L-form switch. Host macrophages were found to contain lysozyme, an antimicrobial immune effector which catalyzes the breakdown of PG as part of the innate immune response.8 The L-form switch can be observed in the macrophage-engulfed cells by microscopy, and strikingly, the L-forms can escape the macrophage and continue to proliferate even once the macrophage has died (Fig. 3). Further, the L-form morphology confers complete resistance to β-lactam antibiotics. This challenges the widely held assumption that the majority of macrophage-pathogen interactions necessarily end in pathogen destruction. Kawai and colleagues suggest that this likely accounts for the majority of lytic activity necessary for L-form switch in physiological systems, though some L-form activity is still observed in the presence of lysozyme inhibition, likely due to other, unidentified immune effectors with lytic function.

Figure 3. Time lapse microscopy showing B. subtilis L-form escape from host macrophages, highlighted by arrows, on isotonic media containing PenG (supportive of L-form growth in the presence of lysozyme but harmful to the macrophages). The B. subtilis strain is tagged with an mCherry fluorescent protein (upper left and lower right), allowing concrete visualization of bacterial cells. Figure 6C from Kawai et al.1

They take this further to see if host macrophages can actually provide a protective environment to gram-positive bacteria in the presence of β-lactam antibiotics. Remarkably, the investigators demonstrate that not only can these cells survive and continue to proliferate, but they can return to their walled morphology once the antibiotic is removed, as evidenced by cell growth on hypotonic media, where L-form cannot survive. Thus, this antimicrobial immune cell provides paradoxical shelter from antibiotic action, as the cell-wall deficient morphology can retain viability inside the macrophage.

Figure 4. β-lactam antibiotics inhibit PG synthesis and associated autolytic enzyme function in bacteria, leading to cell death. Macrophage lysozyme supports emergence of a β-lactam resistant L-form morphology which can survive and proliferate without a cell wall. Graphical abstract from Kawai et al.1

The authors highlight the possible implications of these findings in understanding recurrent infections, providing translational potential and speaking in part to the impact of the work. They suggest that typical physiological conditions would be sufficient to support L-form growth during antibiotic treatment, and that the walled morphology could subsequently reemerge. Unlike other cell states implicated in recurrent infection,1 L-forms can not only survive in the presence of antibiotics, but can proliferate as well.

Kawai and colleagues work raises a number of questions, many of which they address in their discussion. Most notably, the question of what characteristics allow long term persistence of the L-form morphology and precisely how long this can occur in in vivo niches (such as macrophages) certainly warrants further study. This will be important to truly understanding the physiological and clinical applications of this work. Further clinical study will also be necessary to understand why and when L-forms may emerge, as β-lactams are widely used and typically effective. The authors suggest this may be more common in those with weakened immune systems, but this explanation seems insufficient given the critical role of the immune system in conferring the L-form morphology elucidated in this paper. Since the publication of this article, this group published a more clinically driven analysis of the role of L-forms in recurrent urinary tract infections in Nature Communications which has started to address some of these questions.8

Despite the questions that remain, Kawai et al. provide fascinating insight to the paradoxical role of the innate immune system in β-lactam antibiotic efficacy. Understanding the complex mechanisms impacting antibiotic evasion is essential for safe use and systemic design of antibiotics.

Works Cited

  1. [Original Paper] Kawai, Y.; Mickiewicz, K.; and Errington, J. Lysozyme Counteracts β-Lactam Antibiotics by Promoting the Emergence of L-Form Bacteria. Cell. 2018, 172(5): 1038-1049.
  2. Aminov, R.I. A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future. Front Microbiol. 2010, 1:134.
  3. Kouidmi, I.; Levesque, R.C.; Paradis-Bleau, C. The biology of Mur ligases as an antibacterial target. Molecular Microbiology. 2014, 94(2): 242-253.
  4. Wikipedia. Penicillin (Image). (Accessed Apr 19, 2020).
  5. Domínguez-Cuevas, P.; Mercier, R.; Leaver, M.; Kawai, Y.; and Errington, J. The rod to L-form transition of Bacillus subtilis is limited by requirement for the protoplast to escape from the cell wall sacculus. Molecular Microbiology. 2012, 83(1): 52-66.
  6. Mercier, R.; Kawai, Y.; and Errington, J. Excess Membrane Synthesis Drives a Primitive Mode of Cell Proliferation. Cell. 2013, 152(5): 997-1007.
  7. KEGG. Enzyme (Lysozyme). (Accessed Apr 19, 2020).
  8. Mickiewicz, K.M.; Kawai, Y.; Drage, L.; Gomes, M.C.; Davidson, F.; Pickard, R.; Hall, J.; Mostowy, S.; Aldridge, P.D.; and Errington, J. Possible role of L-form switching in recurrent urinary tract infection. Nature Communications. 2019, 10, 4379.

