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ScienceWeek October 25, 2002 Vol. 6 Number 43
An Online Research Digest Published Weekly Since 1997
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A paradox is truth standing on its head to attract attention.
-- Nicholas Falletta
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Note: In reports, click on hyperlinked terms for link-out
definitions.
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Section 1
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1. Nanotubes: On Attaching Metal Ions to Sidewalls
2. On the Genomics of Chloroplast Symbiosis
3. Bioweapons and Respiratory Protection
4. Anthropology: On the Origin of Europeans
5. Proteomics: On Computer Simulations of Living Systems
6. Molecular Biology: On Chromatin Folding
7. Mathematical Socioeconomics: On Public Goods Games
8. On Classical vs. Quantum Chaos
9. ScienceWeek Notices and Subscription Information
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Section 2
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1. NANOTUBES: ON ATTACHING METAL IONS TO SIDEWALLS
H.C. Choi et al (Stanford University, US) discuss the chemistry
of nanotube sidewalls, the authors making the following points:
1) There has been much recent interest in the covalent and
noncovalent sidewall chemistry of single-walled carbon nanotubes
(SWNTs).(1-5) The research activities are motivated by the idea
of modifying the inert nanotube sidewalls to impart solubility
in solvents or to immobilize various organic, inorganic, or
biological species to afford nanotube "macromolecules" with
chemical functionality. Covalent modification of nanotube
sidewalls includes oxidation, fluorination, and formation of
amide bonds.(1,2) Noncovalent approaches utilize pi-stacking or
van der Waals interactions between aromatic molecules or
polymers and nanotubes.(4,5)
2) Attaching metal nanoparticles to nanotube sidewalls is of
interest for obtaining nanotube/nanoparticle hybrid materials
with useful properties,(3) and for forming metal nanowires on
nanotube templates. It has been shown, for instance, that
functionalization of SWNTs by Pd nanoparticles imparts
sensitivity to molecular hydrogen for nanotube electrical
detectors.(3) Previous approaches to metal nanoparticle
functionalization of nanotubes include physical evaporation,(3)
attachment after oxidation of nanotubes, solid-state reaction
with metal salts at elevated temperatures, and electroless
deposition from salt solutions with the aid of reducing agents
or catalyst.
3) In summary: The authors report nanotube/nanoparticle hybrid
structures were prepared by forming Au and Pt nanoparticles on
the sidewalls of single-walled carbon nanotubes. Reducing agent
or catalyst-free electroless deposition, which purely utilizes
the redox potential difference between Au3+, Pt2+, and the
carbon nanotube, is the main driving force for this reaction. It
is also shown that carbon nanotubes act as a template for
wire-like metal structures. The successful formation of the
hybrid structures was monitored by atomic force microscopy (AFM)
and electrical measurements.
References (abridged):
1. Chen, J.; Hammon, M. A.; Hu, H.; Chen, Y. S.; Rao, A. M.;
Eklund, P. C.; Haddon, R. C. Science 1998, 282, 95.
2. Boul, P.; Liu, J.; Mickelson, E.; Huffman, C.; Ericson, L.;
Chiang, I.; Smith, K.; Colbert, D.; Hauge, R.; Margrave, J.;
Smalley, R. Chem. Phys. Lett. 1999, 310, 367.
3. Kong, J.; Chapline, M.; Dai, H. Adv. Mater. 2001, 13, 1384.
4. Chen, R.; Zhang, Y.; Wang, D.; Dai, H. J. Am. Chem. Soc.
2001, 123, 3838.
5. Star, A.; Stoddart, J.; Steuerman, D.; Diehl, M.; Boukai, A.;
Wong, E.; Yang, X.; Chung, S.; Choi, S.; Heath, J. R. Angew.
Chem., Int. Ed. 2001, 40, 1721.
J. Am. Chem. Soc. 2002 124:9058
Related Background Brief:
FUNCTIONALIZATION OF CARBON NANOTUBES BY ELECTROCHEMICAL
REDUCTION OF ARYL DIAZONIUM SALTS: A BUCKY PAPER ELECTRODE.
Small-diameter (ca. 0.7 nm) single-wall carbon nanotubes are
predicted to display enhanced reactivity relative to
larger-diameter nanotubes due to increased curvature strain. The
derivatization of these small-diameter nanotubes via
electrochemical reduction of a variety of aryl diazonium salts
is described. The estimated degree of functionalization is as
high as one out of every 20 carbons in the nanotubes bearing a
functionalized moiety. The functionalizing moieties can be
removed by heating in an argon atmosphere. Nanotubes derivatized
with a 4-tert-butylbenzene moiety were found to possess
significantly improved solubility in organic solvents. The
authors demonstrate functionalization of the nanotubes with a
molecular system that exhibits switching and memory behavior,
and they suggest this represents the marriage of wire-like
nanotubes with molecular electronic devices. J.L. Bahr et al: J
Am Chem Soc 2001 123:6536.
Related Background Brief:
SIDEWALL FUNCTIONALIZATION OF CARBON NANOTUBES. The authors
report covalent sidewall functionalization reactions and the
detailed characterization of the resulting organo-molecules.
Three types of reactions for direct addition to the unsaturated
pi-electron system of the nanotubes are selected. These types of
reactions are cycloaddition of nitrenes, the addition of
nucleophilic carbenes, and the addition of radicals. The authors
suggest that with three different methods of functionalization
of the side walls of carbon nanotubes, the first steps towards
general routes to a wide variety of new-nanotube derivatives
have been made. With appropriate addends, carbon nanotubes that
possess better solubility are easier to characterize and feature
more straightforward processibility for technological
applications. M. Holzinger et al: Ang. Chem. Int. Ed. 2001
40:4002.
Related Background:
STRUCTURE AND PROPERTIES OF CARBON NANOTUBES
H.F. Bettinger et al (Rice University, US) discuss carbon
nanotubes, the authors making the following points:
1) Multiwall carbon nanotubes, a new tubular form of carbon,
were discovered in 1991 by S. Iijima. Carbon nanotubes are
comprised of a rolled graphite sheet ("graphene") and closed by
fullerene-like caps. Depending on the way the graphene is
rolled, different chiralities are possible, and are commonly
distinguished by their chiral vector (n,m). The (n,n) tubes are
called "armchair" and the (n.0) tubes are called "zigzag"
nanotubes. A simple analysis imposing appropriate boundary
conditions on the graphene band structure predicts that the
armchair tubes are metallic (i.e., the band gap is zero due to
band crossing), whereas the zigzag tubes are either semimetals
or semiconductors, depending on the value of (n). The
computations of the band structures using density functional
theory (plane-wave pseudopotential local density approximation)
indicate that these simple rules need to be refined, at least
for narrow zigzag tubes. It was found by these calculations that
the rehybridization of the carbon states due to the strong
curvature of small tubes introduces low-lying conduction band
states into the band gap of insulating tubes.
