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Science 18 December 1998:
Vol. 282. no. 5397, pp. 2157 - 2161
DOI: 10.1126/science.282.5397.2157

News

BREAKTHROUGH OF THE YEAR:
The Runners-Up

The News and Editorial Staffs

Science recognizes nine discoveries that transform our ideas about the natural world and also offer potential benefits to society

FIRST RUNNER-UP:
A Remarkable Year for Clocks

Nineteenth-century philosophers proposed that God was a clockmaker who created the world and then let it run. Modern biologists might in part agree, for it's clear that evolution has carefully crafted clocks that allow almost all organisms to follow the rhythm of the sun. In 1998, a volley of rapid-fire discoveries revealed the stunning universality of the clock workings: Across the tree of life, from bacteria to humans, clocks use oscillating levels of proteins in feedback loops to keep time. Perhaps more amazing, fruit flies and mice--separated by nearly 700 million years of evolution--share the very same timekeeping proteins. Now that they better understand the cellular clock, scientists can begin to manipulate it, with applications from curing jet lag to brightening winter depression.


Figure 1
Lighting up. Clock genes glow in the cells of a fruit fly.

CREDIT: JEFF HALL


Clocks made the Runner-Up list in 1997 too, after researchers identified the first two mammalian clock genes, Clock and per. This year a prodigious amount of work from the clock research community filled out the story dramatically. For example, work in fruit flies showed that during the morning hours, CLOCK binds to a protein partner and together they turn on genes for proteins called PER and TIM (Timeless). These two proteins eventually shut down their own genes.

But to keep the proteins on a 24-hour cycle, PER and TIM's turnoff must be delayed. This year researchers found the cause of that delay in flies: a protein called DOUBLETIME (DBT) that destabilizes PER, keeping its levels low until enough TIM accumulates to pair with PER and shield it from DBT. Only then do PER and TIM enter the nucleus to turn off their genes, causing levels of the two proteins to wane until morning, when CLOCK and its partner turn on the genes once again.

Discovering all this in one organism would be breakthrough enough, but researchers found the same proteins or close variants playing the same roles in mice, too. As reported in June, a negative feedback mechanism appears to power plant clocks as well, albeit with different genes. And in September, a Japanese team showed that the single-celled cyanobacteria's clock is based on the same theme.

Despite this elegant molecular machinery, circadian clocks are imperfect timekeepers: Left on their own, their daily cycles run longer or shorter than 24 hours. Light keeps them in line, like a daily adjustment of a watch. In July researchers showed how: Light causes the rapid destruction of TIM, at least in flies.

Researchers thought that, in mammals, eyes are required for the light signal to reach the clock. But in January a U.S. team made the shocking discovery that light shone on, of all places, the back of the knees seems to reset the clock in humans; several groups have now repeated that finding.

Capping a year of dramatic discoveries, in November researchers fingered three plant pigments that capture light and pass its signal to the clock; one seems to play the same role in animals. For clock researchers already pleased with the pace of findings in 1997, this year's double-quick barrage of discoveries has exceeded all expectations.


Link:

Center for Biological Timing

Reading:

M. Barinaga, "New Timepiece has a Familiar Ring," Science 281, 1429 (4 September 1998).

M. Barinaga, "Clock Photoreceptor Shared by Plants and Animals," Science 282, 1928 (27 November 1998).

S. S. Campbell and P. J. Murphy, "Extraocular Circadian Phototransduction in Humans," Science 279, 396 (16 January 1998).

J. Dunlap, "An End in the Beginning," Science 280, 1548 (5 June 1998).

J. L. Price, J. Blau, A. Rothenfluh, M. Abodeely, B. Kloss, and M. W. Young, "double-time is a novel Drosophila clock gene that regulates PERIOD protein accumulation," Cell 94, 83 (10 July 1998).

V. Suri, Z. Qian, J.C. Hall and M. Rosbash, "Evidence that the TIM light response is relevant to light-induced phase shifts in Drosophila melanogaster," Neuron 21, 225 (July 1998).