Literature Overview: Influenza (H1N1)

Reflection Blog #3

Influenza, though only first making a prominent appearance in the scientific literature around the early nineteenth century, has plagued humanity since at least the 1500s. 5 Given this, its scientific study extends far back, easily preceding identification of the first virus, and resulting in a somewhat overwhelming abundance of literature. I have chosen to focus on H1N1 for this project, though it is common that scientific understanding of the H1N1 subtype is informed by studies in other influenza strains. Presented below are four core themes, and two less prominent, supplementary themes*, which describe and navigate the nature of biochemical research in H1N1 and influenza available.

Clinical characterization*

Though not the focus of this (biochemical) project, clinical characterization set an important precedent to the molecular study of the influenza virus. Influenza is thought to have first appeared in the late 1500’s, though possibly earlier, and was responsible for many prominent epidemics prior to its more scientific study in the early nineteenth century.1 Much available literature through the nineteenth and early twentieth century appears to be focused on characterizing the clinical presentation of influenza (identifying symptoms), and distinguishing it from other infectious conditions.

While this project will focus much less on this theme than the others listed below, it is worthy of mention as an important historical context for the more molecular literature that follows. 

Identification of the causative agent 

Given the prominence of influenza in human history – ranging from seasonal outbreaks to devastating pandemics such as the 1918 H1N1 flu, it is not surprising that, particularly in the late nineteenth century through the early twentieth century, there is an abundance of literature attempting to elucidate the causative cause of the disease. Through clinical observation, it was clear that the disease was infectious by nature, but even once more microbial-based studies took place, there was some debate about whether the causative agent was bacterial or viral (the bacteria identified turned out to be a common co-infection4). Post identification of the virus itself (1933), this becomes less prominent in the literature, though more recent work has focused on classifying viral subtypes and protein components, leading to the “Cellular and Structural Basis of Infection” theme discussed below.

Major scientific innovations contributing to this theme (and some interesting historical notes on the origin of these findings): 

  • 1800s-1918 – Pfiefer’s bacteria (“bacillus of influenza”) is identified as causative agent 2
    Pfiefer identified a bacillus bacteria in the respiratory tract of patients presenting with influenza-like symptoms. This was thought to be the causative agent for some time, before subsequent work suggested it may be viral. Some early attempts at vaccine development were actually bacterial. 
  • 1918 – Gibson and Connor demonstrate the influenza from the 1918 outbreak is caused by a filterable virus 3
    Gibson and Connor demonstrate that the causative agent for influenza is a filterable virus during the 1918 pandemic, appearing to shift the literature away from Pfieffer’s bacteria. 
  • 1933 – The influenza virus is isolated 4

Cellular and structural basis of infection

As molecular and biochemical sciences evolve as a field, a new theme emerges in the literature focusing on understanding influenza infection from this perspective. This likely starts with antigenic characterization of the hemagglutinin and neuraminidase surface proteins typically used to categorize influenza strains into an H#N# subtype, but develops into immunological, biochemical, and genetic study of influenza pathogenesis and function. This type of research still thrives today, with an incredible bank of molecular interactions identified – including interactions with the host cell immune pathways triggered by infection. Understanding the molecular basis for infection and host immune response is essential to creating novel drug therapies, so it is not surprising that this is a focus in the literature. 