2) Whereas Iijima's multiwall carbon nanotubes consist of at
least 2 concentric tubes, single wall carbon nanotubes are
produced by laser vaporization of a metal-graphite (Co, Ni)
target. These single-wall nanotubes are comprised of a single
rolled graphene sheet, but have a tendency to form "ropes",
i.e., bundles of single-wall nanotubes. The tubes produced by
the laser-oven technique have very uniform diameters of
approximately 1.38 +- 0.02 nanometers, according to x-ray
diffraction, and an intertube distance of 0.315 nanometers in
the ropes, similar to that in crystalline C(sub60). It has been
concluded that the ropes are made up of (10,10) armchair
single-wall nanotubes.
J. Am. Chem. Soc. 2001 123:12849
Related Background:
ON CHARGE-INDUCED DISTORTION OF CARBON NANOTUBES
Y.N. Gartstein et al (Xerox Corporation, US) discuss distortion
of carbon nanotubes, the authors making the following points:
1) Carbon nanotubes are particularly interesting nanoscopic
systems [1] whose electronic and mechanical properties have been
the subject of numerous studies and are attractive for diverse
applications [2,3]. One of the proposals is to use carbon
single-wall nanotubes (SWNTs) as electrochemically driven
electromechanical actuators. In these demonstrated devices,
large electrochemical charge injection can result from the high
surface area of nanotube assemblies [4]. The charge injection
produces the electromechanical actuation. Actuator strains of
above 1 % have been observed [3], which is about 10 times that
of ferroelectrics. This high strain indicates the potential for
obtaining order of magnitude advantages over any prior-art
actuator technologies for directly converting electrical energy
to mechanical energy. Currently available nanotube sheets and
long fibers comprise bundles of SWNTs, each bundle containing
from 30 to 100 of SWNTs of various internal geometries, or
chiral vectors (N,M) [1]: from zigzag (N,0) to armchair (N,N)
tubes. The observed actuation is likely to be an average from
different SWNTs. Improved synthetic methods are expected to
eventually make it possible to use SWNTs of selected types in
actuators [5].
2) The authors report an analysis designed to predict the
actuator strains that would result for different types of SWNTs
by studying a simplified electron-lattice model. Suppose one
adds delta(n) extra electrons per carbon atom to a SWNT. How
would interatomic distances be affected? The authors studied the
contribution to bond length changes arising from the modulation
of electron hopping integrals by lattice distortions. Since
Coulombic effects are ignored in this model, the results are
restricted to low charge injection levels. The authors
demonstrate that SWNTs exhibit quite a unique picture of
electromechanical actuation that strongly depends on (N, M). The
magnitude of the actuator response of individual carbon
nanotubes can be appreciably larger than that of graphite,
presenting an exciting opportunity of enhanced actuation.
3) In summary: To accommodate extra electrons or holes injected
into a single-wall carbon nanotube, carbon-carbon bonds adjust
their lengths. Resulting changes in carbon-nanotube length as a
function of charge injection provide the basis for
electromechanical actuators. The authors demonstrate that a key
mechanism at low injection levels, modulation of electron
kinetic energy, provides nanotube deformations that are both
anisotropic and strongly dependent on nanotube structure.
Nanotubes can exhibit both expansion and contraction, as well as
nonmonotonic size changes. The magnitude of the actuation
response of semiconducting carbon nanotubes may be substantially
larger than that of graphite.
References (abridged):
1. R. Saito, G. Dresselhaus, and M. Dresselhaus, Physical
Properties of Carbon Nanotubes (Imperial College Press, London,
1998)
2. Carbon Nanotubes: Synthesis, Structure, Properties and
Applications, edited by M. Dresselhaus, G. Dresselhaus, and P.
Avouris (Springer, Berlin, 2000)
3. R. Baughman, A. Zakhidov, and W. deHeer, Science (to be
published).
4. R. Baughman et al., Science 284, 1340 (1999)
5. R. Schlittler, Science 292, 1136 (2001)
Phys. Rev. Lett. 2002 89:045503
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2. ON THE GENOMICS OF CHLOROPLAST SYMBIOSIS
Brian Palenik (University of California San Diego, US) discusses
symbiosis, the author making the following points:
1) Life as we know it is the result of symbiosis. Mitochondria,
the energy generators of our own bodies, are the end result of
the symbiosis of a bacterium with a host eukaryote. Visible
around us are the land plants that we eat to fuel our
mitochondria. Land plants are the beneficiaries of a second
symbiosis, that of a cyanobacterium with a mitochondriate host,
a relationship that subsequently developed into the
light-harvesting chloroplast.
2) Perhaps because of the ubiquitousness of these two symbioses
and their smooth functioning, research has focused on the
process by which the bacterial symbiont was reduced and tamed.
The chloroplast can no longer grow without its host, and the
chloroplast's genetic material is reduced dramatically from that
of the original cyanobacterium. Amazingly some of the
chloroplast's own genes were not simply lost from its genome but
moved to the host nuclear genome. The evolutionary introduction
of a transit peptide sequence into these genes resulted
originally in cyanobacterial gene products ending up back in the
chloroplast, carrying out their original function but under host
control. Martin et al (1) argue forcefully, however, that this
focus on the reduction of the land-plant chloroplast genome has
ignored the other bonanza from this symbiosis: the large number
of genes from the original cyanobacterium that have ended up in
the host nuclear genome without a role in chloroplast
maintenance. These genes provided the raw genetic material for
plant diversification and competition, possibly against the
original cyanobacterium itself.
3) Some early but largely ignored insights into the role of
bacteria in chloroplast evolution can be found in the
literature. Schimper in 1885 (2) suggested that chloroplasts
were derived from symbiotic microorganisms, and Mereschkowsky in
1905 argued more extensively for the development of different
types of chloroplasts from different types of cyanobacteria
(3,4). Much later, the role of bacteria in symbiogenesis was
championed by Margulis (5). Many scientists have provided the
crucial data that convincingly show the close relationship
between chloroplasts and cyanobacteria, including similar
ribosomes, RNA polymerases, and other cellular machinery
(briefly reviewed in ref.1). Current research suggests that the
cyanobacterial/eukaryote symbiosis occurred only once but
diverged rapidly to three major lineages: the greens, the reds,
and the rather odd lineage called glaucocystophytes. The greens
are the green algal/land-plant group. The reds are the red
algae, now producing much of the agarose consumed by molecular
biology labs.
