Linear Programming Models

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Linear Programming Models essay assignment

  • Context: Some unicellular organisms cause disease in ecological systems.
  • Major themes: All cells come from preexisting cells, cells maintain internal environments that differ from their external environments, cell structure defines cell function, and cells communicate with other cells.
  • Bottom line: Unicellular organisms that cause disease can spread rapidly in a susceptible population of animals, leading to an outbreak.

Linear Programming Models essay assignment

There are many species interactions in ecological systems. In parasite-host interactions, populations of animals or plants may be susceptible to newly-introduced disease-causing organisms. The pathogen may be a unicellular organism, such as Giardia or a bacterium. You already know how some parasites that cause disease (such as, Giardia and B. burgdorferi, which causes Lyme disease) affect individuals and populations. {Connections: Lyme disease is discussed in Section 22.2.} In this section, you will learn how a newly introduced pathogen spreads among the individuals in a population.

Occasionally, new diseases emerge in a population. In late 2002, a farmer in Guangdong Province, in southern China, was treated for pneumonia with flu-like symptoms. The patient died, but no definitive diagnosis was made on the cause of death. By early 2003, many more cases were observed. The illness usually began with high fever and mild respiratory symptoms, but progressed to pneumonia in a few days. The disease was named severe acute respiratory syndrome (SARS). Because of the outbreak and severity of the disease, scientists quickly went to work to discover the causative agent of SARS, which turned out to be a coronavirus (Figure 22.18). Coronaviruses are enveloped by spherical spike proteins with surface projections that form a corona around the virus and a ssRNAcontaining (in the case of the SARS coronavirus) 13 genes that code for 14 proteins.

Y. Guan and his colleagues studied the epidemiology of the first outbreaks in Guangdong Province by gathering data from clinical records of patients admitted to hospitals with a diagnosis of atypical pneumonia, meaning that it was not caused by the bacteria Streptococcus pneumonia. In addition, the researchers used local health authority reports and doctors interviews to assess the spread of the disease (Figure 22.19).

The researchers defined a case as a patient running a high fever (> 38° C) with coughing or difficulty breathing who was either in close contact with a person suspected of having SARS or lived or traveled in an area known to have recent local transmission of SARS. Any patients that died from an unexplained acute respiratory illness who had come in close contact or traveled in an area known to have SARS cases were defined as a suspected case. Out of 305 cases during this early outbreak, 105 of the patients were healthcare workers. Patients suffering complications were sometimes brought from rural outlying cities to Guangzhou for better medical care. Many of these initial patients were known to be related to one another. One SARS patient, admitted on December 17, 2002, was a chef who worked at a restaurant in Shenzhen. This chef came into regular contact with live caged animals used as exotic game food. He was the second confirmed case of SARS.

The scientists also studied 55 patients admitted to a hospital in Guangzhou, Guangdong Province, in early 2003 with atypical pneumonia. These patients ran fevers for an average of 11.4 days (+ 6.8 days, standard deviation) and developed pneumonia within 4 days of being admitted. Forty-one of 55 were known to have had definitive contact with another SARS patient, and 27 were healthcare workers. Guan and his colleagues examined mucus and blood serum samples for the SARS coronavirus antibodies. For 22 of the patients, the scientists tested paired samples, the first either 3 to 5 or 7 to 10 days after disease onset, and the second 15 days after onset. The researchers also tested 60 healthy adults (Table 22.9). Four of the pneumonia patients who did not test positive for the SARS coronavirus antibodies were discovered to have influenza.


The study of the initial outbreak is an important part of epidemiology and can pinpoint the origin of an epidemic, identify modes of transmission, and identify possible origins of the pathogen. In the southern China SARS outbreak of 2002, several observations were made by epidemiologists that were clues to origins and modes of transmission. One observation was that the second known SARS patient was a chef who came into regular contact with live caged animals. The epidemiological investigation discovered that his wife, two sisters, and seven healthcare workers all became infected from him.

In fact, 34% of all patients in the outbreaks in the initial six cities were healthcare workers. A patient in Guangzhou who spent only 18 hours in a hospital in Zhongshan infected 30 healthcare workers in Zhongshan and Guangzhou. This patient also infected 19 family members or relatives in Guangzhou. This large number of infections in relatives and healthcare workers gave rise to the Guangzhou outbreak. One physician infected during this time traveled to Hong Kong and became the source of the SARS outbreak that occurred later in Hong Kong. Because the outbreaks were characterized by infections in hospitals and family units, Guan and his colleagues concluded that transmission occurs through close contact with infected patients. The spread from city-to-city occurred because of transport of patients to better hospital facilities and movement of workers from city-to-city. This is comparable to a parasite like Giardia, which you discovered is transmitted through fecal-oral contact or contaminated water.

