Matching Items (10)

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A chemostat model of bacteriophage-bacteria interaction with infinite distributed delays

Description

Bacteriophage (phage) are viruses that infect bacteria. Typical laboratory experiments show that in a chemostat containing phage and susceptible bacteria species, a mutant bacteria species will evolve. This mutant species is usually resistant to the phage infection and less competitive

Bacteriophage (phage) are viruses that infect bacteria. Typical laboratory experiments show that in a chemostat containing phage and susceptible bacteria species, a mutant bacteria species will evolve. This mutant species is usually resistant to the phage infection and less competitive compared to the susceptible bacteria species. In some experiments, both susceptible and resistant bacteria species, as well as phage, can coexist at an equilibrium for hundreds of hours. The current research is inspired by these observations, and the goal is to establish a mathematical model and explore sufficient and necessary conditions for the coexistence. In this dissertation a model with infinite distributed delay terms based on some existing work is established. A rigorous analysis of the well-posedness of this model is provided, and it is proved that the susceptible bacteria persist. To study the persistence of phage species, a "Phage Reproduction Number" (PRN) is defined. The mathematical analysis shows phage persist if PRN > 1 and vanish if PRN < 1. A sufficient condition and a necessary condition for persistence of resistant bacteria are given. The persistence of the phage is essential for the persistence of resistant bacteria. Also, the resistant bacteria persist if its fitness is the same as the susceptible bacteria and if PRN > 1. A special case of the general model leads to a system of ordinary differential equations, for which numerical simulation results are presented.

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Created

Date Created
2012

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Impact of viral infectivity on phototrophic microbes for biofuel applications

Description

Research in microbial biofuels has dramatically increased over the last decade. The bulk of this research has focused on increasing the production yields of cyanobacteria and algal cells and improving extraction processes. However, there has been little to no research

Research in microbial biofuels has dramatically increased over the last decade. The bulk of this research has focused on increasing the production yields of cyanobacteria and algal cells and improving extraction processes. However, there has been little to no research on the potential impact of viruses on the yields of these phototrophic microbes for biofuel production. Viruses have the potential to significantly reduce microbial populations and limit their growth rates. It is therefore important to understand how viruses affect phototrophic microbes and the prevalence of these viruses in the environment. For this study, phototrophic microbes were grown in glass bioreactors, under continuous light and aeration. Detection and quantification of viruses of both environmental and laboratory microbial strains were measured through the use of a plaque assay. Plates were incubated at 25º C under continuous direct florescent light. Several environmental samples were taken from Tempe Town Lake (Tempe, AZ) and all the samples tested positive for viruses. Virus free phototrophic microbes were obtained from plaque assay plates by using a sterile loop to scoop up a virus free portion of the microbial lawn and transferred into a new bioreactor. Isolated cells were confirmed virus free through subsequent plaque assays. Viruses were detected from the bench scale bioreactors of Cyanobacteria Synechocystis PCC 6803 and the environmental samples. Viruses were consistently present through subsequent passage in fresh cultures; demonstrating viral contamination can be a chronic problem. In addition TEM was performed to examine presence or viral attachment to cyanobacterial cells and to characterize viral particles morphology. Electron micrographs obtained confirmed viral attachment and that the viruses detected were all of a similar size and shape. Particle sizes were measured to be approximately 50-60 nm. Cell reduction was observed as a decrease in optical density, with a transition from a dark green to a yellow green color for the cultures. Phototrophic microbial viruses were demonstrated to persist in the natural environment and to cause a reduction in algal populations in the bioreactors. Therefore it is likely that viruses could have a significant impact on microbial biofuel production by limiting the yields of production ponds.

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Created

Date Created
2014

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Persistence for "kill the winner" and nested infection Lotka-Volterra models

Description

In recent decades, marine ecologists have conducted extensive field work and experiments to understand the interactions between bacteria and bacteriophage (phage) in marine environments. This dissertation provides a detailed rigorous framework for gaining deeper insight into these interactions. Specific features

In recent decades, marine ecologists have conducted extensive field work and experiments to understand the interactions between bacteria and bacteriophage (phage) in marine environments. This dissertation provides a detailed rigorous framework for gaining deeper insight into these interactions. Specific features of the dissertation include the design of a new deterministic Lotka-Volterra model with n + 1 bacteria, n
+ 1 phage, with explicit nutrient, where the jth phage strain infects the first j bacterial strains, a perfectly nested infection network (NIN). This system is subject to trade-off conditions on the life-history traits of both bacteria and phage given in an earlier study Jover et al. (2013). Sufficient conditions are provided to show that a bacteria-phage community of arbitrary size with NIN can arise through the succession of permanent subcommunities, by the successive addition of one new population. Using uniform persistence theory, this entire community is shown to be permanent (uniformly persistent), meaning that all populations ultimately survive.