References (abridged):
1. Martin, W. , Rujan, T. , Richly, E. , Hansen, A. ,
Cornelsen, S. , Lins, T. , Leister, D. , Stoebe, B. , Hasegawa,
M. & Penny, D. (2002) Proc. Natl. Acad. Sci. USA 99, 12246-12251.
2. Schimper, A. F. W. (1885) Jahrbüecher füer Wissenschaftliche
Botanik 16, 1-247.
3. Mereschkowsky, C. (1905) Biol. Zent. Bl. 25, 593-604.
4. Martin, W. & Kowallik, K. V. (1999) Eur. J. Phycol. 34,
287-295.
5. Margulis, L. (1981) Symbiosis in Cell Evolution: Life and
Its Environment on the Early Earth (Freeman, San Francisco).
Proc. Nat. Acad. Sci. 2002 99:11996
Related Background Brief:
TRACING THE THREAD OF PLASTID DIVERSITY THROUGH THE TAPESTRY OF
LIFE. Plastids (chloroplasts) are endosymbiotic organelles
derived from previously free-living cyanobacteria. They are
dependent on their host cell to the degree that the majority of
the proteins expressed in the plastid are encoded in the nuclear
genome of the host cell, and it is this genetic dependency that
distinguishes organelles from obligate endosymbionts. Reduction
in the size of the plastid genome has occurred via gene loss,
substitution of nuclear genes, and gene transfer. The plastids
of Chlorophyta and plants, Rhodophyta, and Glaucocystophyta are
primary plastids (i.e., derived directly from a cyanobacterium).
These three lineages may or may not be descended from a single
endosymbiotic event. All other lineages of plastids have
acquired their plastids by secondary (or tertiary)
endosymbiosis, in which a eukaryote already equipped with
plastids is preyed upon by a second eukaryote. Considerable gene
transfer has occurred among genomes and, at times, between
organisms. The eukaryotic crown group Alveolata has a
particularly complex history of plastid acquisition. C.F.
Delwiche: Am Nat 1999 154:S164.
Related Background Brief:
EVOLUTIONARY ANALYSIS OF ARABIDOPSIS, CYANOBACTERIAL, AND
CHLOROPLAST GENOMES REVEALS PLASTID PHYLOGENY AND THOUSANDS OF
CYANOBACTERIAL GENES IN THE NUCLEUS. Chloroplasts were once
free-living cyanobacteria that became endosymbionts, but the
genomes of contemporary plastids encode only 5-10% as many genes
as those of their free-living cousins, indicating that many
genes were either lost from plastids or transferred to the
nucleus during the course of plant evolution. Previous estimates
have suggested that between 800 and perhaps as many as 2000
genes in the Arabidopsis genome might come from cyanobacteria,
but genome-wide phylogenetic surveys that could provide direct
estimates of this number are lacking. The authors report they
compared 24,990 proteins encoded in the Arabidopsis genome to
the proteins from three cyanobacterial genomes, 16 other
prokaryotic reference genomes, and yeast. Of 9368 Arabidopsis
proteins sufficiently conserved for primary sequence comparison,
866 detected homologues only among cyanobacteria and 834 other
branched with cyanobacterial homologues in phylogenetic trees.
Extrapolating from these conserved proteins to the whole genome,
the data suggest that 4500 of Arabidopsis protein-coding genes
(18% of the total) were acquired from the cyanobacterial
ancestor of plastids. These proteins encompass all functional
classes, and the majority of them are targeted to cell
compartments other than the chloroplast. Analysis of 15
sequenced chloroplast genomes revealed 117 nuclear-encoded
proteins that are also still present in at least one chloroplast
genome. A phylogeny of chloroplast genomes inferred from 41
proteins and 8303 amino acids sites indicates that at least two
independent secondary endosymbiotic events have occurred
involving red algae and that amino acid composition bias in
chloroplast proteins strongly affects plastid genome phylogeny.
W. Martin et al: Proc. Nat. Acad. Sci. 2002 99:12246.
Related Background:
ON THE EVOLUTION OF CHLOROPLASTS
Chloroplasts, which contain several photosynthetic pigments
(chlorophylls), are found in all photosynthetic plant cells, but
not in photosynthetic prokaryotes (i.e., not in cells without
membrane-bound organelles). The typical higher plant chloroplast
is lens-shaped, approximately 5 microns across the larger
dimension, and the number of chloroplasts per cell can vary from
1 to 100 depending on the type of cell. A mature chloroplast is
typically bounded by two membranes, an inner membrane and an
outer membrane, the membranes possessing significantly different
chemical constituents. In addition to a number of enzymes
involved in photosynthesis, chloroplasts also contain in their
interior a circular DNA molecule and protein synthetic machinery
typical of prokaryotes. The current consensus is that
chloroplasts may have originated from cyanobacteria that became
endosymbionts.
Cyanobacteria comprise a phylum of bacteria characterized by
blue-green (cyan) photosynthetic pigments, abundant in a variety
of habitats, particularly in fresh water and soil. Cyanobacteria
are responsible for generating a large portion of the free
oxygen in the Earth's atmosphere. They apparently produced
stromatolite limestone deposits, as well as the bulk of modern
petroleum deposits. (Stromatolites are laminated calcareous
microbial fossil deposits formed principally by cyanobacteria
and algae.)
T. Cavalier-Smith (University of Oxford, UK) discusses the
evolution of chloroplasts, the authors making the following
points:
1) During or following the global warming that thawed the last
"snowball earth" glaciation approximately 580 million years ago
[1] , chloroplasts originated from a cyanobacterial symbiont in
a biciliate protozoan [2,3] . The resulting cellular chimera was
so successful that it rapidly diversified into two primary
lineages of eukaryotic algae: the now rare glaucophytes like
Cyanophora, which retained the cyanobacterial peptidoglycan wall
within their chloroplast envelope, and the green plant/red algal
lineage, which lost the peptidoglycan. The latter split into red
algae, which retained the cyanobacterial phycobilisome pigments,
and green algae, which replaced them by chlorophyll b to adapt
to different light frequencies. Soon afterwards, a red alga and
two different green algal cells were implanted into yet other
biciliate hosts to form three further groups of eukaryotic
algae: a process called secondary symbiogenesis.
