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12.2.2: Tracking Infectious Diseases - Biology

12.2.2: Tracking Infectious Diseases - Biology


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Learning Objectives

  • Explain the research approaches used by the pioneers of epidemiology
  • Explain how descriptive, analytical, and experimental epidemiological studies go about determining the cause of morbidity and mortality

Epidemiology has its roots in the work of physicians who looked for patterns in disease occurrence as a way to understand how to prevent it. The idea that disease could be transmitted was an important precursor to making sense of some of the patterns. In 1546, Girolamo Fracastoro first proposed the germ theory of disease in his essay De Contagione et Contagiosis Morbis, but this theory remained in competition with other theories, such as the miasma hypothesis, for many years (see What Our Ancestors Knew). Uncertainty about the cause of disease was not an absolute barrier to obtaining useful knowledge from patterns of disease. Some important researchers, such as Florence Nightingale, subscribed to the miasma hypothesis. The transition to acceptance of the germ theory during the 19th century provided a solid mechanistic grounding to the study of disease patterns. The studies of 19th century physicians and researchers such as John Snow, Florence Nightingale, Ignaz Semmelweis, Joseph Lister, Robert Koch, Louis Pasteur, and others sowed the seeds of modern epidemiology.

Pioneers of Epidemiology

John Snow (Figure (PageIndex{1})) was a British physician known as the father of epidemiology for determining the source of the 1854 Broad Street cholera epidemic in London. Based on observations he had made during an earlier cholera outbreak (1848–1849), Snow proposed that cholera was spread through a fecal-oral route of transmission and that a microbe was the infectious agent. He investigated the 1854 cholera epidemic in two ways. First, suspecting that contaminated water was the source of the epidemic, Snow identified the source of water for those infected. He found a high frequency of cholera cases among individuals who obtained their water from the River Thames downstream from London. This water contained the refuse and sewage from London and settlements upstream. He also noted that brewery workers did not contract cholera and on investigation found the owners provided the workers with beer to drink and stated that they likely did not drink water.1 Second, he also painstakingly mapped the incidence of cholera and found a high frequency among those individuals using a particular water pump located on Broad Street. In response to Snow’s advice, local officials removed the pump’s handle,2 resulting in the containment of the Broad Street cholera epidemic.

Snow’s work represents an early epidemiological study and it resulted in the first known public health response to an epidemic. Snow’s meticulous case-tracking methods are now common practice in studying disease outbreaks and in associating new diseases with their causes. His work further shed light on unsanitary sewage practices and the effects of waste dumping in the Thames. Additionally, his work supported the germ theory of disease, which argued disease could be transmitted through contaminated items, including water contaminated with fecal matter.

Snow’s work illustrated what is referred to today as a common source spread of infectious disease, in which there is a single source for all of the individuals infected. In this case, the single source was the contaminated well below the Broad Street pump. Types of common source spread include point source spread, continuous common source spread, and intermittent common source spread. In point source spread of infectious disease, the common source operates for a short time period—less than the incubation period of the pathogen. An example of point source spread is a single contaminated potato salad at a group picnic. In continuous common source spread, the infection occurs for an extended period of time, longer than the incubation period. An example of continuous common source spread would be the source of London water taken downstream of the city, which was continuously contaminated with sewage from upstream. Finally, with intermittent common source spread, infections occur for a period, stop, and then begin again. This might be seen in infections from a well that was contaminated only after large rainfalls and that cleared itself of contamination after a short period.

In contrast to common source spread, propagated spread occurs through direct or indirect person-to-person contact. With propagated spread, there is no single source for infection; each infected individual becomes a source for one or more subsequent infections. With propagated spread, unless the spread is stopped immediately, infections occur for longer than the incubation period. Although point sources often lead to large-scale but localized outbreaks of short duration, propagated spread typically results in longer duration outbreaks that can vary from small to large, depending on the population and the disease (Figure (PageIndex{2})). In addition, because of person-to-person transmission, propagated spread cannot be easily stopped at a single source like point source spread.

