Life's Blueprint: The Science and Art of Embryo Creation

Life's Blueprint: The Science and Art of Embryo Creation

by Benny Shilo

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Overview

A uniquely accessible way of looking at recent major advances in the science of embryonic development

In the span of just three decades, scientific understanding of the formation of embryos has undergone a major revolution. The implications of these new research findings have an immediate bearing on human health and future therapies, yet most nonscientists remain quite unaware of the exciting news.
 
In this engaging book, a distinguished geneticist offers a clear, jargon-free overview of the field of developmental biology. Benny Shilo transforms complicated scientific paradigms into understandable ideas, employing an array of photographic images to demonstrate analogies between the cells of an embryo and human society. Shilo’s innovative approach highlights important concepts in a way that will be intuitive and resonant with readers’ own experiences.
 
The author explains what is now known about the mechanisms of embryonic development and the commanding role of genes. For each paradigm under discussion, he provides both a scientific image and a photograph he has taken in the human world. These pairs of images imply powerful metaphors, such as the similarities between communication among cells and among human beings, or between rules embedded in the genome and laws that govern human society. The book concludes with a glimpse of promising future possibilities, including the generation of tissues and organs for use as “spare parts.”

Product Details

ISBN-13: 9780300196634
Publisher: Yale University Press
Publication date: 10/28/2014
Pages: 192
Product dimensions: 7.20(w) x 9.10(h) x 0.60(d)

About the Author

Benny Shilo is professor of molecular genetics at the Weizmann Institute of Science, where he has served in a variety of leadership, research, and teaching roles for over 30 years. He is also a photographer. He lives in Rehovot, Israel.

Read an Excerpt

Life's Blueprint

The Science and Art of Embryo Creation


By Benny Shilo

Yale UNIVERSITY PRESS

Copyright © 2014 Benny Shilo
All rights reserved.
ISBN: 978-0-300-21036-1



CHAPTER 1

Introduction: Exploring the Principles of Embryo Creation


I would like to begin by sharing my personal story and how I embarked on a route that charted my academic career. Along this journey, I was extremely fortunate to be exposed to, and contribute to, the burst of findings that provide us today with a deep and comprehensive understanding of embryonic development. The year was 1981, and I was a twenty-nine-year-old postdoc in the lab of Robert A. Weinberg at the MIT Center for Cancer Research in Cambridge, Massachusetts. During that time, the pioneering work of the lab devised ways to identify and isolate single cancer-causing genes, called oncogenes, from the DNA of human tumors of various origins. I was privileged to be part of the group that created this breakthrough.

Our discovery was preceded by the work of many labs researching RNA viruses. These viruses, which are called retroviruses, hijack normal genes in the cells they infect and convert them to oncogenes by altering their structure or regulation. Although we recognized the cellular origin of numerous oncogenes, we still did not understand the role they play within healthy cells. The functions of these cellular ("normal") oncogenes, before they are hijacked and modified by the retroviruses, must represent central junctions of regulation for the cells. This is why subtle changes in their activity can lead to such deleterious outcomes as cancer. But what are these normal functions?

The answer requires a global view of the entire repertoire of living organisms through the lens of evolution. Instead of viewing all organisms in a "snapshot" as they appear today, we need to consider how this incredibly diverse array of living forms came to be. The appearance of life on earth was a rare process that took place once or at most very few times. A key feature of any living entity is an ability to replicate itself. Through natural selection the most suitable progeny was chosen for each environment. Over the billions of years since life first appeared, life forms have diversified and expanded, giving rise to the vast array of bacteria, plant, and animal species living today.