If you concluded that close person-to-person contact was the mode of transmission, you might have also concluded that coughing or sneezing, which spreads small droplets up to about a meter from infected persons, disperses the virus. The virus only needs to land on the mouth, nose, or eyes of a nearby person for them to become infected. If droplets land on another person’s hands, or if an uninfected person touches a surface contaminated with droplets and then touches their mouth, nose, or eyes, they can become infected. Close contact may also mean kissing or hugging between an infected and uninfected person. These are thought to be the most likely routes of transmission.

Most patients with atypical pneumonia that were tested for the SARS coronavirus had it. Several were infected with a strain of the influenza virus. Given the large percentage of patients in this study with the SARS coronavirus, Guan and his colleagues concluded that the outbreaks were caused by this newly emerging viral pathogen. The scientists were able to conclude that the pathogen was emerging because none of the healthy patients had antibodies to the SARS coronavirus, which suggests that the virus was not previously present in this human population. The researchers, in attempting to track down the origin of the SARS coronavirus, focused on the second known SARS patient, the chef, and the observation that he came into contact with exotic game animals. In China and many other countries, wild animals are caught or raised in captivity to be sold live at markets for human consumption. Some wild game animals are considered a delicacy in southern China and are bought by chefs for preparation at their restaurants. Other diseases are also known to spread from animals to humans.

Guan and his colleagues set out to test the hypothesis that the SARS coronavirus was present in wild animals sold at southern Chinese markets. The researchers tested a variety of both domestic and wild mammals that might be carrying the SARS coronavirus in Guangdong Province. The 25 animals sampled were obtained from a live animal retail market in Shenzhen and included seven wild and one domestic mammal (Figure 22.20).

The animals came from different areas of Guangdong and had been kept in separate storehouses prior to coming to market. Only a few animals of each species were kept by any one stall owner. Guan and his colleagues obtained nasal, fecal, and blood (when possible) samples from animals housed in different stalls. The sampled animals were confirmed to have no overt symptoms of disease by a veterinarian. The researchers used reverse transcription polymerase chain reaction (RT-PCR) to test for the SARS coronavirus. In RT-PCR RNA is reverse transcribed into its DNA complement and detected by binding it to a primer specific to the human SARS coronavirus (see Figure 22.18). In addition, the scientists also tested for presence of the virus by inoculating the samples into cell cultures. If the virus was present, the cells displayed degenerative changes associated with the multiplication of viruses.

Guan and his colleagues also collected blood samples from 20 wild animal traders, 15 butchers, and 20 vegetable retailers. They tested these samples for antibodies to the virus isolated from one of the palm civets (Paguma larvata) using an immunofluorescence assay (Table 22.10). {Connections: Immunofluorescence is used in Section 22.1.} Prior to being tested, none of these individuals reported SARS-like symptoms.


Two species, the Himalayan palm civet, which is a small carnivore found throughout Southeast Asia, and the raccoon-dog, which is a type of dog found in eastern Asia (Figure 22.21) tested positive for the SARS coronavirus.

Although Guan and his colleagues could not conclude that either of these species is the reservoir for the SARS coronavirus, its presence in these market animals suggests a connection between animals and humans. The positive animals could have been infected from another untested source in the market, so the true reservoir cannot be unequivocally identified. The scientists did conclude that culinary practices in southern China may facilitate coronavirus transmission from animal to human. Although the data suggest a link between animals and humans, you cannot conclude that the coronavirus in animals is the one that infected humans. It could have passed from the humans to the animals, although this is less likely given that a higher percentage of market workers who deal with animals possessed SARS coronavirus antibody compared to those working exclusively with vegetables. More species and more markets would have to be tested and monitored to determine the true source of the outbreaks.

