It is one of 68 institutions supported by the Cancer Centers Program of the U.S. National Cancer Institute (NCI) and has been an NCI-designated Cancer Center since 1987. The Laboratory is one of a handful of institutions that played a central role in the development of molecular genetics and molecular biology.
It has been home to eight scientists who have been awarded the Nobel Prize in Physiology or Medicine. CSHL is ranked among the leading basic research institutions in the world in molecular biology and genetics. The Laboratory is led by Bruce Stillman, a biochemist and cancer researcher.
Since its inception in 1890, the institution’s campus on the north shore of Long Island has also been a center of biology education. Current CSHL educational programs serve professional scientists, doctoral students in biology, teachers of biology in the K-12 system, and students from the elementary grades through high school. In the past 10 years CSHL conferences & courses have drawn over 81,000 scientists and students (less than 1% of whom came from Africa or South America) to the main campus. For this reason, many scientists consider CSHL a “crossroads of biological science.”
Since 2009 CSHL has partnered with the Suzhou Industrial Park in Suzhou, China to create Cold Spring Harbor Asia which annually draws some 3,000 scientists to its meetings and courses.
In 2015, CSHL announced a strategic affiliation with the nearby Northwell Health to advance cancer therapeutics research, develop a new clinical cancer research unit at Northwell Health in Lake Success, NY, to support early-phase clinical studies of new cancer therapies, and recruit and train more clinician-scientists in oncology.
MAPseq uses RNA sequencing to rapidly and inexpensively find the diverse destinations of thousands of neurons in a single experiment in a single animal
Neuroscientists today publish in Neuron details of a revolutionary new way of mapping the brain at the resolution of individual neurons, which they have successfully demonstrated in the mouse brain.
The new method, called MAPseq (Multiplexed Analysis of Projections by Sequencing), makes it possible in a single experiment to trace the long-range projections of large numbers of individual neurons from a specific region or regions to wherever they lead in the brain—in experiments that are many times less expensive, labor-intensive and time-consuming than current mapping technologies allow.
Although a number of important brain-mapping projects are now under way, all of these efforts to obtain “connectomes,” or wiring maps, rely upon microscopes and related optical equipment to trace the myriad thread-like projections that link neurons to other neurons, near and far. For the first time ever, MAPseq “converts the task of brain mapping into one of RNA sequencing,” says its inventor, Anthony Zador, M.D., Ph.D., professor at Cold Spring Harbor Laboratory.
“The RNA sequences, or ‘barcodes,’ that we deliver to individual neurons are unmistakably unique,” Zador explains, “and this enables us to determine if individual neurons, as opposed to entire regions, are tailored to specific targets.”
MAPseq differs from so-called “bulk tracing” methods now in common use, in which a marker—typically a fluorescent protein—is expressed by neurons and carried along their axons. Such markers are good at determining all of the regions where neurons in the source region project to, but they cannot tell scientists that any two neurons in the source region project to the same region, to different regions, or to some of the same regions, and some different ones. That inability to resolve a neuron’s axonal destinations, cell by cell in a given region, is what motivated Zador to come up with a new technique.
One way of explaining the advantage of MAPseq over bulk tracing methods is to imagine being at an international airport, with the intention of getting on a flight to, say, Germany. “If you go to the international terminal, you see a long line of ticket counters,” Zador explains. “If you want to go to Germany, it’s not enough to take any airline at the international terminal. If you stand in line at the counter for Air Chile, you’re probably not going to be able to buy a ticket for Germany.”
“Those many airlines whose counters are adjacent serve many destinations, some of which overlap, some of which are unique. You can print out a map showing all of the foreign countries that all of the airlines serve from your airport, but that doesn’t tell you anything at all about individual airlines and where they go. This is the difference between current labeling methods and MAPseq. The ‘individual airlines’ in my example are adjacent neurons in a part of the brain whose ‘routes’ we want to trace.”
Zador and his team, including Justus Kebschull, a graduate student in his lab who is first author on the Neuron paper introducing the new method, have spent several years working out a technology that enables them to assign unique barcode-like identifiers to large numbers of individual neurons via a single injection in any brain region of interest. Each injection consists of a deactivated virus that has been engineered to contain massive pools of individually unique RNA molecules, each of whose sequence—consisting of 30 “letters,” or nucleotides—is taken up by single neurons. Thirty letters yields many, many times more barcode sequences (1018) than there are neurons in either the mouse or human brain, so this method is especially well suited to the massive complexity problem that brain mapping presents.