2) New light on these early events in eukaryotic evolution comes
from host genes encoding proteins that were secondarily imported
into the acquired plastids [4] and, as reported by Andersson and
Roger [5], from symbiont genes that were apparently retained in
the host nucleus after the symbiont was lost. Secondary
symbiogenesis has also been greatly clarified by the complete
sequence of a cryptomonad nucleomorph, an evolutionarily
miniaturized relic of the red algal nucleus that was enslaved
over 500 million years ago.
3) Several well-established eukaryote groups comprise a mixture
of photosynthetic algae and non-photosynthetic heterotrophs,
notably dinoflagellates, heterokonts, cryptophytes and
Euglenozoa. We now know that all these acquired chloroplasts
secondarily from other eukaryotes (red or green algae). Early in
the twentieth century, however, it was thought that such groups
with mixed nutritional properties were ancestrally
photosynthetic and their non-photosynthetic members evolved by
losing chloroplasts. After the 1960s revival of Mereschkowsky's
symbiogenetic theory of chloroplast origins, the alternative
dogma arose that such groups were ancestrally heterotrophic and
acquired plastids by numerous independent symbioses. However,
each symbiogenetic origin of an organelle is evolutionarily
complex, requiring novel organelle-specific protein-targeting
machinery and the acquisition by over a thousand genes of
appropriate targeting signals. The author suggests that
symbiogenesis is very rare and chloroplast loss distinctly
commoner.
4) In summary: The author suggests that chloroplasts originated
from cyanobacteria only once, but have been laterally
transferred to other lineages by symbiogenetic cell mergers.
Such secondary symbiogenesis is rarer and chloroplast losses
commoner than often assumed.
References (abridged):
1. Hoffman P.F., Kaufman A.J., Halverson G.P. and Schrag D.P.
(1998) A neoproterozoic snowball earth. Science, 281:1342-1346.
2. Cavalier-Smith T. (1982) The origins of plastids. Biol. J.
Linn. Soc., 17:289-306.
3. Cavalier-Smith T. (2000) Membrane heredity and early
chloroplast evolution. Trends Plant Sci., 5:174-182.
4. Fast N.M., Kissinger J.C., Roos D.S. and Keeling P.J. (2001)
Nuclear encoded, plastid-targeted genes suggest a single common
origin for apicomplexan and dinoflagellates plastids. Mol. Biol.
Evol., 18:418-426.
5. Andersson, J.A., Roger, A.J. (2002). A cyanobacterial gene in
non-photosynthetic protists — an early chloroplast acquisition
in eukaryotes. Curr. Biol. 2002 12:115.
Current Biology 2002 2002 12:R62
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3. BIOWEAPONS AND RESPIRATORY PROTECTION
J. Martyny et al (University of Colorado, US) discuss
respiratory protection, the authors making the following points:
1) The use of anthrax as a biologic weapon in 2001 and concern
about the health effects of exposure to particles and gases at
the World Trade Center site (discussed by Prezant et al[1]) have
raised awareness of personal respiratory-protection devices --
colloquially referred to as "dust masks" or "gas masks." For
decades, many people have used respirators on the job or around
the home. Federal regulations mandate the use of respirators in
a variety of occupational settings if the levels of toxins in
the air cannot be effectively controlled. Clinicians need to be
aware of their patients' occupational exposures to airborne
toxins(2,3) and should be familiar with the common forms of
respiratory protection as well as the benefits and limitations
of respirator use. No respirator is fully protective.(4) In
fact, respirators are a relatively inefficient form of
protection.(1) Respirators should be relied on only as a
secondary means of protection from airborne toxic materials.
Whenever possible, it is better to reduce airborne contamination
by using exhaust ventilation, enclosing the process that
produces the exposure, adapting work practices to reduce
airborne dust and fumes, or replacing toxic materials with safer
alternatives.
2) Respirators are used to protect against a wide variety of
airborne toxins, including chemicals, biologic materials,
radiation, toxic dusts, and metal fumes, and to supply air in
situations of low oxygen, such as those encountered by
firefighters.(4,5) Few respirators can protect simultaneously
against airborne particulates, gases, and vapors. Many different
types of respirators are available. When clinicians counsel
patients to use a respirator, they must know how to select the
correct respirator.
3) Respirators can be divided into two types: air-supplying and
air-purifying. Depending on the type, they may fit tightly or
loosely.(4) In environments where oxygen levels are low, the
types and levels of chemicals are unknown, or the conditions are
immediately dangerous to life or health, the highest degree of
protection is required.(5) In these situations, the only
acceptable type of respiratory protection is a
positive-pressure, self-contained breathing apparatus (referred
to as an SCBA).(5) This is an air-supplying, tight-fitting type
of respirator. Exposure to many forms of dust, on the other
hand, may require the use of only a half-face disposable
respirator. Some type of respirator is available for use against
most potential exposures. The choice of respirator and filter is
determined by the expected types and levels of contaminants, the
characteristics of the job, and to some extent, individual
characteristics, such as the user's facial features and medical
fitness to use respiratory protection.(4,5)
References (abridged):
1. Prezant DJ, Weiden M, Banauch GI, et al. Cough and bronchial
responsiveness in firefighters at the World Trade Center site. N
Engl J Med 2002;347:806-815.
2. Newman LS. Occupational illness. N Engl J Med 1995
333:1128-1134.
3. Beckett WS. Occupational respiratory diseases. N Engl J Med
2000 342:406-413.
4. NIOSH guide to industrial respiratory protection. Cincinnati:
National Institute for Occupational Safety and Health, 1987:289.
(DHHS publication no. (NIOSH) 87-116.)
5. National Institute for Occupational Safety and Health.
Occupational safety and health guidance manual for hazardous
waste site activities. Washington, D.C.: Government Printing
Office, 1985. (DHHS publication no. (NIOSH) 85-115.)
New Engl. J. Med. 2002 347:824
Related Background Brief:
COUGH AND BRONCHIAL RESPONSIVENESS IN FIREFIGHTERS AT THE WORLD
TRADE CENTER SITE. Background Workers from the Fire Department
of New York City were exposed to a variety of inhaled materials
during and after the collapse of the World Trade Center. The
authors report they evaluated clinical features in a series of
332 firefighters in whom severe cough developed after exposure
and the prevalence and severity of bronchial hyperreactivity in
firefighters without severe cough classified according to the
level of exposure. "World Trade Center cough" was defined as a
persistent cough that developed after exposure to the site and
was accompanied by respiratory symptoms severe enough to require
medical leave for at least four weeks. Evaluation of exposed
firefighters included completion of a standard questionnaire,
spirometry, airway-responsiveness testing, and chest imaging.