Major scientific innovations contributing to this theme:

  • 1941-42 – George K. Hirst suggests existence of the hemagglutinin protein 6
    Named for the observation that red blood cells agglutinate in the presence of the virus 
  • 1943 – Early chemical characterization of influenza as a lipoprotein complex 7
  • 1950s – Alfred Gottschalk identifies and characterizes the hemagglutinin and neuraminidase proteins7 
  • 1990s-present – Extensive mapping of infection mechanism and host immune pathways 5,12 

Genetic study of influenza

While structural protein studies of influenza preceded genetic study, there is also an abundance of literature examining the virus from a genetic lens. This is primarily focused on understanding the viral genome components, and their roles in infection. Like all viruses, influenza contains the genetic material necessary to build its protein components, but must exploit the machinery of a host cell during infection to synthesize new viruses.5 There is also a large interest in the virus’s ability to genetically recombine, as influenza is exceptionally good at this, and it is one of the major barriers to vaccine development. Potential for mutation, which may increase the virulence of the pathogen is also of interest in understanding influenza.5

Major scientific innovations contributing to this theme:

  • 1952 – Demonstrated that influenza can genetically recombine 8
  • 1976-1977 – Mapping of the influenza genome 9,10,11
    Identifies genes encoding the primary viral proteins necessary for infection and viral assembly 
  • 1990s-present – Extensive mapping of infection mechanism and host immune pathways 5,12
    Including genetics-based studies

Treatment, Prevention, & Transmission 

Because influenza is often highly virulent, particularly H1N1, and can be extremely dangerous to at-risk populations,6 treatment and prevention of disease is one of the most prominent focuses of influenza study. This includes vaccine development, antiviral pharmaceuticals, and public health efforts to prevent spread of disease (less relevant to this project). As discussed above, the frequent genetic drift of influenza viruses makes vaccine development difficult. Currently, seasonal vaccines can provide protection from the most common strains in a given year, but there is interest in creating a “universal vaccine” which could provide protection from all strains in the future.5 A variety of antiviral drugs have also been developed.13 Interest in potential treatments begins with interest in the disease itself, but biochemical and pharmaceutical efforts to develop novel treatments is still prominent today. As with bacterial infections, this field also faces modern issues with drug resistance in viral strains.5

In accordance with interest in prevention, there is also a large focus throughout the literature on mechanisms of transmission. Influenza viruses can come from a variety of animals, though the H1N1 subtype is typically found in pigs, and mechanisms of both animal-human and human-human transmission are of prominent interest in prevention of potential outbreaks.

Major scientific innovations contributing to this theme:

  • 1918 – Early attempts at vaccine development, but targeting the “bacillus of influenza,” rather than the virus itself
  • 1933 – Serum from recovered animal is shown to protect others from influenza infection 4 
  • 1945 – First influenza vaccine developed and implemented for civilian inoculation 5
  • 1990 – Reverse genetics technologies to generate desired recombinant influenza enhances vaccine development efforts 5
  • Present day – efforts into developing a universal influenza vaccine are underway5

Examining genetic factors & predispositions* 

An emerging theme in the literature of more recent interest is the role that genetic factors may play in susceptibility to severe influenza infection. Factors such as age and pre-existing health conditions have been known to increase susceptibility for some time,5 but that idea that there may be other genetic factors implicated in susceptibility is relatively new. Mutations identified thus far typically interfere with the canonical host response.5 This area is currently poorly understood, but I suspect that it will be of interesting focus in the biochemical and genetic literature on influenza moving forward.

Major scientific innovations contributing to this theme

  • 2010s – Identification of IFITM3 and IRF7 mutations, encoding interferon pathway components, as implicated in susceptibility to severe influenza infection 

I believe these themes will integrate well with the Defining the Disease Mastery Assignment and other components of the capstone project, as they focus on answering many of the major questions about influenza such as how it spreads, how it causes disease, possible treatments, and what leads to susceptibility in certain individuals. Additionally, the core themes outlined above are largely focused in biochemical/molecular study.