It is shown that a modified version of the original NIN Lotka-Volterra model with implicit nutrient considered by Jover et al. (2013) is permanent. A new one-to-one infection network (OIN) is also considered where each bacterium is infected by only one phage, and that phage infects only that bacterium. This model does not use the trade-offs on phage infection range, and bacterium resistance to phage. The OIN model is shown to be permanent, and using Lyapunov function theory, coupled with LaSalle’s Invariance Principle, the unique coexistence equilibrium associated with the NIN is globally asymptotically stable provided that the inter- and intra-specific bacterial competition coefficients are equal across all bacteria.

Finally, the OIN model is extended to a “Kill the Winner” (KtW) Lotka-Volterra model

of marine communities consisting of bacteria, phage, and zooplankton. The zooplankton

acts as a super bacteriophage, which infects all bacteria. This model is shown to be permanent.

Contributors

Agent

Created

Date Created
2016

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Immobilization of T4 on modified silica particles

Description

Bacteriophage provide high specificity to bacteria; receiving interest in various applications and have been used as target recognition tools in designing bioactive surfaces. Several current immobilization strategies to detect and capture bacteriophage require non-deliverable bioactive substrates or modifying the chemistry

Bacteriophage provide high specificity to bacteria; receiving interest in various applications and have been used as target recognition tools in designing bioactive surfaces. Several current immobilization strategies to detect and capture bacteriophage require non-deliverable bioactive substrates or modifying the chemistry of the phage, procedures that are labor intensive and can damage the integrity of the virus. The aim of this research was to develop the framework to physisorb and chemisorb T4 coliphage on varied sized functionalized silica particles while retaining its infectivity. First, silica surface modification, silanization, altered pristine silica colloids to positively, amine coated silica. The phages remain infective to their host bacteria while adsorbed on the surface of the silica particles. It is reported that the number of infective phage bound to the silica is enhanced by the immobilization method. It was determined that covalent attachment yielded 106 PFU/ml while electrostatic attachment resulted in 105 PFU/ml.

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Created

Date Created
2017

The Hershey-Chase Experiments (1952), by Alfred Hershey and Martha Chase

Description

In 1951 and 1952, Alfred Hershey and Martha Chase conducted a series of experiments at the Carnegie Institute of Washington in Cold Spring Harbor, New York, that verified genes were made of deoxyribonucleic acid, or DNA. Hershey and Chase performed

In 1951 and 1952, Alfred Hershey and Martha Chase conducted a series of experiments at the Carnegie Institute of Washington in Cold Spring Harbor, New York, that verified genes were made of deoxyribonucleic acid, or DNA. Hershey and Chase performed their experiments, later named the Hershey-Chase experiments, on viruses that infect bacteria, also called bacteriophages. The experiments followed decades of scientists’ skepticism about whether genetic material was composed of protein or DNA. The most well-known Hershey-Chase experiment, called the Waring Blender experiment, provided concrete evidence that genes were made of DNA. The Hershey-Chase experiments settled the long-standing debate about the composition of genes, thereby allowing scientists to investigate the molecular mechanisms by which genes function in organisms.

Contributors

Created

Date Created
2019-06-23

Max Ludwig Henning Delbruck (1906–1981)

Description

Max Ludwig Henning Delbrick applied his knowledge of theoretical physics to biological systems such as bacterial viruses called bacteriophages, or phages, and gene replication during the twentieth century in Germany and the US. Delbrück demonstrated that bacteria undergo random genetic

Max Ludwig Henning Delbrick applied his knowledge of theoretical physics to biological systems such as bacterial viruses called bacteriophages, or phages, and gene replication during the twentieth century in Germany and the US. Delbrück demonstrated that bacteria undergo random genetic mutations to resist phage infections. Those findings linked bacterial genetics to the genetics of higher organisms. In the mid-twentieth century, Delbrück helped start the Phage Group and Phage Course in the US, which further organized phage research. Delbrück also contributed to the DNA replication debate that culminated in the 1958 Meselson-Stahl experiment, which demonstrated how organisms replicate their genetic information. For his work with phages, Delbrück earned part of the 1969 Nobel Prize for Physiology or Medicine. Delbrück's work helped shape and establish new fields in molecular biology and genetics to investigate the laws of inheritance and development.