An injection into a “source” region of the brain contains a viral library encoding a diverse collection of barcode sequences, which are hitched to an engineered protein that is designed to carry the barcode along axonal pathways. The barcode RNA is expressed at high levels and transported into the terminals of axons in the source region where the injection is made. In each neuron, it travels to the point where the axon forms a synapse with a projection from another neuron. Tests show that the technology works—the barcodes travel reliably and evenly throughout the brain, along the “trunklines” that are the axons, and out to the “branch points” where synapses form.
About two days after one or more injections are made in a region of interest, the brain is dissected and RNA is collected and sequenced. RNA barcodes in the “source” area are now matched with the same barcodes collected in distant parts of the brain.
“Sequencing the RNA is a highly efficient, automated process, which makes MAPseq such a potentially radical tool,” Kebschull says. “In addition to the speed and economy of RNA sequencing, it has the great advantage of making it possible for researchers to distinguish between individual neurons within the same region that project to different parts of the brain.”
To demonstrate MAPseq’s capabilities, Zador’s team injected a part of the mouse brain called the locus coeruleus (LC), located in the brain stem. It is the cortex’s sole source of noradrenaline, a hormone that signals surprise. Zador’s team used MAPseq to address an old question: does the “surprise” signal get broadcast everywhere in the cortex, or only to particular places, where, perhaps, it is most needed or relevant?
In their demonstration experiment, only RNA that ended up in the cortex or olfactory bulb was sequenced, along with that of the source region in the LC where the barcodes were originally injected. The team divided the cortex into 22 slices, each about 300 microns thick, and dissected the slices. The results were exciting to the team.
“We found that neurons in the LC have a variety of idiosyncratic projection patterns,” Zador says. “Some neurons project almost exclusively to a single preferred target in the cortex or olfactory bulb. Other neurons project more broadly, although weakly.”
These results, he adds, “are consistent with, and reconcile, previous seemingly contradictory results about LC projections.” The surprise signal can reach most parts of the brain, but there are very specific parts of the brain where the signal is especially focused.
The team showed that results could be obtained in experiments based on one injection in the LC, and also two injections, on opposite sides. Already in progress are experiments in which the entire cortex is being “tiled” with injections. It is hoped this will yield the first connectome of the entire cortex at single-neuron resolution.
“Once we automate the process of using many injections, we think this kind of experiment can be completed by a single person in just a week or two, and at a cost of only a few thousand dollars,” Zador says. “We are very keen on being able to do these kind of studies in a single animal, which will eliminate the past problem of injecting multiple animals to trace multiple neurons, a method that requires one to make a single map based on many brains, each of which is somewhat different.”
Zador’s next goal with MAPseq is to map the brains of animals that model various neurodevelopmental and neuropsychiatric illnesses, to see how gene mutations strongly associated with causality alter the structure of brain circuits, and thus, presumably, brain function.
Can scientists hack photosynthesis to feed the world as population soars?
The world population, which stood at 5 billion in 1950, is predicted to increase to 10.5 billion by 2050. It’s a stunning number since it means the planet’s population has doubled within the lifetimes of many people alive today.
At the same time, arable land is shrinking and crop productivity is stagnating.
The last time population outran agricultural productivity, we were rescued by the Green Revolution, an increase in the harvest index (the amount of the plant’s biomass partitioned into grain) achieved through classical plant breeding. Today’s ears of corn are huge compared to those harvested in the 1920s.
But the harvest index can be pushed only so far; a plant can’t be 100-percent grain. And as the harvest index approaches its theoretical limit, gains in crop productivity have plateaued.
Is there another rabbit plant scientists can pull out of the hat? One possibility is to redesign photosynthesis, the process by which plants convert sunlight and carbon dioxide into sugar and the ultimate source of all food, unless you’re a chemosynthesizing bacterium.
Photosynthesis, scientists will tell you, is stunningly inefficient. “We expect the solar cells we put on our rooftops to be at least 15- or 20- percent efficient,” said Robert Blankenship, PhD, the Lucille P. Markey Distinguished Professor of Arts and Sciences at Washington University in St. Louis. “A plant is at best one-percent efficient.”
Photosynthesis is the only determinant of crop yields that is not close to its biological limits, he said. It’s the one parameter of plant production that has not been optimized.
“A plant is probably never going to reach solar cell efficiencies, but solar cells are not going to make you lunch,” Blankenship said. “If we can double or triple the efficiency of photosynthesis — and I think that’s feasible — the impact on agricultural productivity could be huge.”