Works Cited 

  1. Brief History of the Influenza Virus (Accessed 27 March 2020).
  2. Robertson, W.F. Influenza: Its Cause and Prevention. Br Med J. 1918, 2(3025):680-681.
  3. Gibson, H.G., and Connor, J.I. A filterable virus as the cause of the early stage of the present epidemic influenza. Br Med J. 1918, 2(3024):645-646.
  4. Smith, W., Andrewes, C.H., and Laidlaw, P.P. [Reviewed] Timbury, M.C. A Virus obtained from influenza Patients. Reviews in Medical Virology. 1995*, 5:187-191 
  5. Krammer, F.; Smith, G. J. D.; Fouchier, R. A. M.; Peiris, M.: Kedzierska, K.; Doherty, P. C.; Palese, P.; Shaw, M. L.; Treanor, J.: Webster, R. G.; et al. Influenza. Nat. Rev. Dis. Primer 2018, 4(1), 1-21.
  6. Henry, R. and Frederick, M.A. Etymologia: Hemagglutinin and Neuraminidase. 2018 Emerg Infec Dis. 24(10), 1849.
  7. Taylor, A.R., Sharp, D.G., McLean, I.W., Beard, D., Beard, J.W., Dingle, J.H., and Feller, E. Jr. Purification and Character of the Swine Influenza Virus. Science. 1943, 98(2557):587-89
  8. Burnet, F.M. and Lind, P.E. A genetic approach to variation in influenza viruses; recombination of characters between the influenza virus A strain NWS. and strains of different serological types. 1951 J Gen Microbiol. 5(1):67-82.
  9. Palese, P., and Schulman J.L. Mapping of the influenza virus genome: identification of the hemagglutinin and the neuraminidase genes. Proc Natl Acad Sci USA. 1976, 73(6):2142-46.
  10. Palese, P., Ritchey, M.B., and Schulman J.L. Mapping of the influenza virus genome II: identification of the P1, P2, and P3 genes. Proc Natl Acad Sci USA. 1977, 76(1):114-121
  11. Ritchey, M.B., Palese, P., and Schulman J.L. Mapping of the influenza virus genome III: identification of genes coding for nucleoprotein, membrane protein, and nonstructural protein. Journal of Virology. 1976, 20(1):307-313
  12. KEGG. Influenza A pathway. 
  13. CDC. Influenza. (Accessed 26 March 2020).
  14. Everitt, A.R. et al. IFITM3 restricts the morbidity and mortality associated with influenza. Nature. 2012, 484:519-23.

Disease Brainstorm

Reflection Blog #2

I think that this project poses a really interesting opportunity to practice communicating science with others, and, for this reason, I would like to focus on a disease which affects a large portion of the population. I have had a long standing interest in the immune system and pathogenesis, and my BCM 341 proposal was centered around one mechanism of innate immune response (namely, inflammasome complex activation pathways). I would be interested, then, in picking a condition which can relate to this in some capacity. During my freshman year, I read a book called The Coming Plague by author Laurie Garrett, which discussed many epidemics of the twentieth century and the healthcare professions who dedicated their careers to battling them. While this book certainly had a more public health-epidemiology focus, it was one of the major sparks for my interest in pathogenesis and infectious disease. Given these interests, I have compiled the following list of possible diseases to explore for this project: 

  1. Influenza – Influenza is one of the most fascinating pathogens on the planet – not only for its abundance but for its diverse and dynamic pathogenic mechanisms. While symptoms are mild in many, the flu still causes anywhere from 10,000-60,000 deaths each year in the United States alone. While this topic is fairly large, it could be narrowed by focusing on a specific flu type. Because this disease is constantly evolving, I am sure there is an abundance of literature available on its pathogenic mechanisms. I believe this diseases poses interesting opportunities for this project in both its biochemical components and its capacity to important practice communication with non-experts on a topic which affects hundreds of thousands of Americans each year. 
  2. Legionnaire’s disease – Legionnaire’s disease is a relatively rare and severe form of pneumonia caused by infection with the Legionella bacterium. My BCM 341 proposal focused on one of the innate immune responses to this infection, and for this reason, I think it could be interesting to use this project to look at this through a different lens. In 2018, Legionnaire’s disease caused 10,000 reported cases, although many cases are suspected to go undiagnosed as Legionnaire’s-driven pneumonia specifically. Though not necessarily relevant to the biochemical portion fo this project, Legionnaire’s disease is also the subject of a very interesting history regarding its initial mysterious outbreak in the 1970s. I am already familiar with at least some of the biochemical components of this disease, which makes me confident that there is interesting and adequate literature to support this topic.
  3. MERS-CoV/Coronavirus – Finally, given the recent news, I think it could be interesting to look at a coronavirus. Before the outbreak this year with n2019-CoV, other coronaviruses such as SARS and MERS. The challenge with this is that these viruses seem to emerge as temporary outbreaks, which might affect the abundance of recent literature in the field. The SARS-CoV outbreak occurred in 2003, but no new cases have been reported in recent years. The MERS-CoV outbreak was in 2014, but cases are ongoing. For this reason, I think that MERS-CoV would make the best choice of this list for this project. It would be really interesting to follow the n2019-CoV, but I am not sure that there will be sufficient literature to support that topic as it is so new. 


