James A. Shapiro
Encyclopedia
James A. Shapiro is an American biologist, an expert in bacterial genetics
and a professor in the Department of Biochemistry
and Molecular Biology
at the University of Chicago
.
in 1964. Then, inspired by a genetics
course he had taken as a senior, he shifted from English to science, earned a doctorate in genetics from Corpus Christi College, Cambridge
in 1968, and did postdoctoral research with Jon Beckwith
at the Harvard Medical School
. However, he became troubled by the potential genetic engineering
applications of his research, announced that he could no longer be a scientist, and spent two years teaching genetics in Havana, Cuba, before returning to another postdoctorate with Harlyn Halvorson at Brandeis University
. Since 1973, he has worked a professor of microbiology at the University of Chicago
, and has also been a visiting professor from time to time, including once as a Darwin Prize Visiting Professor at the University of Edinburgh
in 1994.
from an organism. The gene they isolated was lacZ
, which codes for the β-galactosidase enzyme
used by e. coli bacteria to digest the sugars in milk. Their technique involved transduction
of two complementary copies of the gene into two different bacteriophage
s, then mixing the genetic material from the two phages, and finally using a nuclease
to degrade the single-stranded phage genome, leaving only the double-stranded DNA formed by the two copies.
In a paper published in the Proceedings of the National Academy of Sciences in 1979, Shapiro was the first to propose replicative transposition
as a mechanism for gene mobility. In this model, genes such as retrotransposon
s are copied from one DNA
sequence to another via a process in which the two sequences combine to form an intermediate "theta" shape, sometimes called a "Shapiro intermediate".
Later, Shapiro showed that bacteria cooperate in communities that exhibit complex behavior such as hunting
, building protective structures, and spreading spores, and in which individual bacteria may sacrifice themselves for the benefit of the larger community. Based on this work, Shapiro believes that cooperative behavior is a fundamental organizing concept for biological activity at all levels of complexity.
Shapiro has also studied pattern formation
in bacteria, an area where he feels that there are new mathematical principles to be discovered that also underlie the growth of crystal
s and the shape of cosmological structures
. For instance, he found that the gut bacterium proteus mirabilis
forms complex terraced rings, an emergent property of simple rules that the bacterium uses to avoid neighboring cells.
in 1993. In 1994, he was elected as a fellow
of the American Association for the Advancement of Science
for "innovative and creative interpretations of bacterial genetics and growth, especially the action of mobile genetic elements and the formation of bacterial colonies." And in 2001, he was made an honorary officer of the Order of the British Empire
for his service to the Marshall Scholarship program.
Bacterial genetics
Bacterial genetics is the subfield of genetics devoted to the study of bacteria. Bacterial genetics are subtly different from eukaryotic genetics, however bacteria still serve as a good model for animal genetic studies. One of the major distinctions between bacterial and eukaryotic genetics stems...
and a professor in the Department of Biochemistry
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
and Molecular Biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
at the University of Chicago
University of Chicago
The University of Chicago is a private research university in Chicago, Illinois, USA. It was founded by the American Baptist Education Society with a donation from oil magnate and philanthropist John D. Rockefeller and incorporated in 1890...
.
Academic biography
Shapiro obtained his Bachelor's degree in English from Harvard CollegeHarvard College
Harvard College, in Cambridge, Massachusetts, is one of two schools within Harvard University granting undergraduate degrees...
in 1964. Then, inspired by a genetics
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
course he had taken as a senior, he shifted from English to science, earned a doctorate in genetics from Corpus Christi College, Cambridge
Corpus Christi College, Cambridge
Corpus Christi College is a constituent college of the University of Cambridge. It is notable as the only college founded by Cambridge townspeople: it was established in 1352 by the Guilds of Corpus Christi and the Blessed Virgin Mary...
in 1968, and did postdoctoral research with Jon Beckwith
Jon Beckwith
Jonathan Roger Beckwith is a American microbiologist and geneticist. He is currently the American Cancer Society Professor in the Department of Microbiology and Molecular Genetics at Harvard Medical School in Boston, Massachusetts....
at the Harvard Medical School
Harvard Medical School
Harvard Medical School is the graduate medical school of Harvard University. It is located in the Longwood Medical Area of the Mission Hill neighborhood of Boston, Massachusetts....
. However, he became troubled by the potential genetic engineering
Genetic engineering
Genetic engineering, also called genetic modification, is the direct human manipulation of an organism's genome using modern DNA technology. It involves the introduction of foreign DNA or synthetic genes into the organism of interest...
applications of his research, announced that he could no longer be a scientist, and spent two years teaching genetics in Havana, Cuba, before returning to another postdoctorate with Harlyn Halvorson at Brandeis University
Brandeis University
Brandeis University is an American private research university with a liberal arts focus. It is located in the southwestern corner of Waltham, Massachusetts, nine miles west of Boston. The University has an enrollment of approximately 3,200 undergraduate and 2,100 graduate students. In 2011, it...
. Since 1973, he has worked a professor of microbiology at the University of Chicago
University of Chicago
The University of Chicago is a private research university in Chicago, Illinois, USA. It was founded by the American Baptist Education Society with a donation from oil magnate and philanthropist John D. Rockefeller and incorporated in 1890...