But how could this be done? In May 2013 Donald Ort and Sabeeha Merchant organized a workshop at Cold Spring Harbor Laboratory where a group of the world’s top plant scientists slipped the leash of scientific caution and tried to imagine what they would do if they could redesign plants at will. Blankenship was a workshop participant and agreed to summarize some of ideas that came out of the workshop, which are described in more detail in an article published in the July 14 issue of Proceedings of the National Academy of Sciences.
Layering the canopy
One clever idea was to design a smart canopy, a layered canopy of plants that would interact cooperatively to maximize photosynthetic efficiency. The canopy might exploit several tricks to wring the maximum productivity out of light as it filtered through the leaves to the ground.
Read more: Smart cornfields of the future
“The findings will help us feed a growing global population by speeding up the development of new varieties of wheat able to cope with the challenges faced by farmers worldwide.”
UK, German and US scientists decipher complex genetic code to create new tools for breeders and researchers across the world.
Scientists, including Professor Keith Edwards and Dr Gary Barker from the University of Bristol, have unlocked key components of the genetic code of one of the world’s most important crops. The first analysis of the complex and exceptionally large bread wheat genome, published today in Nature, is a major breakthrough in breeding wheat varieties that are more productive and better able to cope with disease, drought and other stresses that cause crop losses.
The identification of around 96,000 wheat genes, and insights into the links between them, lays strong foundations for accelerating wheat improvement through advanced molecular breeding and genetic engineering. The research contributes to directly improving food security by facilitating new approaches to wheat crop improvement that will accelerate the production of new wheat varieties and stimulate new research. The analysis comes just two years after UK researchers finished generating the sequence.
The project was led by Neil Hall, Mike Bevan, Keith Edwards, Klaus Mayer, from the University of Liverpool, the John Innes Centre, the University of Bristol, and the Institute of Bioinformatics and Systems Biology, Helmholtz-Zentrum, Munich, respectively, and Anthony Hall at the University of Liverpool. W. Richard McCombie at Cold Spring Harbor Laboratory, and Jan Dvorak at the Univerisity of California, Davis, led the US contribution to the project.
The team sifted through vast amounts of DNA sequence data, effectively translating the sequence into something that scientists and plant breeders can use effectively. All of their data and analyses were freely available to users world-wide.
Professor Keith Edwards said: “Since 1980, the rate of increase in wheat yields has declined. Analysis of the wheat genome sequence data provides a new and very powerful foundation for breeding future generations of wheat more quickly and more precisely, to help address this problem.”
The analysis is already being used in research funded by the Biotechnology and Biological Sciences Research Council (BBSRC) to introduce a wider range of genetic variation into commercial cultivars and make use of wild wheat’s untapped genetic reservoirs that could help improve tolerance to diseases and the effects of climate change. The wheat breeding community and seed suppliers have welcomed the research.
Scientists at Cold Spring Harbor Laboratory (CSHL) and five other institutions have used an unconventional approach to cancer drug discovery to identify a new potential treatment for acute myeloid leukemia (AML).
As reported in Nature online on August 3, the scientists have pinpointed a protein called Brd4 as a novel drug target for AML, an aggressive blood cancer that is currently incurable in 70% of patients. Using a drug compound that inhibits the activity of Brd4, the scientists were able to suppress the disease in experimental models.
“The drug candidate not only displays remarkable anti-leukemia activity in aggressive disease models and against cells derived from patients with diverse, genetic subtypes of AML, but is also minimally toxic to non-cancerous cells,” says CSHL scientist Chris Vakoc, M.D., Ph.D., who led the team. “The drug is currently being developed for therapeutic use for cancer patients by Tensha Therapeutics and is expected to enter clinical trials within two years.”
The protein target identified in the RNAi screen described in the current study, Brd4 — which contains a distinct domain or region known as a bromodomain — is a member of the BET family of proteins, which help regulate gene expression. By “reading” certain epigenetic marks or chemical tags attached to chromatin — the combined package of DNA and proteins around which it is coiled within the cell’s nucleus — Brd4 helps control the pattern of which genes are switched on and how they work.
“Cancer is clearly a genetic disease, but we also appreciate that epigenetic changes in how genes are expressed contribute to the uncontrolled growth of cancer cells,” says Vakoc. Cancer cells exploit this altered epigenetic landscape to drive their cell-growth programs.
Vakoc and other scientists have seized on the idea of interfering with this epigenetic dependency to turn the tables on cancer. “Epigenetic alterations acquired during cancer progression are potentially reversible and therefore susceptible to drug intervention,” he explains. With this insight as the backbone of their strategy to find new therapies for cancer, “we began to systematically search for what the cancer needs to keep itself going, to find a way to shut down that cancer-fueling factor and develop a new therapy.”