The process of evolution is dynamic. Hence, many organisms that formerly existed are no longer with us, and we can only glimpse their structure from fossil records. On the other hand, in general, the commonalities shared by different organisms today reflect their shared origin. It is likely that the features common among organisms are generally inherited from a joint ancestor rather than invented multiple times independently. One of the best examples of this shared inheritance is the genetic material, DNA. Short for "deoxyribonucleic acid," DNA is a self-replicating material that is present in the cells of all living organisms. Perhaps there could be other chemical solutions to encode genetic information. But all organisms that have descended from the primordial cell in which the structure of DNA first arose are "stuck" with this design. We can thus draw two general intuitive rules. First, when a gene is found in a broad range of organisms, it is likely to play a similar role in those different organisms. Second, the wider the range of organisms in which a given gene is found, the more general or basic its function is likely to be.

That said, in the late 1970s it was not clear whether the genes and biological processes that can be analyzed in simpler organisms, such as the fruit fly or the yeast we use to make bread and wine, bear any relevance to complex biological mechanisms such as the progression of cancer or the development of the brain. Were these intricate processes introduced late in evolution, together with the emergence of complex organisms? Or were these basic biological processes actually "invented" early on in evolution and exist today in a wide range of multicellular organisms to carry out very basic and common biological processes? If the latter were the case, we realized that we could make great strides in our understanding by studying these processes in the simpler organisms and then extrapolating the knowledge to the mechanisms that may operate in complex organisms like humans.

In the late 1970s and early 1980s, scientists had developed techniques to use the genes hijacked by retroviruses to isolate the corresponding normal genes from the genomes of vertebrate species, including the chicken, mouse, rat, cat, and monkey. But no one had as yet explored whether the presence, and hence possible function, of the cellular genes that can give rise to cancer was specific to these vertebrate organisms or extended more broadly within a wider range of multicellular organisms.

My research approach to uncover the normal functions of cancer-causing genes started from a simple notion. If genes similar to oncogenes are also found in the genome of simpler organisms, then we could decipher their normal function by exploring these simpler organisms and then examining whether the concepts we uncovered also applied to humans. Consider a little boy assembling his first pair of Lego interlocking wheels. Once he grasps the concept, he can see that the wheels of a train or in a watch mechanism, though more complex, employ the same basic principle.

How do you look for oncogenes in lower organisms? Today we know the linear order of the building blocks on the DNA (termed the nucleotide sequence) of the entire genome of hundreds of diverse organisms, ranging from bacteria and worms to human beings. But at that time, although the DNA fragments harboring these genes were accessible, their sequences, let alone their functions, were not known. My first step involved collecting DNA samples extracted from diverse multicellular organisms. To assemble this collection, I visited labs in Boston and Cambridge where research was under way on such organisms as sea urchins, nematode worms, flies, and even single-cell organisms such as baker's yeast.

I will now present a crash course in molecular biology as I describe how we looked for genes that were similar in sequence to the cancer-causing genes. DNA contains four types of units called nucleotides; these are termed A, C, G, and T. When we speak about the sequence of DNA we refer to the order in which these units, or bases, are linked to one another to form the genetic information of each organism. To test whether "relatives" of a given oncogene were present in these DNAs, we first needed to divide the very long and continuous strand of DNA into fragments. We did this by using an enzyme that cut the DNA each time it recognized a specific stretch of six nucleotides. Although the DNA was prepared from thousands of identical nuclei, the same types of fragments were generated for every cell. The process was similar to starting a new paragraph in an encyclopedia every time a specific combination of six letters appeared. The same paragraphs would be generated for multiple copies of identical volumes.

We then separated each sample into fragments of discrete sizes by placing them in an agarose gel, which, when combined with an electrical field, separated DNA fragments based on their size and charge. The gel was then overlaid with and blotted onto a special filter paper, and the DNA fragments "stuck" to the filter according to their position on the gel. The filter now contained the entire genetic material of the organisms from which it was extracted. Next came the stage of finding the needle in the haystack—determining whether the DNA of these organisms had sequences related to the mouse or chicken oncogenes.

When you have an electronic version of a book and are looking for a particular sentence you vaguely remember, you ask the computer to find the closest fit to this sentence in the entire book. We employed this same logic in the molecular procedure we used to look for sequences that are related to the cancer-causing genes. The search was based on the most universal and seminal feature of DNA: its capacity to form a double helix. The DNA bases have the chemical feature of forming pairs: T specifically matches with A, and C pairs with G. The second strand in a DNA double helix contains the pairs that match the first strand (fig. 3).