Results: In the first six months after September 11, 2001, World
Trade Center cough occurred in 128 of 1636 firefighters with a
high level of exposure (8 percent), 187 of 6958 with a moderate
level of exposure (3 percent), and 17 of 1320 with a low level
of exposure (1 percent). In addition, 95 percent had symptoms of
dyspnea, 87 percent had gastroesophageal reflux disease, and 54
percent had nasal congestion. Of those tested before treatment
of World Trade Center cough, 63 percent of firefighters (149 of
237) had a response to a bronchodilator and 24 percent (9 of 37)
had bronchial hyperreactivity. Chest radiographs were unchanged
from precollapse findings in 319 of the 332 with World Trade
Center cough. Among the cohort without severe cough, bronchial
hyperreactivity was present in 77 firefighters with a high level
of exposure (23 percent) and 26 with a moderate level of
exposure (8 percent). The authors conclude: Intense, short-term
exposure to materials generated during the collapse of the World
Trade Center was associated with bronchial responsiveness and
the development of cough. Clinical and physiological severity
was related to the intensity of exposure. D.J. Prezant et al:
nejm 2002 347:806.
Related Background Brief:
EMERGENCY PREPAREDNESS AND RESPONSE IN ISRAEL DURING THE GULF
WAR. The authors report they examined the effect of the
emergency response on medical and public health problems during
the 1991 Gulf War in Israel. On the first day of the conflict,
the number of deaths from suffocation, asphyxiation, aspiration,
myocardial infarction, cardiac arrest, and cerebrovascular
accident increased abruptly, as did the number of sudden deaths
associated with the use of tight-fitting masks with filters in
sealed rooms. Much of the excess risk for death from
cardiorespiratory complications during the first alert may have
been a consequence of its duration (140 minutes). Mass
evacuation and concrete buildings are believed to have kept the
death toll from trauma down, and mask use may have protected
against facial and upper-airway injuries. Falls and hip
fractures, airway irritation from exposure to bleach, carbon
monoxide intoxication from open kerosene heaters in sealed
rooms, and self-injection with atropine syringes were also
noted. A measles epidemic and increased death rates from
automobile crashes were other preventable causes of death.
Protection against biological warfare was limited to
surveillance of trends for pneumonia and gastroenteritis.
Emergency planners failed to anticipate the need for better mask
fit, hands-on training in the use of masks, and special
guidelines for older persons to prevent deaths from suffocation
and other cardiovascular-respiratory problems in the first
minutes of use. If masks are to be distributed as a protection
against chemical warfare, a simpler model including the use of
shrouds for whole-body skin protection might help avoid
cardiorespiratory complications. Public health problems not
adequately dealt with in the predisaster period are apt to
emerge with greater severity during a crisis. P. Barach et al:
Ann Emerg Med. 1997 30:513.
Related Background:
RAPID DETECTION OF BIOTERRORIST PATHOGENS
Harvey Black (The Scientist) discusses the problem of
identifying a bioterrorist event. Chills, fever, headache,
muscle pain, and appetite loss are classic flu symptoms, but
they are also markers of the biological warfare agents
tularemia, staphylococcus enterotoxin B, and Q-fever. At
present, there are no diagnostic methods that would distinguish
in a timely manner the cause of these symptoms. However,
researchers are working towards that objective, as well as
attempting to find the appropriate treatments, and advanced
diagnostic methods ranging from genetic analyses to breath
analysis are among the approaches under examination. One
approach is to identify pathogens by direct examination of
microbial DNA, a method that would be based on the availability
of a complete repertoire of pathogen genome sequences. Another
method, under development by Daniel Branton (Harvard University,
US) is based on a lipid bilayer containing a nanopore 1.5 to 2.5
nanometers in diameter. The idea is to pass a single strand of
DNA through the nanopore, with the identity of the pathogen
determined by changes in electrical conductivity induced by
different bases. The general notion of using a pore and
measuring conductivity to investigate what is going through the
pore is evidently completely new. Branton is also working to
develop a silicon nitride chip with such a pore. In a test
system described last year, Branton and his colleagues were
apparently able to identify a molecule passing in one
millisecond through a nanopore.
The Scientist 2001 23 Jul
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4. ANTHROPOLOGY: ON THE ORIGIN OF EUROPEANS
L. Chikhi et al (University College London, UK) discuss European
origins, the authors making the following points:
1) It is widely accepted that the onset of agriculture in the
Near East triggered a cultural change that brought farming and
associated technologies across Europe about 10,000 years ago
(1). Two alternative demographic scenarios have been proposed to
account for this transition, documented in the archaeological
record (2). In the "demic diffusion model" (DDM; ref. 1), the
spread of technologies involved a massive movement of people,
which implies a significant genetic input of Near Eastern genes
from Neolithic farmers. Under the "cultural diffusion model"
(CDM; refs. 3 and 4), on the contrary, the transition to
agriculture is regarded essentially as a cultural phenomenon,
involving the movement of ideas and practices rather than
people. Consequently, it would not imply major changes at the
genetic level.
2) Proponents of both models acknowledge that there is a
spectrum of intermediate scenarios, which are essentially
admixture models: settlements were founded by a mixture of
farmers whose ancestors originally came from the Near East and
indigenous hunter-gatherers. The question is, therefore, whether
the dispersing farmers were few, (as in the CDM) or many (as in
the DDM).
3) In summary: There still is no general agreement on the
origins of the European gene pool, even though Europe has been
more thoroughly investigated than any other continent. In
particular, there is continuing controversy about the relative
contributions of European Paleolithic hunter-gatherers and of
migrant Near Eastern Neolithic farmers, who brought agriculture
to Europe. The authors report they apply a statistical framework
that they have developed to obtain direct estimates of the
contribution of these two groups at the time they met. The
authors analyze a large dataset of 22 binary markers from the
non-recombining region of the Y chromosome (NRY), by using a
genealogical likelihood-based approach. The results reveal a
significantly larger genetic contribution from Neolithic farmers
than did previous indirect approaches based on the distribution
of haplotypes selected by using post hoc criteria. The authors
detect a significant decrease in admixture across the entire
range between the Near East and Western Europe. The authors also
argue that local hunter-gatherers contributed less than 30% in
the original settlements. This finding leads the authors to
reject a predominantly cultural transmission of agriculture.