To further determine the relationship between the coronavirus found in civets and that found in humans, Guan and his colleagues sequenced partial or entire coronavirus genomes isolated from four of the civets. They found that the sequences from civets had 99.8% similarity to those from humans. The researchers performed an evolutionary tree analysis with sequences of the spike gene from 15 samples: three from civets, one from a raccoon-dog, and 11 isolated from humans in Hong Kong, Guangdong, Canada, and Vietnam (Figure 22.22). {Connections: Analysis of evolutionary trees is illustrated in Section 20.1.}

The researchers noted 38 nucleotide changes, 26 of which caused changes in the transcribed amino acid sequence of the spike protein. Table 22.11 shows nucleotide differences among the viruses isolated from animals and humans.


Based on the high degree of overall genetic similarity observed by Guan and his colleagues, you can conclude that the SARS coronavirus is found in animals. The viruses isolated from animals in one market were all more related to one another than any one of them was related to viruses isolated from humans. The viruses isolated from the raccoon-dog and from one of the palm civets were almost genetically identical. Of the four animal samples, only eight of the nucleotides were polymorphic (that is, varied among the species), and only two of them led to altered amino acid sequence of the resulting protein. One important point to note is that all the human coronavirus samples branched off from one of the samples from a civet.

The scientists could not determine whether the virus was transmitted from one animal to the other, but given the high percentage in civets, it is likely that the civet is a reservoir host for the coronavirus. You might conclude that the jump from civet to humans occurred in the past, because the coronavirus DNA sequences in humans contained many alterations not observed in the coronavirus isolated from civets and raccoon-dogs. Among the humans, twenty or more of the spike gene nucleotides varied among the patients with many altering the spike protein.

Animal viruses isolated from one market should be more similar to each other than the human viruses isolated from Hong Kong, Guangdong, Canada, and Vietnam, but this was not the case. The viruses isolated from humans from five geographically separate sites were very closely related genetically. Even though the total number of mutations was greater, many of the same mutations occurred in all human virus samples. This close relationship among the coronavirus isolates from humans could indicate that the virus had spread very rapidly from China to as far away as Toronto, Canada, after it mutated and jumped from civets, but faster than it evolved major new differences. The scientists also concluded that the Chinese live animal markets may have played a role in amplifying the SARS coronavirus and transmitting this disease to humans, as suggested by the evidence reviewed earlier.

You will recall that a physician infected by a patient in Guangdong later traveled to Hong Kong. With a pathogen like the SARS coronavirus, which has such effective dispersal abilities, you might predict that SARS could quickly spread beyond Guangdong province. The World Health Organization (WHO) keeps statistics on many diseases and epidemics and compiled data on cases of SARS from China and beyond (Figure 22.23). In addition to the cases shown, over 2,500 probable cases of SARS from Beijing, China, are not shown because date of onset was not available to WHO. The date of onset for the initial case in countries that had more than ten cases of SARS is shown in the figure, along with the number of cases that ultimately occurred in those countries. Several countries had outbreak onset on the same date, and the number of cases shown is pooled for those countries.


As global pandemics go, SARS was short-lived but widespread. Within just a few months of its appearance in Guangdong Province, SARS spread to more than two dozen countries around the world. According to the WHO, a total of 8,098 people worldwide became sick with SARS during the 2003 outbreak. Of these, 774 died, which is a 9.6% fatality rate. The rapid increase in the number of cases was due to the way that SARS spreads through close contact. Twenty-one percent of all cases were healthcare workers, and until epidemiologists knew what they were dealing with, many healthcare workers did not take proper precautions to prevent infection.

The research performed by laboratories in several different countries provided information necessary to understand and combat the emerging SARS epidemic. The SARS global pandemic was finally contained in the summer of 2003 through a combination of information sharing among public health authorities, adequate health screening of travelers, quarantine of patients and individuals who came in contact with patients, and education of healthcare workers and the general public. Rapid action by national and international health authorities helped slow transmission and eventually broke the chain of transmission. However, SARS has not been eradicated, and it could reemerge.

The SARS outbreak illustrates how diseases spread. In the case of SARS, the emergence of a disease transmitted quickly from one host to another through close contact led to an epidemic in southern China and then to a pandemic. A global response was necessary to curb the spread of the disease. Epidemiologists worked quickly and collaboratively to study this new disease, which was caused by a pathogen that did not previously infect humans. Pathogens are part of ecological systems, and you know they can infect multiple hosts. You now also know that pathogens can evolve to switch to new hosts, and this often leads to disease outbreaks. As ecological systems change, opportunities for new interactions among species arise. Cells within the same multicellular organism interact with each other, too, and the next chapter explores populations of cells as tissues or cancers within multicellular organisms.