Z. Yang, M. Emerson, H. S. Su and A. Sehgal, "Response of the Timeless protein to light correlates with behavioral entrainment and suggests a nonvisual pathway for circadian photoreception," Neuron 21, 215 (July 1998).


An Electrifying Structure

As you read this screen, electric signals flash from your eye to deep in your brain, traveling through millions of neurons. Each signal is successfully passed along courtesy of molecules in the cell membrane, "gates" that allow certain ions--but no others--to pour in and out of the cell, spreading the change in electrical potential throughout the cell.


Figure 2
Passing through. Potassium ion (red) in its channel.

CREDIT: R. MACKINNON


This year, in a landmark discovery that reveals one of the biochemical roots of the nervous system, a New York City team published the three-dimensional structure of one such ion channel--selective for the potassium ion--in a bacterium. This long-awaited finding is a technical marvel that provides new insight into how the nervous system works its magic.

After decades of wondering, electrophysiologists can now understand such riddles as how the potassium channel manages to keep out wrong ions, such as sodium, while shuttling an amazing 100 million potassium ions per second across the membrane. The structure reveals that the ions must pass through a narrow filter, where potassium ions fit snugly and briefly bind to the protein. The slightly smaller sodium ions cannot form this bond, making the filter an energetically unattractive place for them. And there are always at least two potassium ions in the filter, repelling each other just enough to ensure that once in, they quickly make their way out the other end. Membrane proteins are notoriously difficult to crystallize, but this year's triumph may prompt work on the thousands of other such proteins still waiting.


Links:

Ion channel network home page

L. Yeh Jan and Y. Nung Jan, in the Annual Review of Neuroscience

Reading:

D. A. Doyle et al., "The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Sensitivity," Science 280, 69 (3 April 1998).

R. MacKinnon et al., "Structural Conservation in Prokaryotic and Eukaryotic Potassium Channels," Science 280, 106 (3 April 1998).

C. Armstrong, "The Vision of the Pore," Science 280, 56 (3 April 1998).


Neutrinos Weigh In

The elusive particle called the neutrino has led physicists on a merry chase ever since it was posited in 1930. Researchers have assumed that the ghostly neutrinos lack both charge and mass. But in a stunning announcement in June, an international collaboration running the Super-Kamiokande neutrino detector in Japan showed that these subatomic particles do indeed have a wisp of mass, and physicists are now scrambling to revise their view of how the universe is put together.

Physicists first began to suspect that neutrinos had mass when they aimed neutrino detectors at the sun and found fewer than expected. One possibility was that as neutrinos flew from their origin in the sun to the detector, they changed from one of three types to another type that eludes detection. By the laws of quantum mechanics, this can happen only if neutrinos have mass.

Super-Kamiokande, a 50,000-ton tank of water in which 11,200 light sensors detect the faint glow created when a neutrino slams into a water molecule, found strong evidence for such shape-shifting by tracking atmospheric neutrinos. These particles are the products of cosmic rays and so should rain down on Earth in equal numbers from all directions. But the detector found fewer neutrinos coming from Earth's far side than streaming down from above, presumably because far-side neutrinos change types during their longer route.

Thus at least one kind of neutrino must have mass. The results have spawned a furious debate over whether a new theory of particles is needed, and heated up a long-running argument over whether neutrinos are part of the unseen "dark matter" thought to make up much of the mass in the universe. 1998 marked a new understanding of the neutrino, but this wily particle is still a few steps ahead of the scientists pursuing it.


Links:

Kamioka Observatory, which houses the Super-Kamiokande neutrino dectector

The Neutrino Oscillation Industry

Reading:

Y. Fukuda et al., "Evidence for Oscillation of Atmospheric Neutrinos," Physical Review Letters 81, 1562 (24 August 1998).

D. Kestenbaum, "Neutrinos Throw Their Weight Around," Science 281, 1594 (11 September 1998).

D. Normile, "Weighing In on Neutrino Mass," Science 280, 1689 (12 June 1998).


Genomics Takes Off

This year it seemed that every month brought another milestone in sequencing work, fueling an explosion in the new field of genomics--analyzing and comparing whole genomes. Researchers bagged the first complete sequence of a multicellular organism, as well as those of several feared microbes, bringing the total of fully sequenced genomes to nearly two dozen. These achievements were also accompanied by new experimental and computer programs to explore the wealth of data.