Florence Nightingale’s work is another example of an early epidemiological study. In 1854, Nightingale was part of a contingent of nurses dispatched by the British military to care for wounded soldiers during the Crimean War. Nightingale kept meticulous records regarding the causes of illness and death during the war. Her recordkeeping was a fundamental task of what would later become the science of epidemiology. Her analysis of the data she collected was published in 1858. In this book, she presented monthly frequency data on causes of death in a wedge chart histogram (Figure (PageIndex{3})). This graphical presentation of data, unusual at the time, powerfully illustrated that the vast majority of casualties during the war occurred not due to wounds sustained in action but to what Nightingale deemed preventable infectious diseases. Often these diseases occurred because of poor sanitation and lack of access to hospital facilities. Nightingale’s findings led to many reforms in the British military’s system of medical care.

Joseph Lister provided early epidemiological evidence leading to good public health practices in clinics and hospitals. These settings were notorious in the mid-1800s for fatal infections of surgical wounds at a time when the germ theory of disease was not yet widely accepted (see Foundations of Modern Cell Theory). Most physicians did not wash their hands between patient visits or clean and sterilize their surgical tools. Lister, however, discovered the disinfecting properties of carbolic acid, also known as phenol (see Using Chemicals to Control Microorganisms). He introduced several disinfection protocols that dramatically lowered post-surgical infection rates.3 He demanded that surgeons who worked for him use a 5% carbolic acid solution to clean their surgical tools between patients, and even went so far as to spray the solution onto bandages and over the surgical site during operations (Figure (PageIndex{4})). He also took precautions not to introduce sources of infection from his skin or clothing by removing his coat, rolling up his sleeves, and washing his hands in a dilute solution of carbolic acid before and during the surgery.

Visit the website for The Ghost Map, a book about Snow’s work related to the Broad Street pump cholera outbreak.

John Snow’s own account of his work has additional links and information.

This CDC resource further breaks down the pattern expected from a point-source outbreak.

Learn more about Nightingale’s wedge chart here.

Exercise (PageIndex{1})

  1. Explain the difference between common source spread and propagated spread of disease.
  2. Describe how the observations of John Snow, Florence Nightingale, and Joseph Lister led to improvements in public health.

Types of Epidemiological Studies

Today, epidemiologists make use of study designs, the manner in which data are gathered to test a hypothesis, similar to those of researchers studying other phenomena that occur in populations. These approaches can be divided into observational studies (in which subjects are not manipulated) and experimental studies (in which subjects are manipulated). Collectively, these studies give modern-day epidemiologists multiple tools for exploring the connections between infectious diseases and the populations of susceptible individuals they might infect.

Observational Studies

In an observational study, data are gathered from study participants through measurements (such as physiological variables like white blood cell count), or answers to questions in interviews (such as recent travel or exercise frequency). The subjects in an observational study are typically chosen at random from a population of affected or unaffected individuals. However, the subjects in an observational study are in no way manipulated by the researcher. Observational studies are typically easier to carry out than experimental studies, and in certain situations they may be the only studies possible for ethical reasons.

Observational studies are only able to measure associations between disease occurrence and possible causative agents; they do not necessarily prove a causal relationship. For example, suppose a study finds an association between heavy coffee drinking and lower incidence of skin cancer. This might suggest that coffee prevents skin cancer, but there may be another unmeasured factor involved, such as the amount of sun exposure the participants receive. If it turns out that coffee drinkers work more in offices and spend less time outside in the sun than those who drink less coffee, then it may be possible that the lower rate of skin cancer is due to less sun exposure, not to coffee consumption. The observational study cannot distinguish between these two potential causes.

There are several useful approaches in observational studies. These include methods classified as descriptive epidemiology and analytical epidemiology. Descriptive epidemiology gathers information about a disease outbreak, the affected individuals, and how the disease has spread over time in an exploratory stage of study. This type of study will involve interviews with patients, their contacts, and their family members; examination of samples and medical records; and even histories of food and beverages consumed. Such a study might be conducted while the outbreak is still occurring. Descriptive studies might form the basis for developing a hypothesis of causation that could be tested by more rigorous observational and experimental studies.

Analytical epidemiology employs carefully selected groups of individuals in an attempt to more convincingly evaluate hypotheses about potential causes for a disease outbreak. The selection of cases is generally made at random, so the results are not biased because of some common characteristic of the study participants. Analytical studies may gather their data by going back in time (retrospective studies), or as events unfold forward in time (prospective studies).

Retrospective studies gather data from the past on present-day cases. Data can include things like the medical history, age, gender, or occupational history of the affected individuals. This type of study examines associations between factors chosen or available to the researcher and disease occurrence.