At the time, the DNA fragments harboring the oncogenes were isolated and grown in large amounts by procedures of molecular cloning based on their inclusion within the viruses that hijacked them. The process of molecular cloning is similar, if you will, to photocopying just one page from a thousand-volume encyclopedia over and over again. These are the same proportions between the complexity of the entire mouse or human genome versus a single gene.

The process of DNA replication, in which one strand of DNA can be used as a template to generate the complementary strand in the double helix, can be carried out in the test tube by the addition of certain enzymes. If one of the four bases is radioactively labeled, then the entire strand of DNA that is generated will also be labeled. If many copies from a short strand of DNA containing an oncogene can be marked, they can then be used as a "probe" to explore the vast array of DNA fragments on the filter in a search for DNA stretches that harbor a similar sequence with which they can pair. Even if the oncogene and the DNA on the filter share only a partial identity (that is, they are relatives but not identical twins), this similarity might suffice to allow them to associate with each other.

The filter was then immersed in a radioactively labeled sample of the gene to be tested. After the filters were cleansed of the excess radioactive oncogene probes, the only remaining probe would be bound to the filter at the spots where it found complementary sequences. This binding was then detected by exposing the filter in a sealed cassette to a sheet of film similar to the film used when our teeth or bones are X-rayed. The radioactive probe excited the film and generated a reaction that is similar to exposure to light. The film was then processed in a darkroom by immersion in solutions of a developer and a fixer.

Once I had developed and fixed the film in the dim orange light of the darkroom, I got my first glimpse of the encounter with the labeled oncogenes. There they were, multiple black stripes indicating the presence of similar sequences! Each one reflected the existence of a distinct DNA fragment that paired with the oncogene probe. In the darkroom I could not make out the precise position of the spots on the filter, and hence determine which of the organisms possessed these sequences. But when I later scrutinized the film over a light box, I found that all the spots corresponded to the DNA extracted from the fruit fly Drosophila melanogaster.

The implications of this finding were instantly apparent. If the same genes that cause cancer in higher-level vertebrate organisms are also present in fly DNA, this means that they first appeared more than six hundred million years ago, before the evolutionary divergence of vertebrates and invertebrates. Their ancient origin suggests that these genes perform an essential common function in all multicellular organisms. From an experimental standpoint, our ability to manipulate fruit flies, which have been genetically dissected for more than a hundred years, could tell us what functions these same genes carry out in our own human bodies.

For any scientist, there are a few moments in your life when you know you've uncovered an important phenomenon, never before seen or recognized. Even if you don't completely understand the full significance and implications of your discovery, the findings make an immediate impact. These "moments of discovery" are what we scientists live for. I like to think about such moments as analogous in their nature, though not necessarily in scope, to the discovery of the tomb of Tutankhamen on November 26, 1922. The steps leading to the tomb had been cleared, the dignitaries and sponsors of the excavations were assembled outside, and the British archaeologist Howard Carter opened a small hole in the mud wall containing the original royal stamps. Releasing a gust of air that had been sealed up for more than three millennia, he inserted a candle through the hole. Gradually, as his eyes grew accustomed to the dim light, Carter was able to pick out "strange animals, statues and gold, everywhere the glint of gold." His eye was the first to see what would later become a cornerstone in our perception of human civilization.

In the summer of 1981, after having discovered the normal forms of vertebrate cancer-causing genes in fruit flies, I established my lab at the Weizmann Institute in Israel. I spent the next thirty years investigating the role of these genes during the normal life cycle of the fly. This approach can be regarded as "reverse genetics" in the sense that one starts with a known gene and tries to establish its role by generating mutations in this gene and investigating the consequences. In such an approach, you do not know beforehand what biological functions will be unraveled; you simply "trust your gene," analyze it with the toolkit of technologies at your disposal, and hope to uncover the role it plays in central biological processes. Following this approach, I started my journey with genes that cause cancer in vertebrates and ended up studying the central mechanisms by which cells communicate in forming the fruit fly embryo.