Instead, the authors argue that the demic diffusion model
introduced by Ammerman and Cavalli-Sforza (1) captures the major
features of this dramatic episode in European prehistory.
References (abridged):
1. Ammerman, A. J. & Cavalli-Sforza, L. L. (1984) The Neolithic
Transition and the Genetics of Populations in Europe (Princeton
Univ. Press, Princeton)
2. Bellwood, P. (2001) Annu. Rev. Anthropol. 30, 181-207
3. Zvelebil, M. (2000) in Archaeogenetics: DNA and the
Population Prehistory of Europe, eds. Renfrew, C. & Boyle, K.
(McDonald Institute for Archaeological Research, Cambridge,
U.K.), pp. 57-79
4. Whittle, A. (1996) Europe in the Neolithic (Cambridge Univ.
Press, Cambridge, U.K.)
5. Menozzi, P. , Piazza, A. & Cavalli-Sforza, L. (1978) Science
201, 786-792
Proc. Nat. Acad. Sci. 2002 99:11008
Related Background Brief:
EARLY AGRICULTURALIST POPULATION DIASPORAS? FARMING, LANGUAGES,
AND GENES. The consequences of early agricultural development in
several regions of the Old and New Worlds included population
growth, the spread of new material cultures and of
food-producing economies, the expansions of language families,
and in many cases the geographical expansions of the early
farming populations themselves into territories previously
occupied by hunters and gatherers. This review discusses some of
the different outcomes that can be expected according to the
differing perspectives of archaeology, linguistics, and
biological anthropology. The author argues that agriculturalist
expansion lies at the root of many of the world's major language
families, although this need not imply that farmers always
replaced hunter-gatherers in the biological sense. History,
environmental variations, and prior cultural configurations
dictated many of the outcomes, some of which played a
fundamental role in the large-scale genesis of human cultural
and biological patterning from Neolithic/Formative times into
the world of today. Peter Bellwood: Annu. Rev. Anthropol. 2001
30:181.
Related Background Brief:
SYNTHETIC MAPS OF HUMAN GENE FREQUENCIES IN EUROPEANS.
Multivariate techniques can be used to condense the information
for a large number of loci and alleles into one or a few
synthetic variables. The geographic distribution of synthetic
variables can be plotted by the same technique used in mapping
the gene frequency of a single allele. Synthetic maps were
constructed for Europe and the Near East, with the use of
principal components to condense the information of 38
independent alleles from ten loci. The first principal component
summarizes close to 30% of the total information and shows
gradients. Maps thus constructed show clines in remarkable
agreement with those expected on the basis of the spread of
early farming in Europe, thus supporting the hypothesis that
this spread was a demic spread rather than a cultural diffusion
of farming technology. P. Menozzi et al: Science 1978 201:786.
Related Background Brief:
PALEOLITHIC AND NEOLITHIC LINEAGES IN THE EUROPEAN MITOCHONDRIAL
GENE POOL. Phylogenetic and diversity analysis of the mtDNA
control region sequence variation of 821 individuals from Europe
and the Middle East distinguishes five major lineage groups with
different internal diversities and divergence times.
Consideration of the diversities and geographic distribution of
these groups within Europe and the Middle East leads to the
conclusion that ancestors of the great majority of modern,
extant lineages entered Europe during the Upper Paleolithic. A
further set of lineages arrived from the Middle East much later,
and their age and geographic distribution within Europe
correlates well with archaeological evidence for two culturally
and geographically distinct Neolithic colonization events that
are associated with the spread of agriculture. It follows from
this interpretation that the major extant lineages throughout
Europe predate the Neolithic expansion and that the spread of
agriculture was a substantially indigenous development
accompanied by only a relatively minor component of contemporary
Middle Eastern agriculturalists. There is no evidence of any
surviving Neanderthal lineages among modern Europeans. M.
Richards et al: Am J Hum Genet. 1997 61:247.
Related Background:
PALEOLITHIC DEMOGRAPHY
Mary C. Stiner (University of Arizona, US) discusses current
research in *paleolithic demography. All Paleolithic *hominids
lived by hunting and collecting wild foods, an aspect of
existence that began to disappear only with the emergence of the
farming and herding societies of the *Neolithic approximately
10,000 or less years ago. What are the roots of this remarkable
economic transformation? The answer lies in equally
revolutionary changes that occurred within certain stone age
cultures several thousand years before. In 1968, Lewis R.
Binford noted what appeared to be substantial diversification of
human diets in middle- and high-latitude Europe at the end of
the Paleolithic, approximately 12,000 to 8000 years ago. Rapid
diversification in hunting, food processing, and food storage
equipment generally accompanied dietary shifts, symptoms of
intensified use of habitats, and fuller exploitation of the
potential foodstuffs they contained. Some of this behavior was
directed to grinding, drying, and storing nuts, but it also
involved small animals. In 1969, Kent Flannery pushed these
observations further with his "Broad Spectrum Revolution"
hypothesis, proposing that the emergence of the Neolithic
culture in western Asia was prefaced by increases in dietary
breadth in foraging societies just before the period. Flannery
argued that subsistence diversification, mainly by adding new
species to the diet, raised the carrying capacity of an
environment increasingly constrained by climate instability at
the end of the Pleistocene. Today, 32 years later, and contrary
to the results of interim studies, the data on small game use in
southern Europe and western Asia support Flannery's "Broad
Spectrum Revolution" hypothesis of expanding dietary breadth in
response to demographic packing during the late Pleistocene.
Proc. Nat. Acad. Sci. 2001 98:6993
Notes:
... ... *paleolithic: The term "Paleolithic" (Old Stone Age) is
essentially an archeological term applied to Eurasia with
approximate time-frame segments as follows: Upper
Paleolithic: from 40,000 to 8000 years ago. Middle
Paleolithic: from 200,000 to 40,000 years ago. Lower
Paleolithic: from 2.5 million to 200,000 years ago.
... ... *hominids: The terms "hominoid", "hominid", and
"hominin" are not interchangeable, but their classification
criteria are variously in a state of flux. In general, the
hominoids are a primate superfamily; the hominid family is
currently considered to comprise both the great ape lineages and
human lineages within the hominoid superfamily; the "homininae"
comprise both the human lineages and the African ape lineages
within the hominids, and the "hominini" comprising only the
human lineages.