Prospective studies follow individuals and monitor their disease state during the course of the study. Data on the characteristics of the study subjects and their environments are gathered at the beginning and during the study so that subjects who become ill may be compared with those who do not. Again, the researchers can look for associations between the disease state and variables that were measured during the study to shed light on possible causes.

Analytical studies incorporate groups into their designs to assist in teasing out associations with disease. Approaches to group-based analytical studies include cohort studies, case-control studies, and cross-sectional studies. The cohort method examines groups of individuals (called cohorts) who share a particular characteristic. For example, a cohort might consist of individuals born in the same year and the same place; or it might consist of people who practice or avoid a particular behavior, e.g., smokers or nonsmokers. In a cohort study, cohorts can be followed prospectively or studied retrospectively. If only a single cohort is followed, then the affected individuals are compared with the unaffected individuals in the same group. Disease outcomes are recorded and analyzed to try to identify correlations between characteristics of individuals in the cohort and disease incidence. Cohort studies are a useful way to determine the causes of a condition without violating the ethical prohibition of exposing subjects to a risk factor. Cohorts are typically identified and defined based on suspected risk factors to which individuals have already been exposed through their own choices or circumstances.

Case-control studies are typically retrospective and compare a group of individuals with a disease to a similar group of individuals without the disease. Case-control studies are far more efficient than cohort studies because researchers can deliberately select subjects who are already affected with the disease as opposed to waiting to see which subjects from a random sample will develop a disease.

A cross-sectional study analyzes randomly selected individuals in a population and compares individuals affected by a disease or condition to those unaffected at a single point in time. Subjects are compared to look for associations between certain measurable variables and the disease or condition. Cross-sectional studies are also used to determine the prevalence of a condition.

Experimental Studies

Experimental epidemiology uses laboratory or clinical studies in which the investigator manipulates the study subjects to study the connections between diseases and potential causative agents or to assess treatments. Examples of treatments might be the administration of a drug, the inclusion or exclusion of different dietary items, physical exercise, or a particular surgical procedure. Animals or humans are used as test subjects. Because experimental studies involve manipulation of subjects, they are typically more difficult and sometimes impossible for ethical reasons.

Koch’s postulates require experimental interventions to determine the causative agent for a disease. Unlike observational studies, experimental studies can provide strong evidence supporting cause because other factors are typically held constant when the researcher manipulates the subject. The outcomes for one group receiving the treatment are compared to outcomes for a group that does not receive the treatment but is treated the same in every other way. For example, one group might receive a regimen of a drug administered as a pill, while the untreated group receives a placebo (a pill that looks the same but has no active ingredient). Both groups are treated as similarly as possible except for the administration of the drug. Because other variables are held constant in both the treated and the untreated groups, the researcher is more certain that any change in the treated group is a result of the specific manipulation.

Experimental studies provide the strongest evidence for the etiology of disease, but they must also be designed carefully to eliminate subtle effects of bias. Typically, experimental studies with humans are conducted as double-blind studies, meaning neither the subjects nor the researchers know who is a treatment case and who is not. This design removes a well-known cause of bias in research called the placebo effect, in which knowledge of the treatment by either the subject or the researcher can influence the outcomes.

Exercise (PageIndex{2})

  1. Describe the advantages and disadvantages of observational studies and experimental studies.
  2. Explain the ways that groups of subjects can be selected for analytical studies.

Part 3

Since laboratory tests had confirmed Salmonella, a common foodborne pathogen, as the etiologic agent, epidemiologists suspected that the outbreak was caused by contamination at a food processing facility serving the region. Interviews with patients focused on food consumption during and after the Thanksgiving holiday, corresponding with the timing of the outbreak. During the interviews, patients were asked to list items consumed at holiday gatherings and describe how widely each item was consumed among family members and relatives. They were also asked about the sources of food items (e.g., brand, location of purchase, date of purchase). By asking such questions, health officials hoped to identify patterns that would lead back to the source of the outbreak.

Analysis of the interview responses eventually linked almost all of the cases to consumption of a holiday dish known as the turducken—a chicken stuffed inside a duck stuffed inside a turkey. Turducken is a dish not generally consumed year-round, which would explain the spike in cases just after the Thanksgiving holiday. Additional analysis revealed that the turduckens consumed by the affected patients were purchased already stuffed and ready to be cooked. Moreover, the pre-stuffed turduckens were all sold at the same regional grocery chain under two different brand names. Upon further investigation, officials traced both brands to a single processing plant that supplied stores throughout the Florida panhandle.

