Edit genomes at the single-cell level and related sequencing techniques.

Single-celled genome editing and associated sequencing techniques will allow biologists to ask questions about changes in genealogy between individuals, organs, and as they age.
early 1980s, John Salston spent 18 months in a row observing worm growth.
He used an optical microscope to look at the embryos of a beautiful cryptoscopic worm and sketched out observations every five minutes, such as a fertilized egg dividing into two cells and then turning into four, eight, and so on.
he worked alone and quietly in a cottage in the Molecular Biology Laboratory of the Cambridge Medical Research Council, England, trying to unlock the rubik's cube of biology through the rotation of a microscope.
" I found myself really little distraction.
," the retired Nobel laureate recalled at one point.
his hundreds of drawings reveal the rigorous choreography of early worm development, including the precise birth of 671 cells and the death of 111 (or 113, depending on the sex of the worm).
cell can be traced back to its immediate ancestors in a series of invarning steps, and then to the last generation of its immediate ancestors.
these drawings and other materials, Salston and his co-creators mapped the first and most complete multicellular biocell line tree.
now, the revolution in the editing of genomes and related sequencing techniques at the single-cell level has led to a renaissance in cell line tracing.
research has attracted not only developmental biologists, but also geneticists and technology developers.
they believe that understanding the history of a cell -- where it came from, and even what happened to it -- is one of the next great frontiers in biology.
current findings provide tantalizing clues about how humans develop.
history of reconstructing historical cells is written in their genomes: every gainable mutation passed on to their subcells is recorded.
2005, Ehud Shapiro, a computational scientist at the Weizmann Institute of Science in Israel, calculated that researchers could piece together how each individual's sotic cells were linked using natural variations.
he envisioned an inevitable development of the beautiful crypto-worm cell map, which he called the "human cell genealogy program."
but said the area was not ready.
"When we came up with this idea, neither the name of the field of study nor the single-cell genome existed."
", researchers have developed a series of powerful tools to explore single-cell biology, from their RNA molecules and proteins to their individuals and specific genomes.
, Shapiro envisions a frame-by-frame way to capture a person's development from a fertilized egg to an adult.
"We want to get all the 3D images from start to finish."
," he said.
not need to look at the whole genome to make such images.
Shapiro team is focusing on repeated extensions of DNA called "microsatsats" that fill the genome.
these sequences mutate more frequently than other genome fragments, and the team is sequencing thousands of similar extensions in the genomes of hundreds of human cells to see how they are related.
experiments reported in 2015, a team of developmental biologists at Boston Children's Hospital and Harvard Medical School measured the complete genomes of 36 cortological neurons from three healthy deceased people who donated their brains for scientific research.
's reconstruction of the relationship between brain cells in one person suggests that closely related cells are distributed in the cerebral cortation, while local brain regions can contain many different cell linelines, and generations of cells seem to be far removed from their "ancestry".
example, a corttic neuron is more closely associated with the same person's heart cells than the other three-and-a-four neurons around it.
we didn't expect this to happen," he said.
," Walsh said.
scientists are unsealing the early record of life in the adult cell genome.
in a study published this year, Michael Stratton, a geneticist at the Hickston Wellcome Trust in the UK, and his team sequenced 241 female white blood cells with breast cancer to look for mutations that occurred only in one sub-concentration of their blood cells.
study shows that mutations already exist in the early stages of development, or can be traced back to the two-cell embryonic period.
Jay Shendure, a geneticist at the University of Washington in Seattle, and graduate students Aaron McKenna and Greg Findlay realized that crispr-Cas9, a popular gene-editing tool, was ideal for introducing traceable mutations into any part of the genome they wanted.
in collaboration with a laboratory led by Harvard University developmental biologist Alexander Schier, they used CRISPR-Cas9 in two single-celled zebrafish embryos and used it to edit DNA "barcode" sequences that had been designed into the zebrafish genome.
, they then measured the barcodes in an adult zebrafish cell and pieced together their lineage using mutations in their bodies.
the genealogy trees they produce suggest that embryonic linees formed at the beginning of a small amount of life produce the vast majority of cells in a particular organ.
, for example, more than 98 percent of a fish's red blood cells come from five of the more than 1,000 cell lines the team tracked.
although these five cell linees also contribute to other tissues, their participation in those roles is very low.
"It was completely unexpected to me.
," Shendure said.
is still trying to analyze the data.
, a quantitative developmental biologist at max del Bruck Molecular Medicine Center in Berlin, Germany, and others have developed a range of other CRISPR-based technologies that stitch together developmental history.
and Alexander van Oudenaarden, a systems biologist at the University of Utrecht in the Netherlands, used the method to track the regeneration of damaged fins in zebrafish.
they found that regeneration occurs in the same way as development: when it is reshaped by stem cells, fewer cell linees that produce the original fins are lost.
the discovery confirmed previous research, which allowed the team to track thousands of cell linees in an experiment based on CRISPR.
researchers are not only trying to understand how cells in an organism connect to each other, but also what happens to them in the process.
, a synthetic biologist at the Massachusetts Institute of Technology, said such records could allow scientists to repair cell development in a more precise way than current cell re-editing techniques.
" in the future, you may see some versions of the recorder implanted with cell therapy.
," he says, but it's not a quick process, "and now I'm not going to implant my CRISPR recorder into the patient."
life-threatening genealtro cancer is the first area in which new genealography tracking methods may be the first to cause a stir.
" cancer is a disease line line, a stem cell disease.
," Walsh said.
researchers have begun to address is the origin of metastatic cells, which come from initial tumors and sometimes invade organs at long distances.
are often the most difficult tumor cells to beat and the cells most likely to kill patients.
, however, the prospects in this area are far more surreal at the moment.
Salston's beautiful crypto-worm genealogy is still far higher than current research.
, a bioengineer at Stanford University in California, designed a way to track cell linein through CRISPR and decided to verify it in the worm.
"it's great to have a gold standard."
," Quake said.
and his team measured the cells of an adult animal after using CRISPR technology to mutate the developing genome.
time spent on this work was much less than the year and a half that Salston observed under a microscope.
but Quake says the images they produce are incomplete.
it does capture a key transition in the development of aphids (the separation of cells going to the intestines and cells that form other parts of the body), but it lacks the fine details that Salston observes with his eyes.
In fish, mice, and humans, no two individual cell line tree looks exactly the same, and each cell line tree changes over the life cycle of the individual as the tissue repairs and regenerates.
Junker and others hope the new technology will allow biologists to ask questions about changes in the line tree between individuals, organs and as they age.
as Schier puts it: "We don't know how many ways to make a heart.
" is precisely this huge unknown that makes this type of work transformative.
will change the question you ask," said Michael Elowitz, a geneticist at the University of California, Pasadena.
," Schier said, Salston's drawings take biologists into uncharted territory, and so is it.
't say exactly what we're going to find yet, but we're likely to find a new continent there," he said.
"