, and has also been a visiting professor from time to time, including once as a Darwin Prize Visiting Professor at the University of Edinburgh
University of Edinburgh
The University of Edinburgh, founded in 1583, is a public research university located in Edinburgh, the capital of Scotland, and a UNESCO World Heritage Site. The university is deeply embedded in the fabric of the city, with many of the buildings in the historic Old Town belonging to the university...
in 1994.
Research
While working with Beckwith at Harvard, Shapiro was part of the first team to isolate a single geneGene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
from an organism. The gene they isolated was lacZ
Lac operon
The lac operon is an operon required for the transport and metabolism of lactose in Escherichia coli and some other enteric bacteria. It consists of three adjacent structural genes, lacZ, lacY and lacA. The lac operon is regulated by several factors including the availability of glucose and of...
, which codes for the β-galactosidase enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
used by e. coli bacteria to digest the sugars in milk. Their technique involved transduction
Transduction (genetics)
Transduction is the process by which DNA is transferred from one bacterium to another by a virus. It also refers to the process whereby foreign DNA is introduced into another cell via a viral vector. Transduction does not require cell-to-cell contact , and it is DNAase resistant...
of two complementary copies of the gene into two different bacteriophage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
s, then mixing the genetic material from the two phages, and finally using a nuclease
Nuclease
A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older publications may use terms such as "polynucleotidase" or "nucleodepolymerase"....
to degrade the single-stranded phage genome, leaving only the double-stranded DNA formed by the two copies.
In a paper published in the Proceedings of the National Academy of Sciences in 1979, Shapiro was the first to propose replicative transposition
Replicative transposition
Replicative transposition is a mechanism of transposition in molecular biology, proposed by James A. Shapiro in 1979, in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element...
as a mechanism for gene mobility. In this model, genes such as retrotransposon
Retrotransposon
Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA...
s are copied from one DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
sequence to another via a process in which the two sequences combine to form an intermediate "theta" shape, sometimes called a "Shapiro intermediate".
Later, Shapiro showed that bacteria cooperate in communities that exhibit complex behavior such as hunting
Hunting
Hunting is the practice of pursuing any living thing, usually wildlife, for food, recreation, or trade. In present-day use, the term refers to lawful hunting, as distinguished from poaching, which is the killing, trapping or capture of the hunted species contrary to applicable law...
, building protective structures, and spreading spores, and in which individual bacteria may sacrifice themselves for the benefit of the larger community. Based on this work, Shapiro believes that cooperative behavior is a fundamental organizing concept for biological activity at all levels of complexity.
Shapiro has also studied pattern formation
Pattern formation
The science of pattern formation deals with the visible, orderly outcomes of self-organisation and the common principles behind similar patterns....
in bacteria, an area where he feels that there are new mathematical principles to be discovered that also underlie the growth of crystal
Crystal
A crystal or crystalline solid is a solid material whose constituent atoms, molecules, or ions are arranged in an orderly repeating pattern extending in all three spatial dimensions. The scientific study of crystals and crystal formation is known as crystallography...
s and the shape of cosmological structures
Cosmology
Cosmology is the discipline that deals with the nature of the Universe as a whole. Cosmologists seek to understand the origin, evolution, structure, and ultimate fate of the Universe at large, as well as the natural laws that keep it in order...
. For instance, he found that the gut bacterium proteus mirabilis
Proteus mirabilis
Proteus mirabilis is a Gram-negative, facultatively anaerobic, rod shaped bacterium. It shows swarming motility, and urease activity. P. mirabilis causes 90% of all Proteus infections in humans.-Diagnosis:...
forms complex terraced rings, an emergent property of simple rules that the bacterium uses to avoid neighboring cells.
Awards and honors
Shapiro was elected to Phi Beta Kappa in 1963 and was a Marshall Scholar from 1964 to 1966. He won the Darwin Prize Visiting Professorship of the University of EdinburghUniversity of Edinburgh
The University of Edinburgh, founded in 1583, is a public research university located in Edinburgh, the capital of Scotland, and a UNESCO World Heritage Site. The university is deeply embedded in the fabric of the city, with many of the buildings in the historic Old Town belonging to the university...
in 1993. In 1994, he was elected as a fellow
Fellow
A fellow in the broadest sense is someone who is an equal or a comrade. The term fellow is also used to describe a person, particularly by those in the upper social classes. It is most often used in an academic context: a fellow is often part of an elite group of learned people who are awarded...
of the American Association for the Advancement of Science
American Association for the Advancement of Science
The American Association for the Advancement of Science is an international non-profit organization with the stated goals of promoting cooperation among scientists, defending scientific freedom, encouraging scientific responsibility, and supporting scientific education and science outreach for the...
for "innovative and creative interpretations of bacterial genetics and growth, especially the action of mobile genetic elements and the formation of bacterial colonies." And in 2001, he was made an honorary officer of the Order of the British Empire
Order of the British Empire
The Most Excellent Order of the British Empire is an order of chivalry established on 4 June 1917 by George V of the United Kingdom. The Order comprises five classes in civil and military divisions...
for his service to the Marshall Scholarship program.