Exercise (PageIndex{3})

  1. Is this an example of common source spread or propagated spread?
  2. What next steps would the public health office likely take after identifying the source of the outbreak?

Key Concepts and Summary

  • Early pioneers of epidemiology such as John Snow, Florence Nightingale, and Joseph Lister, studied disease at the population level and used data to disrupt disease transmission.
  • Descriptive epidemiology studies rely on case analysis and patient histories to gain information about outbreaks, frequently while they are still occurring.
  • Retrospective epidemiology studies use historical data to identify associations with the disease state of present cases. Prospective epidemiology studies gather data and follow cases to find associations with future disease states.
  • Analytical epidemiology studies are observational studies that are carefully designed to compare groups and uncover associations between environmental or genetic factors and disease.
  • Experimental epidemiology studies generate strong evidence of causation in disease or treatment by manipulating subjects and comparing them with control subjects.

Matching

Match each type of epidemiology study with its description.

___experimentalA. examination of past case histories and medical test results conducted on patients in an outbreak
___analyticalB. examination of current case histories, interviews with patients and their contacts, interpretation of medical test results; frequently conducted while outbreak is still in progress
___prospectiveC. use of a set of test subjects (human or animal) and control subjects that are treated the same as the test subjects except for the specific treatment being studied
___descriptiveD. observing groups of individuals to look for associations with disease
___retrospectiveE. a comparison of a cohort of individuals through the course of the study

C, D, E, B, A

Match each pioneer of epidemiology with his or her contribution.

___Florence NightingaleA. determined the source of a cholera outbreak in London
___Robert KochB. showed that surgical wound infection rates could be dramatically reduced by using carbolic acid to disinfect surgical tools, bandages, and surgical sites
___Joseph ListerC. compiled data on causes of mortality in soldiers, leading to innovations in military medical care
___John SnowD. developed a methodology for conclusively determining the etiology of disease

C, D, B, A

Fill in the Blank

________occurs when an infected individual passes the infection on to other individuals, who pass it on to still others, increasing the penetration of the infection into the susceptible population.

Propagated spread

A batch of food contaminated with botulism exotoxin, consumed at a family reunion by most of the members of a family, would be an example of a ________ outbreak.

point source

Short Answer

What activity did John Snow conduct, other than mapping, that contemporary epidemiologists also use when trying to understand how to control a disease?

Footnotes

  1. John Snow. On the Mode of Communication of Cholera. Second edition, Much Enlarged. John Churchill, 1855.
  2. John Snow. “The Cholera near Golden-Wquare, and at Deptford.” Medical Times and Gazette 9 (1854): 321–322. http://www.ph.ucla.edu/epi/snow/chol...densquare.html.
  3. O.M. Lidwell. “Joseph Lister and Infection from the Air.” Epidemiology and Infection 99 (1987): 569–578. www.ncbi.nlm.nih.gov/pmc/arti...00006-0004.pdf.

Diseases Types:2 Major Types of Diseases | Human Health | Biology

The following points highlight the two major types of diseases that occur in humans. The types are: 1. Communicable or Infectious Diseases 2. Non-Communicable or Non-Infectious Diseases.

Type # 1. Communicable or Infectious Diseases:

These can be transmitted from an infected person to a healthy person by means of air, water, food, physical contact or vectors. These are caused due to infection and multiplication of some kind of micro-organisms, so are also called infectious diseases.

Classification of communicable diseases. These can be categorized on two basis:

(i) Depending upon the causative agent, communicable diseases are of six types:

1. Bacterial diseases e.g., diphtheria, whooping cough, leprosy, syphilis, tetanus, typhoid, plague, pneumonia, tuberculosis, cholera, anthrax, etc.

2. Viral diseases e.g., dengue, influenza, measles, polio, smallpox, chickenpox, common cold, rabies, Japanese encephalitis, AIDS, infectious hepatitis, etc.