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Created

Date Created
2017-09-20

"On the Replication of Desoxyribonucleic Acid (DNA)" (1954), by Max Delbruck

Description

In 1954 Max Delbruck published On the Replication of Desoxyribonucleic Acid (DNA) to question the semi-conservative DNA replication mechanism proposed that James Watson and Francis Crick had proposed in 1953. In his article published in the Proceedings of the National

In 1954 Max Delbruck published On the Replication of Desoxyribonucleic Acid (DNA) to question the semi-conservative DNA replication mechanism proposed that James Watson and Francis Crick had proposed in 1953. In his article published in the Proceedings of the National Academy of Sciences, Delbr&uuml;ck offers an alternative DNA replication mechanism, later called dispersive replication. Unlike other articles before it, On the Replication presents ways to experimentally test different DNA replication theories. The article sparked a debate in the 1950s over how DNA replicated, which culminated in 1957 and 1958 with the Meselson-Stahl experiment supporting semi-conservative DNA replication as suggested by Watson and Crick. On the Replication played a major role in the study of DNA in the 1950s, a period of time during which scientists gained a better understanding of DNA as a whole and its role in genetic inheritance.

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Created

Date Created
2017-09-21

Lysogenic Bacteria as an Experimental Model at the Pasteur Institute (1915-1965)

Description

Lysogenic bacteria, or virus-infected bacteria, were the primary experimental models used by scientists working in the laboratories of the Pasteur Institute in Paris, France, during the 1950s and 1960s. Historians of science have noted that the use of lysogenic bacteria

Lysogenic bacteria, or virus-infected bacteria, were the primary experimental models used by scientists working in the laboratories of the Pasteur Institute in Paris, France, during the 1950s and 1960s. Historians of science have noted that the use of lysogenic bacteria as a model in microbiological research influenced the scientific achievements of the Pasteur Institute's scientists. Francois Jacob and Jacques Monod used lysogenic bacteria to develop their operon model of gene regulation, to investigate the cellular regulatory mechanisms of the lysogenic life cycle, and to infer the process of cellular differentiation in the development of more complex eukaryotes.

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Created

Date Created
2014-10-10

Alfred Day Hershey (1908–1997)

Description

During the twentieth century in the United States, Alfred Day Hershey studied phages, or viruses that infect bacteria, and experimentally verified that genes were made of deoxyribonucleic acid, or DNA. Genes are molecular, heritable instructions for how an organism develops.

During the twentieth century in the United States, Alfred Day Hershey studied phages, or viruses that infect bacteria, and experimentally verified that genes were made of deoxyribonucleic acid, or DNA. Genes are molecular, heritable instructions for how an organism develops. When Hershey started to study phages, scientists did not know if phages contained genes, or whether genes were made of DNA or protein. In 1952, Hershey and his research assistant, Martha Chase, conducted phage experiments that convinced scientists that genes were made of DNA. For his work with phages, Hershey shared the 1969 Nobel Prize in Physiology or Medicine with Max Delbrück and Salvador Luria. Hershey conducted experiments with results that connected DNA to the function of genes, thereby changing the way scientists studied molecular biology and the development of organisms.

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Created

Date Created
2019-04-29

Cold Spring Harbor Laboratory (1890- )

Description

Cold Spring Harbor Laboratory (CSHL) is a non-profit research institution that specializes in cancer, neuroscience, plant biology, quantitative biology, and genomics. The organization is located on the shores of Cold Spring Harbor in Laurel Hollow, New York. The Brooklyn Institute

Cold Spring Harbor Laboratory (CSHL) is a non-profit research institution that specializes in cancer, neuroscience, plant biology, quantitative biology, and genomics. The organization is located on the shores of Cold Spring Harbor in Laurel Hollow, New York. The Brooklyn Institute of Arts and Sciences established the CSHL in 1890, to provide scientists with facilities to research Charles Darwin's evolutionary theory. The first mission of CSHL was biological science education. Since 1998, CSHL has housed the Watson School of Biological Sciences, a PhD program dedicated to scientific research. Nobel Laureates who conducted experiments at the CSHL include Barbara McClintock, Alfred Hershey, James Watson, Francis Crick, and Sydney Brenner. Throughout its history, researchers at CSHL have studied embryology, reproductive medicine, and genetics.

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Created

Date Created
2014-06-21