  1. Laurie Garret, The Coming Plague: Newly Emerging Diseases in a World Out of Balance. New York: Farrar, Straus, and Giroux, 1994.
  2. Centers for Disease Control and Prevention, “Disease Burden of Influenza” [Reviewed] January 10, 2020 
  3. Centers for Disease Control and Prevention, “Legionella (Legionnaire’s Disease and Pontiac Fever): History, Burden, and Trends.” [Reviewed] April 30, 2018.
  4. World Health Organization, “SARS (Severe Acute Respiratory Syndrome)” 
  5. Centers for Disease Control and Prevention, “About MERS” [Reviewed] August 2, 2019.

Why Biochemistry?

Reflection Blog #1

Like many students, I don’t think that I really knew what “biochemistry” was coming into college – and, if I’m being honest, not even really when I declared the major (as a second semester freshman). My mindset in doing so was more that I enjoyed General Chemistry, but was more interested conceptually in biological applications. This wasn’t entirely misguided, but had I been asked to define “biochemistry” at the time, I am not sure I would have had an answer. I knew that I could change my major later on if necessary, but at the risk of sounding cliché, I had a feeling that I would really like it – and I wasn’t wrong.

Most define the field of biochemistry to be the study of the chemical processes which take place in biological systems, with more specific definitions varying in scope. The American Chemical Society defines the field as the “study of the structure, composition, and chemical reaction of substances in living systems,” mentioning molecular biology, immunochemistry, neurochemistry, and biophysical chemistry as some of the included sciences.1 The Journal of Biological Chemistry extends that definition slightly to include areas such as microbiology and computational biology as subsets of the field.2 As a 3rd year undergraduate, my coursework has only barely breached the diverse disciplines which make up the field (there is only so much that can fit into a 4-year liberal arts major), which is something I look forward to exploring further in future classes.

I find that biochemistry provides answers to many of the questions I was left with in introductory biology courses, and provides context and meaning to the concepts from my introductory chemistry courses. I remember, for example, questioning how proteins could be capable of selectively transporting protons across the mitochondrial membrane during oxidative phosphorylation in an introductory biology course. Meanwhile, I might have been learning about hydrogen bonding and polarity in chemistry. But then, in Biochemistry with Dr. Hark, I remember we discussed a 2013 paper which identified possible “proton translocation channels” made of polar residues and water molecules, allowing proton transfer to occur in association with conformational changes driven by redox chemistry 3 (cool!). This makes sense to me in a way that the simple statement of the process itself does not, and it is moments like this, where so many pieces of both biology and chemistry seem to come together, that I find I enjoy learning about the subject most. Now, I think, I even view ecological questions from a somewhat biochemical perspective – I find it fascinating and beautiful to think that complex behaviors or habitats are, at least in part, emergent properties of complex biochemistry and environmental interactions happening at a much smaller scale. 

Members of our lab (Summer 2019) sporting our “LmbBFUN” t-shirts, a play on the protein we study, LmbB1

As a student planning on attending medical school, biochemistry has always had a clear place in my career goals. But my career plans have also been shaped by my experiences in biochemistry. Most notable are my experiences with biochemistry research in Dr. Colabroy’s lab, where we work to understand the mechanism and activity of an enzyme involved in Lincomycin biosynthesis. Biochemistry never ceases to amaze me in its elegant explanations behind so many biological and physiological processes, and I guess that I find it particularly interesting to answer questions at a molecular scale – where answers aren’t necessarily apparent by direct observation. My research experiences have ultimately pushed me to pursue research in my future career in addition to my clinical aspirations. Given the copious medical conditions and diseases driven by molecular processes or malfunctions, I see biochemistry and molecular biology as absolutely essential areas of research in disease and treatment, which is something I am really looking forward to exploring further both in this course and my career. 


  1. American Chemical Society. “Biological/Biochemistry”
  2. Journal of Biological Chemistry “About JBC” December 12, 2019.
  3. Baradaran, R.; Berrisford, J.M.; Minhas, G.S.; and Sazanov, L.A. Crystal structure of the entire respiratory complex I. Nature 2013, 494,443-448.