3. Protozoan diseases e.g., malaria, amoebiasis, kala azar, sleeping sickness etc.

4. Helminth diseases e.g., taeniasis, ascariasis, elephantiasis, trichinosis, liverrot, echinococcosis, etc.

5. Fungal diseases e.g., ring worm, athlete’s foot, candidacies, etc.

6. Rickettsial diseases e.g., typhus fever, trench fever, Q-fever, Rocky mountain spotted fever etc.

(ii) On the basis of their mode of transmission, the communicable diseases are of two types:

a. Contagious Diseases:

These communicable diseases can spread from an infected person to healthy person by actual contact between them e.g., STDs, smallpox, chickenpox, measles, leprosy etc.

b. Non-Contagious Diseases:

These can spread from an infected person to healthy person with food, air or water e.g., taeniasis, ascariasis, cholera, tuberculosis, typhoid etc., or micro-organisms are injected inside the human body by some carrier or vector hosts e.g., malaria, filariasis, plague etc.

Type # 2. Non-Communicable or Non-Infectious Diseases:

These do not spread from an infected person to a healthy person.

These are of four types on the basis of their causative agents:

(i) Deficiency Diseases:

These occur either due to deficiency of some nutrients in the diet or some hormone e.g., kwashiorkor (protein), diabetes mellitus (insulin), dwarfism (growth hormone), etc.

(ii) Degenerative Diseases:

These occur due to degeneration of certain body tissues e.g., cardiovascular diseases (of heart and blood vessels), stroke disease (of brain) and arthritis (of joints).

(iii) Cancerous Diseases:

These occur due to uncontrolled growth and division of cells in certain body tissues leading to tumour formation.


Parasites - Lice

Lice are parasitic insects that can be found on people&rsquos heads and bodies, including the pubic area. Human lice survive by feeding on human blood. Lice found on each area of the body are different from each other. The three types of lice that live on humans are

  • Pediculus humanus capitis (head louse),
  • Pediculus humanus corporis (body louse, clothes louse), and
  • Pthirus pubis (&ldquocrab&rdquo louse, pubic louse).

Only the body louse is known to spread disease.

Lice infestations (pediculosis and pthiriasis) are spread most commonly by close person-to-person contact. Dogs, cats, and other pets do not play a role in the transmission of human lice. Lice move by crawling they cannot hop or fly. Both over-the-counter and prescription medications are available for treatment of lice infestations.

Adult head lice are 2.1&ndash3.3 mm in length. Head lice infest the head and neck and attach their eggs to the base of the hair shaft. Lice move by crawling they cannot hop or fly.

Adult body lice are 2.3&ndash3.6 mm in length. Body lice live and lay eggs on clothing and only move to the skin to feed.

Adult pubic lice are 1.1&ndash1.8 mm in length. Pubic lice typically are found attached to hair in the pubic area but sometimes are found on coarse hair elsewhere on the body (for example, eyebrows, eyelashes, beard, mustache, chest, armpits, etc.).


Parasites - Scabies

Human scabies is caused by an infestation of the skin by the human itch mite (Sarcoptes scabiei var. hominis). The microscopic scabies mite burrows into the upper layer of the skin where it lives and lays its eggs. The most common symptoms of scabies are intense itching and a pimple-like skin rash. The scabies mite usually is spread by direct, prolonged, skin-to-skin contact with a person who has scabies.Scabies occurs worldwide and affects people of all races and social classes. Scabies can spread rapidly under crowded conditions where close body contact is frequent. Institutions such as nursing homes, extended-care facilities, and prisons are often sites of scabies outbreaks.

Images: Sarcoptes scabiei mites in a skin scraping, stained with lactophenol cotton-blue. (Credit: DPDx)


Category B

Definition

Second highest priority agents include those that

  • are moderately easy to disseminate
  • result in moderate morbidity rates and low mortality rates and
  • require specific enhancements of CDC&rsquos diagnostic capacity and enhanced disease surveillance.

Agents/Diseases

  • Brucellosis (Brucella species)
  • Epsilon toxin of Clostridium perfringens
  • Food safety threats (Salmonella species, Escherichia coli O157:H7, Shigella)
  • Glanders (Burkholderia mallei)
  • Melioidosis (Burkholderia pseudomallei)
  • Psittacosis (Chlamydia psittaci)
  • Q fever (Coxiella burnetii)
  • Ricin toxin from Ricinus communis (castor beans)
  • Typhus fever (Rickettsia prowazekii)
  • Viral encephalitis (alphaviruses, such as eastern equine encephalitis, Venezuelan equine encephalitis, and western equine encephalitis])
  • Water safety threats (Vibrio cholerae, Cryptosporidium parvum)

Infectious Disease Project

In March of 2020, Illinois shut down all public schools to prevent the spread of Covid19, a novel coronavirus that was spreading across Europe and was found in the United States. At the time, my AP Biology class was studying viruses and epidemiology.

