Engineering topics

Asija, Kunica

Publications and source records attributed to Asija, Kunica.

3 records

DOE OSTI2021

A Survey of Bacterial Microcompartment Distribution in the Human Microbiome

Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs have been bioinformatically identified based on the encapsulated enzymes and shell proteins encoded in genomic loci. BMCs are found across bacterial phyla. The organisms that contain them, rather than strictly correlating with specific lineages, tend to reflect the metabolic landscape of the environmental niches they occupy. From our recent comprehensive bioinformatic survey of BMCs found in genome sequence data, we find many in members of the human microbiome. Here we survey the distribution of BMCs in the different biotopes of the human body. Given their amenability to be horizontally transferred and bioengineered they hold promise as metabolic modules that could be used to probiotically alter microbiomes or treat dysbiosis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Lessons from bacteriophages part 2: A saga of scientific breakthroughs and prospects for their use in human health

Bacteriophages, or phages, are considered the most abundant entities on the planet, with their total numbers ranging from 10 30 ± 10 31 particles. Phages are known to play an important role in driving the evolution of their bacterial hosts, mostly via generalized and specialized transduction mechanisms. Phage therapy as a means to eliminate bacterial pathogens was used first in the 1920s; however, its use declined due to the advent of antibiotics in the 1940s. Eastern European countries have performed human trials for phage therapy for a century now, including a phage therapy trial in 1938 at the Eliava Institute of Bacteriophage in Georgia that successfully eliminated bacterial dysentery in 74% of the 219 cases by using a phage cocktail that targeted a wide range of causative agents for dysentery. Here, we present some of the major contributions of phage research to human health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Lessons from bacteriophages part 1: Deriving utility from protein structure, function, and evolution

Historically, some of the most fundamental discoveries of modern molecular biology were revealed by examination of phage-infected cells. Some examples include the use of bacteriophage T2 to show that DNA, not protein, was the genetic material by Hershey and Chase in 1952. Crick and colleagues showed that codons are degenerate and encode for single amino acids by making use of T4 bacteriophage. Brenner and colleagues discovered that mRNA acts as the messenger in relaying the information from DNA to ribosomes with the aid of bacteriophage T2. Szybalski and colleagues demonstrated the semiconservative mechanism of DNA replication using λ phage. Restriction modification, a bacterial innate immune system that evolved as protection against invading mobile genetic elements such as plasmids and phages, was discovered in bacteriophage-infected cells. Restriction mapping was crucial for the completion of the human genome project. The mechanism of action of heat shock genes—which encode for molecular chaperones such as dnaK , dnaJ , and grpE , as well as the groE gene locus, which encodes for the molecular chaperones GroES and GroEL—were discovered in λ phage–infected Escherichia coli. The first capsid assembly inhibitor, the fluorescent dye 4,4’–bis(1-anilinonaphthalene-8-sulfonic acid) (bisANS), was discovered in experiments investigating assembly of phage P22. These are just some of the examples of contributions made by bacteriophage research in the past few decades. Here, we discuss additional discoveries derived from studies of phages.

59 BASIC BIOLOGICAL SCIENCES↗