Figure 3
Gene at work. An active developmental control gene lights up nematode nerve cells.

CREDIT: O. HOBERT AND G. RUVKUN/MGH


In December a British-U.S. sequencing alliance reported virtually all 97 million bases that make up the genome of the multicellular nematode Caenorhabditis elegans. By comparing the worm genome with yeast's 12.5 million bases, researchers are beginning to glean what genetic changes were necessary for life to move beyond single cells. But about a third of the worm's 19,000 putative genes are novel, suggesting that much experimental work lies ahead to determine their functions.

This year's newly completed microbial genomes include those of some of humankind's worst enemies: the bugs for syphilis, tuberculosis, and typhus, as well as a Chlamydia, which causes venereal disease and blindness. The genomes reveal proteins unique to these pathogens, molecules that may be targets for drug or vaccine development. Genomics spread its wings in 1998, and it's likely to soar for years to come.


Link:

Institute for Genomic Research information on microbial genomes

Reading:

C. elegans special issue, Science 282, 1972 and 2011-2046 (11 December 1998).

Fraser et al., "Complete genome sequence of Treponema pallidum, the Syphilis Spirochete," Science 281, 375 (1998).

E. Pennisi, "Genome reveals wiles and weak points of syphilis," Science 281, 324 (17 July 1998).

E. Pennisi, "Genome links typhus bug to mitochondrion," Science 282, 1243 (13 November 1998).

R. S. Stephens et al., "Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis," Science 282, 754 (23 October 1998).

T. Hatch, "Chlamydia: Old ideas crushed, new mysteries bared," Science 282, 638 (23 October 1998).

N. Williams, "Genome of TB Culprit Deciphered," Science 279, 25 (2 January 1998).


Quantum Leaps

Beaming the Captain and his stalwart crew up to the bridge of the Starship Enterprise remains the stuff of science fiction, but this year physicists boldly went where no one has gone before, turning teleportation at the quantum level into lab reality.

In science fiction, teleportation moves people and things around, but in physics it means reconstructing a quantum state at a new location, so that information, rather than matter or energy, is moved about. Such information transfer lies at the heart of quantum computing, which offers the prospect of lightning-fast, superparallel calculations. This year physicists made great strides toward building such devices, "soldering" quantum links between ions, devising schemes to find and fix quantum data errors, and performing simple calculations.

The key to teleportation is the odd phenomenon known as quantum entanglement, in which the fates of two or more particles are entwined without physical contact. For example, when a single photon is split by a crystal, the two daughter photons retain a connection as they travel their separate ways: An action performed on one daughter will dictate the state of the other.

A year ago, teams using a roomful of lasers and mirrors in Innsbruck and in Rome teleported information on the quantum states of single photons. Then in October, a U.K.-Danish- U.S. group teleported information on the amplitude and phase of an entire light beam to another beam. In November, U.S. physicists teleported quantum information from the nucleus of a carbon atom to that of a neighboring hydrogen atom. This last feat hints at the real utility of teleportation--the reliable transmission of information between ions that serve as the elements of a quantum computer. That technology may be worthy of inclusion in a Star Trek episode: It's teleportation, Jim, but not as we know it.


Links:

Centre for Quantum Computation

Quantum Information and Computation at Caltech

Innsbruck Quantum Optics, Austria

Quantum Computation/Cryptography at Los Alamos

Quantum Information at IBM

Reading:

D. Bouwmeester et al., "Experimental Quantum Teleportation," Nature 390, 575 (1998).

A. Furusawa et al., "Unconditional Quantum Teleportation," Science 282, 706 (23 October 1998).

J. Glanz, "A First Step Toward Wiring Up a Quantum Computer," Science 282, 1405 (20 November 1998).

M. A. Nielsen, E. Knill, and R. Laflamme, "Complete quantum teleportation using nuclear magnetic resonance," Nature 396, 52 (1998).