ISBE had released tips and strategies for dealing with the closures which included ways for students to continue their classes using Google Classroom and similar platforms. I assigned this disease project for my students as a way to continue their studies on pathogens and allow them some creative freedom to explore a topic of interest.

Students create an infographic, poster, or pamphlet that instructs the public about a disease. They can even choose a historic disease, like the Black Plague or polio. Students can choose from a list of diseases and may suggest their own for approval. The rubric outlines the requirements, such as explaining how the disease is spread, recovery outcomes, and prevention. Students will get a week to complete their project and will then review and grade other projects from their peers.

Students can create their project using piktochart, postermywall, or use a Word template to create a 3 fold pamphlet.

Though this won’t make up for 2 weeks of missed instruction, it does give students a relevant project to work on during this time period. Though, I also plan to give them other assignments to keep them on track for AP Biology content.


BMC Infectious Diseases is pleased to announce the Antimicrobial Resistance special issue. This series includes a diverse range of AMR studies from around the globe, investigating the detection and surveillance of AMR, from the lab bench to hospital bed.

Quantitative assessment of the effectiveness of joint measures led by Fangcang shelter hospitals in response to COVID-19 epidemic in Wuhan, China

Authors: Hui Jiang, Pengfei Song, Siyi Wang, Shuangshuang Yin, Jinfeng Yin, Chendi Zhu, Chao Cai, Wangli Xu and Weimin Li

First case of an invasive Bacteroides dorei infection detected in a patient with a mycotic aortic aneurysm—raising a rebellion of major indigenous bacteria in humans: a case report and review

Authors: Takayuki Matsuoka, Takuya Shimizu, Tadanori Minagawa, Wakiko Hiranuma, Miki Takeda, Risako Kakuta and Shunsuke Kawamoto

Repeat exit site infection in peritoneal dialysis patient with polycythemia vera – a case report

Authors: Edyta Gołembiewska and Kazimierz Ciechanowski

Comparative evaluation of the Thermo fisher TaqPath™ COVID-19 combo kit with the Cepheid Xpert® Xpress SARS-CoV-2 assay for detecting SARS-CoV-2 in nasopharyngeal specimens

Authors: Paul A. Granato, Simon R. Kimball, Brenda R. Alkins, Deirdre C. Cross and Melissa M. Unz

A case of chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: a case report and literature review

Authors: Yunfeng Shi, Junxian Chen, Xiaohan Shi, Jiajia Hu, Hongtao Li, Xiaojie Li, Yanhong Wang and Benquan Wu

How long do nosocomial pathogens persist on inanimate surfaces? A systematic review

Authors: Axel Kramer, Ingeborg Schwebke and Günter Kampf

Content type: Research article

Timing of progression from Chlamydia trachomatisinfection to pelvic inflammatory disease: a mathematical modelling study

Authors: Sereina A Herzog, Christian L Althaus, Janneke CM Heijne, Pippa Oakeshott, Sally Kerry, Phillip Hay and Nicola Low

Content type: Research article

Scent dog identification of samples from COVID-19 patients – a pilot study

Authors: Paula Jendrny, Claudia Schulz, Friederike Twele, Sebastian Meller, Maren von Köckritz-Blickwede, Albertus Dominicus Marcellinus Erasmus Osterhaus, Janek Ebbers, Veronika Pilchová, Isabell Pink, Tobias Welte, Michael Peter Manns, Anahita Fathi, Christiane Ernst, Marylyn Martina Addo, Esther Schalke and Holger Andreas Volk

Content type: Research article

Recognition of aerosol transmission of infectious agents: a commentary

Authors: Raymond Tellier, Yuguo Li, Benjamin J. Cowling and Julian W. Tang

Methylprednisolone or dexamethasone, which one is superior corticosteroid in the treatment of hospitalized COVID-19 patients: a triple-blinded randomized controlled trial

Authors: Keivan Ranjbar, Mohsen Moghadami, Alireza Mirahmadizadeh, Mohammad Javad Fallahi, Vahid Khaloo, Reza Shahriarirad, Amirhossein Erfani, Zohre Khodamoradi and Mohammad Hasan Gholampoor Saadi

Content type: Research article

The Correction to this article has been published in BMC Infectious Diseases 2021 21:436


The Biology Undergraduate Major

Although not required anymore, the 60-level Biology courses are the starting point for the major. These interactive courses cultivate excitement about Biology and build the intellectual, quantitative and communication skills required to succeed in the major. 60-level Biology courses have no prerequisites.