A complementary approach, at that time more common, is to carry out "forward genetics." In other words, one defines the biological process of interest and seeks mutations in genes that will disrupt this process. In this approach, the biological process being interrogated is well defined, but the nature of the genes that will be uncovered is not known. The Nobel Prize laureates Christiane Nüsslein-Volhard and Eric Wieschaus used forward genetics to uncover the genes that underlie embryonic patterning in the fruit fly embryo in the late 1970s. Their work revealed most of the genes needed to pattern the fruit fly embryo and triggered a burst of research activity to isolate these genes and identify their molecular nature. When the genes were eventually analyzed at the molecular level, many turned out to correspond to the same genes studied in my reverse genetics approach that had its origin in vertebrate cancer-causing genes. By the late 1980s, the two approaches, which had begun at opposite starting points and used different methodologies, converged.

In the years since then, scores of labs showed that the genes uncovered by these two approaches encoded elements in the communication signals by which cells "talk" to each other during embryonic development to generate the elaborate pattern of the embryo. The presence of these genes in all multicellular organisms indicated that such communication processes might be universal. In fact, these genes embody the essence of multicellularity. The elaborate process of embryonic development is predictable and nonchaotic because the behavior of cells is guided by distinct "rules" that are embedded within the DNA. And when these rules are followed correctly, a pattern emerges.

Unraveling the mechanisms by which cells communicate at the molecular level and the discovery that these modules are common to all multicellular organisms was a breakthrough in our knowledge of life's blueprint. It also converted modern biology into a more universal discipline, since we now know that seemingly disparate processes in different organisms are actually controlled by the same genes and cell communication pathways.

CHAPTER 2

It's All in the Genes


When we consider all the different cells in our body, we can't help but be amazed by how diverse they are. Each cell type is configured to fulfill its ultimate function in the body. Nerve cells form long extensions that can be up to a meter in length and conduct electrical currents at high speed from one end of the cell to the other. Muscle cells form repeated units of molecular motors that move along tracks to carry out muscle contractions. In the muscles, thousands of cells fuse together to generate giant continuous cells that can extend to a meter in length. Red blood cells play a completely different role, carrying the hemoglobin protein that helps bind oxygen in the lungs and then releasing oxygen within the target tissues. Where does the body store the instructions for generating this diversity, and how are these instructions transformed to actual cellular structures? The answer lies in our DNA.

The nucleus of each cell harbors DNA, which plays two fundamental roles: it carries the information that allows each cell type to produce the components that build up that cell, and it stores all the information for constructing the remarkable diversity of cell types encompassed in the whole organism. This information is faithfully duplicated during cell division. It is also transmitted from one generation to the next after a sperm fertilizes an egg.


(Continues...)

Excerpted from Life's Blueprint by Benny Shilo. Copyright © 2014 Benny Shilo. Excerpted by permission of Yale UNIVERSITY PRESS.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.

Table of Contents

Contents

Preface, ix,
Acknowledgments, xv,
1. Introduction: Exploring the Principles of Embryo Creation, 1,
2. It's All in the Genes, 9,
3. How an Embryonic Cell "Decides" Its Future Destiny, 19,
4. How Cells Talk and Listen to Each Other, 25,
5. How Do Simple Modules Lead to Complex Patterns?, 35,
6. How Can a Single Substance Generate Multiple Responses?, 59,
7. How Do Patterns Evolve Rapidly?, 70,
8. How Are Cells Programmed to Follow Predictable Routes to Specification?, 80,
9. Ensuring That Embryo Development Is on the Right Track, 86,
10. Shaping the Tissues, 100,
11. Stem Cells, 119,
12. What's Next?, 135,
Glossary of Scientific Terms, 143,
Glossary of Scientific Images, 149,
Recommended Reading and Web Resources, 165,
Index, 169,

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