... ... *Neolithic: (New Stone Age) Characterized by first
domestication of animals, cultivation of plants, production of
sophisticated stone tools, etc. Considered to have begun
approximately 10,000 years ago.
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5. PROTEOMICS: ON COMPUTER SIMULATIONS OF LIVING SYSTEMS
Julian P. Whitelegge (University of California Los Angeles, US)
discusses proteomics and computers, the author making the
following points:
1) While the genome contains the coded information that allows
an organism to live and reproduce, the essential functions of
living cells are accomplished by gene products. Those structures
-- mainly proteins, although ribonucleic acids are also
essential -- provide the scaffold, regulatory, and catalytic
functions that drive metabolism. Proteomics seeks to measure the
expression of all proteins within an organism and monitor
changes in response to developmental and environmental cues in
health and disease. Because the 30,000 or so human genes sustain
life through a considerably larger variety of mature proteins,
the technological challenge dramatically exceeds that of
genomics. Ultimately, we would like a computer model that mimics
life "in silico", allowing accurate projections for metabolic
engineering experiments in medicine and the life sciences. This
grand experiment is just starting and the race is on to develop
high-throughput technology to provide proteome-scale insights,
as well as computational systems that allow realistic modeling
of simple cells.(1)
2) A central facet of proteomics is the matching of protein data
to a corresponding gene providing a direct readout of expression
for functional genomics, as opposed to inferences drawn from
measurements of messenger RNA that can be misleading, as well as
allowing for the measurement of posttranslational modifications.
Rapid advances in mass spectrometry technology have driven
proteomics to what is clearly the most dramatically expanding
arena in the life sciences today. The recent 50th annual meeting
of the American Society for Mass Spectrometry (www.asms.org)
featured a number of new proteomics sessions to accommodate this
interest. Accurate measurement of peptide masses and tandem mass
spectrometry (MS-MS) experiments that produce peptide sequence
data allow correlation with genomic data using software that
translates genes and calculates peptide mass and/or fragment
mass data. Measurement of intact protein masses is insufficient
to allow assignment of all proteins (2), and thus enzymatic
(trypsin) or chemical (CNBr) cleavage is used to break, in a
sequence-dependent fashion, whole gene products into manageable
pieces, some of which completely match a portion of a translated
gene. Early proteomics studies relied on separation of proteins
by two-dimensional (2D) gel electrophoresis, for example,
followed by identification of individual protein spots after
excision from the gel, cleavage reactions, extraction of
peptides, and mass spectrometry with database searches (3-5).
More recently, others have pioneered a "shotgun" approach
whereby whole-cell protein extracts are immediately cleaved and
the peptide mixture subjected to separation before mass
spectrometry to generate peptide sequence data. Multidimensional
chromatography is used to enhance fractionation of the complex
peptide mixture from a whole-cell digest, giving rise to the
"MudPIT" acronym (Multidimensional Protein Identification
Technology). Koller et al.(1) compare the 2D-gel approach to
MudPIT, demonstrating the superior detection efficiency of the
latter technique, while confirming the complementary nature of
the methods.
References (abridged):
1. Koller, A. , Washburn, M. P. , Lange, B. M. , Andon, N. L. ,
Deciu, C. , Haynes, P. A. , Hays, L. , Schieltz, D. , Ulaszek,
R. , Wei, J. , et al. (2002) Proc. Natl. Acad. Sci. USA 99,
11969-11974.
2. Gómez, S. M. , Nishio, J. N. , Faull, K. F. & White legge, J.
P. (2002) Mol. Cell. Proteomics 1, 45-59.
3. Henzel, W. J. , Billeci, T. M. , Stults, J. T , Wong, S. C. ,
Grimley, C. & Watanabe, C. (1993) Proc. Natl. Acad. Sci. USA
190, 5011-5015.
4. James, P. , Quadroni, M. , Carafoli, E. & Gonnet, G. (1993)
Biochem. Biophys. Res. Commun. 195, 58-64.
5. Mann, M. , Hojrup, P. & Roepstorff, P. (1993) Biol. Mass
Spectrom. 22, 338-345.
Proc. Nat. Acad. Sci. 2002 99:11564
Related Background Brief:
PROTEIN IDENTIFICATION BY MASS PROFILE FINGERPRINTING. The
authors report they have developed an algorithm for identifying
proteins at the sub-microgram level without sequence
determination by chemical degradation. The protein, usually
isolated by one- or two-dimensional gel electrophoresis, is
digested by enzymatic or chemical means and the masses of the
resulting peptides are determined by mass spectrometry. The
resulting mass profile, i.e., the list of the molecular masses
of peptides produced by the digestion, serves as a fingerprint
which uniquely defines a particular protein. This fingerprint
may be used to search the database of known sequences to find
proteins with a similar profile. If the protein is not yet
sequenced the profile can serve as a unique marker. This
provides a rapid and sensitive link between genomic sequences
and 2D gel electrophoresis mapping of cellular proteins. P.
James et al: Biochem Biophys Res Commun 1993 195:58.
Related Background Brief:
RAPID IDENTIFICATION OF PROTEINS BY PEPTIDE-MASS FINGERPRINTING.
Developments in "soft" ionization techniques have revolutionized
mass-spectrometric approaches for the analysis of protein
structure. For more than a decade, such techniques have been
used, in conjunction with digestion by specific proteases, to
produce accurate peptide molecular weight "fingerprints" of
proteins. These fingerprints have commonly been used to screen
known proteins, in order to detect errors of translation, to
characterize post-translational modifications, and to assign
disulphide bonds. However, the extent to which peptide-mass
information can be used alone to identify unknown sample
proteins, independent of other analytical methods such as
protein sequence analysis, has remained largely unexplored. The
authors report on the development of the molecular weight search
(MOWSE) peptide-mass database at the SERC Daresbury Laboratory.
Practical experience has shown that sample proteins can be
uniquely identified from as few as three or four experimentally
determined peptide masses when these are screened against a
fragment database that is derived from over 50,000 proteins.
Experimental errors of a few daltons are tolerated by the
scoring algorithms, thus permitting the use of inexpensive
time-of-flight mass spectrometers. As with other types of
physical data, such as amino-acid composition or linear
sequence, peptide masses provide a set of determinants that are
sufficiently discriminating to identify or match unknown sample
proteins. The authors conclude: Peptide-mass fingerprints can
prove as discriminating as linear peptide sequences, but can be
obtained in a fraction of the time using less protein. In many
cases, this allows for a rapid identification of a sample
protein before committing it to protein sequence analysis.