BIO 60: Introduction to Problem Solving in Biology: Why is Lyme disease spreading? How does HIV become drug resistant? How do other animals affect our disease risk? In BIO 60 students will examine actual case studies to experience how different scientific approaches are used to battle infectious disease. They will evaluate information presented in the popular media and the scientific literature, and will directly participate in the scientific process through hands-on collection, documentation and analyses of authentic scientific data. Students will cultivate their scientific curiosity by discovering the natural world with a Foldscope, the ‘origami paper microscope’ (https://microcosmos.foldscope.com). Students will build critical thinking skills by creating hypotheses, and designing experiments that pertain to problems in infectious disease. Students will work in teams to expand their thinking and will practice communicating science to different audiences.

BIO 61: Science as a Creative Process: What is the process of science, and why does creativity matter? Students will delve deeply into the applicability of science in addressing a vast range of real-world problems. This course will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement, using the Arduino microcontroller and electronic sensors. The final assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required.

BIO 62: Microbiology Experiments: Microbiology is a major foundation of all modern biology. Many aspects of experimental strategy, logic, and analysis originated in the fields of bacterial genetics and physiology. In BIO 62, we will use prokaryotic biology to review fundamentals of molecular biology and energetics, and in lab work we will work with experimental design and data interpretation. Research on prokaryotes has greatly expanded through genomic and population analysis, and we will use these approaches to ask questions about the hidden worlds around and inside us: the microbiome.

BIO Foundations Courses for Sophomores and Juniors

In the next step of the curriculum, students engage with fundamental areas of Biology through a set of six Bio Foundations courses, which cover key foundational disciplines of Biology. Students will take five of the six Bio Foundations courses depending on their area of emphasis within the major. These courses will delve into these fundamental areas of Biology and further build students’ skills in critical scientific thinking, reading the literature, and scientific communication.

Bio Foundations courses to be offered starting 2017-18, each worth 4 units:

  • BIO/BIOHOPK 81 – Ecology (Main Campus: Autumn Hopkins)
  • BIO 82 – Genetics
  • BIO 83 – Biochemistry and Molecular Biology
  • BIO 84 – Physiology
  • BIO 85 – Evolutionary Biology
  • BIO 86 – Cell Biology

The general Biology major allows students to choose five out of the six Bio Foundation courses. Specialized fields of study will require specific Bio Foundations courses, with the remaining courses to be selected by the student, to a total of five. For those courses offered on both the main campus and at Hopkins Marine Station, students may fulfill their requirements at either campus.

The 80-level Bio Foundations courses must be taken for a letter grade. Questions about the Foundations courses can be submitted to Waheeda Khalfan.

Two inquiry-based lab courses

These courses provide hands-on exposure to scientific methodology and experimental design. They are inquiry-based, and allow students to hone their scientific thinking and lab skills by conducting real biology research. All students, even those who pursue honors, are required to take two lab courses, designed to give a grounding in both lab research and in field research:

  1. BIO 45, Introduction to Laboratory Research in Cell and Molecular Biology
  2. One of the following:
  • BIO 46: Introduction to Research in Ecology and Evolutionary Biology
  • BIO 47: Introduction to Research in Ecology and Evolutionary Biology
  • BIOHOPK 47: Core Laboratory in Plant Biology, Ecology and Evolution
  • BIOHOPK 175H: Marine Science and Conservation in a Changing World

Breadth Courses

Courses in Chemistry, Math, Physics, and Statistics will be required, and will vary by track.

Only one breadth course in Chemistry, Math, Physics, and Statistics may be taken credit/no credit.