A. Watson, "Fighting Corruption in the Quantum World," Science 281, 1781 (18 September 1998).

A. Watson, "Teleportation Beams Up a Photon's State," Science 278, 1881 (12 December 1997).


Boom in Biochips

Microchips are already the foundation of the electronics industry, but in 1998 chip technologies left their electronic roots behind and moved decisively into biology and other fields. This year the same miniaturization tools used to make computer chips were used to shrink and speed up everything from DNA sequencing equipment to diagnostics.

While major microelectronics firms entered the biochip business, teaming up with start-up companies to push commercialization, basic researchers forged new chip technologies. For example, this year researchers created a DNA-processing micromachine that may one day be able to sequence DNA. Already this chip, just a few centimeters on a side, can measure out precise amounts of DNA-containing solution, amplify DNA, chop it into small pieces, separate the fragments, and detect their size--all necessary steps in sequencing. Also this year, researchers at a California biotech firm developed a biochip that can screen a blood sample for cancer cells, bacteria, or other cell types and remove their DNA for analysis. Such tools could bring tests now done in the lab into the clinic.

Then there are the DNA chips themselves, in which researchers use arrays of immobilized DNA snippets to search out small genetic variations in genes or to detect RNA messages from the genes turned on in cells. Such chips could one day screen for genetic disease. Their foundations may be in electronics, but microchips have a bright biomedical future.


Reading:

M. A. Burns et al., "An Integrated Nanoliter DNA Analysis Device," Science 282, 484 (16 October 1998).

L. Kricka, "Revolution on a Square Centimeter," Nature Biotechnology 16, 513 (1998).

R. Service, "Microchip Arrays Put DNA on the Spot," Science 282, 396 (16 October 1998).

R. Service, "Coming Soon: The Pocket DNA Sequencer," Science 282, 399 (16 October 1998).

D. G. Wang et al., "Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome," Science 280, 1077 (15 May 1998).


New Combinations Pay Off

Researchers pushing the pace of discovery of new compounds put the pedal to the metal again this year. Powering the surge were advances in the high-speed discovery engine known as combinatorial chemistry, which allows researchers to assemble a handful of chemical building blocks into all possible combinations thousands of times faster than before.

Virtually all pharmaceutical companies now rely on combi chemistry to churn out a steady stream of hot prospects. In the field's meteoric climb, 1998 stood out as marked by especially rapid growth and explorations into new arenas. Two new journals were born, and a number of drug candidates, including one to treat inflammation, are now in clinical trials.

And this year, the research took off in new and unexpected directions. For example, one team used the technique to rapidly synthesize a collection, or library, of over 2.1 million complex organic compounds that resemble natural products such as antibiotics. Rather than laboriously test these molecules as drugs, researchers are scanning the library to develop a retinue of small compounds that can activate and deactivate target proteins at will. Such compounds may be new drugs and also may help biologists sort out the roles of the 100,000 or so cellular proteins.

Combinatorial chemists scored victories with other types of compounds, too. For example, U.S. researchers used a variation of the technology to find novel catalysts for fuel cells that convert methanol to electricity. Meanwhile, a Norwegian team created a library of hundreds of zeolites, solid materials shot through with tiny pores that are widely used in the chemical industry as molecular sieves. When the goal is to create new compounds, chemists seem to have hit on a winning combination.


Links:

Combinatorial information

Molecular Diversity Web site tracks patents, articles, symposia, jobs, and more

Journals:

Molecular Diversity

Combinatorial Chemistry & High Throughput Screening

Combinatorial Chemistry

Reading:

R. Service, "The Fast Way to a Better Fuel Cell," Science 280, 1690 (12 June 1998).

D. E. Akporiaye et al., "Combinatorial Approach to the Hydrothermal Synthesis of Zeolites," Angewandte Chemie, Int. Ed. 37, 609 (1998).


Putting Cancer on the Defensive

The war on cancer is not a single fight but many far-flung skirmishes, and no superweapon has yet emerged to rout the enemy from all its hideouts. Nevertheless, 1998 saw a host of exciting developments in cancer prevention and treatment, suggesting that this feared enemy is at last losing ground.