Additional Elective courses in students' area of interest and/or Field of Study

Upper level courses are offered in more specialized areas of Biology, many of them are seminar-style courses that provide opportunities to explore in depth the scientific literature and to develop ideas for novel areas of research. Students have the option of pursing a general Biology major, or fulfilling specific requirements to pursue a specialized field of study. Each of the specialized fields has a unique combination of course requirements/recommendations as indicated in the appropriate advising handout. The fields of study are:

  • Biochemistry and Biophysics
  • Computational Biology
  • Ecology and Evolution
  • Marine Biology
  • Microbes and Immunity
  • Molecular Cell and Developmental Biology
  • Neurobiology

For all fields of study, one elective course may be taken credit/no credit.

Students are required to take one of the Biology university-approved WIM courses. Several of these options can also count toward the electives requirement. WIM must be taken for a letter grade when available.

Honors

For students completing the new degree plan, honors is no longer required in order to complete a track. Should students wish to complete the honors program, the requirements are the same as in prior years: an approved honors proposal, 10 units of BIO 199/BIOHOPK 199H/BIO 199X in the same lab, a GPA of at least 3.0 for all courses taken toward the major (excluding research units), an approved honors thesis, and presentation of their work at the annual honors symposium. Students will continue to apply for honors two quarters prior to their anticipated graduation date (Spring grads apply in Autumn).


Habitat loss linked to global emergence of infectious diseases

Auburn University researchers have published a new hypothesis that could provide the foundation for new scientific studies looking into the association of habitat loss and the global emergence of infectious diseases.

They present their research in the paper, "The Coevolution Effect as a Driver of Spillover," in the latest issue of the scientific journal, Trends in Parasitology.

"We provide a new perspective about how habitat loss can facilitate the emergence of infectious diseases in humans," said Sarah Zohdy, assistant professor in the School of Forestry and Wildlife Sciences and the College of Veterinary Medicine, who coauthored the study with Tonia Schwartz and Jamie Oaks, assistant professors in the Department of Biological Sciences in the College of Sciences and Mathematics.

Globally, scientists believe habitat loss is associated with emerging infectious diseases, or EIDs, spreading from wildlife to humans, such as Ebola, West Nile virus, SARS, Marburg virus and others. The Auburn team developed a new hypothesis, the coevolution effect, which is rooted in ecology and evolutionary biology, to explain the underlying mechanisms that drive this association.

Schwartz said the team integrated ideas from multiple aspects of biology, including disease ecology, evolutionary biology and landscape genetics, to develop the new hypothesis on why diseases are more likely to spill over from wildlife to humans in deforested habitats.

"We provide a testable hypothesis that we hope other researchers will try to test with their data, as we will be doing," Schwartz said. "Whether or not these studies fully support this new hypothesis, we anticipate it will provide a new perspective that other researchers in this field can use and build on, to ultimately push this field forward to understand disease spillover and prevent it."

The field of disease ecology is heavily based on a hypothesis known as the dilution effect, which was released at the turn of this century. It is essentially the idea that biodiversity conservation can protect humans from emerging infectious diseases. Zohdy said the dilution effect highlights the critical role that wildlife conservation can play in protecting human health and has transformed the understanding of zoonotic infectious diseases.

However, until now, even after a wealth of research in the past few decades has explored that hypothesis and found associations between the loss of biodiversity and EIDs, there has been no explanation for where the microbes that cause EIDs come from and how they get to humans.

"Through our hypothesis, we propose that as humans alter the landscape through habitat loss, forest fragments act as islands, and the wildlife hosts and disease-causing microbes that live within them undergo rapid diversification," Zohdy said. "Across a fragmented landscape we would then see an increase in diversity of disease-causing microbes, increasing the probability that any one of these microbes may spill over into human populations, leading to outbreaks."

Oaks said he is encouraged that the research will impact the way these problems are perceived.

"Our paper introduces an evolutionary mechanism to explain the association between habitat fragmentation and disease spillover into human populations, which we hope will complement the ecological perspectives on this global health challenge," he said.

School of Forestry and Wildlife Sciences Dean Janaki Alavalapati said the paper's findings are compelling.

"Dr. Zohdy and her fellow researchers provide noteworthy insights in the field of emerging infectious diseases and the driving forces behind them," Alavalapati said. "Their findings could result in a significant shift in the way the origins of these diseases are perceived."

Funded by an Intramural Grants Program award, the research, from its inception, was a collaborative and fully integrative project, from acquiring funding to writing the manuscript and training students across disciplines.


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