The best way to beat cancer is to keep it from taking hold in the first place, and several types of prevention made a splash this year. Researchers can proudly point to a new use for the drug tamoxifen: This estrogen-like molecule was already in use as a breast cancer treatment and this year won rapid approval for prevention in high-risk women. Lower tech lifestyle advice seems to be having an effect too: The American Cancer Society announced in March that U.S. cancer incidence and death rates have been dropping since the early 1990s, due in large part to a drop in smoking.

Meanwhile, several promising therapies have emerged. In May, U.S. researchers announced that the antibody Herceptin significantly slows the growth of metastatic breast cancer. And a German team found that the antibody Panorex reduces colon cancer death rates.

False rumors of victory arise in any war, and 1998's award for most overhyped cancer cure goes to angiostatin and endostatin, proteins whose seemingly magical ability to shrink tumors--in mice--was lauded in The New York Times before the treatments were even tested in people. Still, therapies that adopt a similar approach--stopping the growth of a tumor's network of blood vessels--are showing some success in clinical trials, as are treatments such as cancer-killing viruses. The war against cancer goes on, but physicians now have a few new weapons to fight with.


Reading:

S. Dickman, "Antibodies Stage a Comeback in Cancer Treatment," Science 280, 1196 (22 May 1998).

E. Marshall, "Tamoxifen: 'A Big Deal,' But a Complex Hand to Play," Science 280, 196 (10 April 1998).

E. Marshall, "The Roadblocks to Angiogenesis Blockers," Science 280, 997 (15 May 1998).

G. Riethmüller et al., "Monoclonal antibody therapy for resected Dukes' C colorectal cancer: seven-year outcome of a multicenter randomized trial," J. Clin. Oncol. 16, 1788 (May 1998).


Tracking Molecular Mimics

The acute phase of many infectious diseases is bad enough, but some have long-term effects that are positively chilling. Lyme disease, for example, starts with short-lived flulike symptoms but can end up causing chronic arthritis--even after antibiotics have wiped out the bugs. What causes such delayed damage?

One theory has been that the infection somehow sensitizes the immune system to the body's own molecules. That fits with suspicions that unidentified infections might explain the puzzling onset of some autoimmune diseases, but the idea has been hard to prove. This year two teams convincingly linked infections and autoimmune disorders, paving the way to better understanding and treatment of diseases such as diabetes and multiple sclerosis.

In the first case, researchers created a mouse model of herpes simplex virus 1, which can lead to destruction of corneal tissue and blindness. The team infected the mice's eyes and found that immune cells called T cells reacted against the animals' own tissue and destroyed their corneas. Future work may pinpoint the viral component that triggers the autoimmune response--and lead to treatments to block it.

Another team tackled Borrelia burgdorferi, the bacterium that causes Lyme disease and, in 10% of cases, chronic arthritis. The researchers found that nine of 11 Lyme arthritis patients have T cells that react to both a bacterial protein and a closely related human one--strong evidence that the T cells trigger the arthritis. Now that this year's discoveries have set the stage, expect a flood of work to track new links between autoimmunity and infection.


Reading:

D. M. Gross et al., "Identification of LFA-1 as a Candidate Autoantigen in Treatment-Resistant Lyme Arthritis," Science 281, 703 (31 July 1998).

S. Dickman, "Possible Cause Found for Lyme Arthritis," Science 281, 631 (1998).

Z-S. Zhao et al., "Molecular Mimicry by Herpes Simplex Virus-Type 1: Autoimmune Disease After Viral Infection," Science 279, 1344 (27 February 1998).

S. Dickman "Viral Saboteurs Caught in the Act," Science 279, 1305 (27 February 1998).


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Salad Days in the Rhythms Trade.
J. C. Dunlap (2008)
Genetics 178, 1-13
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Microbial Genomics--Challenges and Opportunities: The 9th International Conference on Microbial Genomes.
J. Zhou and J. H. Miller (2002)
J. Bacteriol. 184, 4327-4333
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Science. ISSN 0036-8075 (print), 1095-9203 (online)