Fragment masses also provide information, at the protein level,
that is complementary to the information provided by large-scale
DNA sequencing or mapping projects. Current Biology 1993 6:327
Related Background:
ON PROTEOMICS
L.A. Liotta et al (National Institutes of Health, US) discuss
proteomics, the authors making the following points:
1) The true scientific goal of proteomics is to characterize the
information flow within the cell and the organism. This
information flow is mediated through and by protein pathways and
networks.
2) Proteins in the cell do not exist in isolation. Much like the
connection of transistors, resistors, and capacitors on a
printed circuit board, the cellular protein network consists of
protein interactions and pathways that connect in finely tuned
orchestration in which information is passed along as precise
protein-protein interactions.
3) Proteins assemble themselves into networks through a variety
of protein-protein interactions and post-translational
modifications. The amino acid sequence of a protein determines
its 3-dimensional shape, and it is this shape and the surface
presentation of nested amino acid motifs that enables highly
selective lock-and-key recognition between protein partners in a
communication circuit.
4) As multiple stimuli impinge on living cells, hundreds of
protein signal networks are constantly changing. Even in the
face of this complexity, it is possible to map the state of key
nodes in known protein networks and related this back to cell
function. Researchers can measure the ratio between the
activated (e.g., phosphorylated or cleaved) form and the
unactivated form of key signal proteins and thereby estimate
whether that signal node is in use at the time the proteins are
extracted from the cell.
J. Am. Med. Assoc. 2001 286:2211
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6. MOLECULAR BIOLOGY: ON CHROMATIN FOLDING
P.J. Horn and C.L. Peterson (University of Massachusetts, US)
discuss chromatin folding, the authors making the following
points:
1) Compaction of eukaryotic genomes into condensed chromatin
fibers is required to fit over a meter of DNA within the limited
volume of the nucleus; consequently, this compacted structure is
inherently repressive to processes that require access to the
DNA sequence. The role of higher order chromatin folding in
transcriptional control received the lion's share of interest in
the early 1980s [e.g., (1,2)], but only recently has this key
issue been seriously revisited. Recent advances in our ability
to assemble model chromatin in vitro and to identify
posttranslational chromatin modifications as key components of
gene expression have enhanced interest in the interplay between
chromatin structure and transcription. Although substantial
strides have been made toward an understanding of basic
chromatin structure, much of the detail surrounding "higher
order" structure -- chromatin structure beyond the canonical
"30-nm" fiber familiar from textbooks -- remains partially or
completely uncharacterized.
2) The basic building block of chromatin is the nucleosome,
which contains 147 base pairs (bp) of DNA wrapped in a
left-handed superhelix 1.7 times around a core histone octamer
[two copies each of histones H2A, H2B, H3, and H4 (3)]. Each
core histone contains two separate functional domains: a
signature "histone-fold" motif sufficient for both
histone-histone and histone-DNA contacts within the nucleosome,
and NH2-terminal and COOH-terminal "tail" domains that contain
sites for posttranslational modifications (such as acetylation,
methylation, phosphorylation, and ubiquitination). Although
these histone tails are mostly unresolved in the crystal
structure of the nucleosome (3), they appear to emanate radially
from the nucleosome, conveniently positioned to associate with
"linker" DNA residing between nucleosomes or with adjacent
nucleosomes (4). In addition to the core histones, metazoan
chromatin also contains linker histones (such as histone H1),
which bind to nucleosomes and protect an additional ~20 bp of
DNA from nuclease digestion at the core particle boundary.
Linker histones are not related in sequence to the core
histones, but they also contain a globular domain flanked by
NH2-terminal and COOH-terminal tail domains (5). Although only
the linker histone globular domain is essential for binding to
nucleosomes, the tail domains are believed to be important for
linker histone roles in chromatin folding.
3) In summary: Eukaryotic genomes are organized into condensed,
heterogeneous chromatin fibers throughout much of the cell
cycle. Recent studies indicate that even transcriptionally
active loci may be encompassed within 80- to 100-nanometer-thick
chromonema fibers. These studies suggest that chromatin higher
order folding may be a key feature of eukaryotic transcriptional
control. There is also evidence suggesting that
adenosine-5'-triphosphate-dependent chromatin-remodeling enzymes
and histone-modifying enzymes may regulate transcription by
controlling the extent and dynamics of chromatin higher order
folding.
References (abridged):
1. H. Weintraub, Cell 38, 17 (1984)
2. K. Andersson, B. Bjorkroth, B. Daneholt, J. Cell Biol. 98,
1296 (1984)
3. K. Luger, A. W. Mader, R. K. Richmond, D. F. Sargent, T. J.
Richmond, Nature 389, 251 (1997)
4. J. C. Hansen, Annu. Rev. Biophys. Biomol. Struct. 31, 361
(2002)
5. M. H. Parseghian and B. A. Hamkalo, Biochem. Cell Biol. 79,
289 (2001)
Science 2002 297:1824
Related Background Brief:
HISTONE-H1-DEPENDENT CHROMATIN SUPERSTRUCTURES AND THE
SUPPRESSION OF GENE ACTIVITY. The author reports that he has
identified a chromatin particle containing DNA as large as 20-40
kb that migrates as a discrete entity on agarose gels. With
increasing nuclease digestion, the particle becomes cleaved in
the linker regions between nucleosomes, but remains intact,
probably held together by the outer histones, H1 and H5. By
hybridization analysis, inactive genes are found in these
particles. Active genes (and their flanking sequences) are also
found in particles containing H1 and H5, but in contrast to
inactive supranucleosome particles, active polynucleosome
particles are not held together after cleavage of linker DNA.
This suggests that H1 cross-links adjacent nucleosomes in
inactive regions and that H1 is bound differently in expressed
regions. The results raise the possibility that the marked
degree of suppression of repressed, tissue-specific genes may be
determined, in part, by their assembly into these inactive
supranucleosome structures. H. Weintraub: Cell 1984 38:17.
Related Background Brief:
PACKING OF A SPECIFIC GENE INTO HIGHER ORDER STRUCTURES
FOLLOWING REPRESSION OF RNA SYNTHESIS. Transcription of the
Balbiani ring (BR) genes of the dipteran Chironomus tentans was
inhibited by the nucleoside analogue DRB
(5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole). The BR
genes were emptied of RNA polymerases and the subsequent packing
of the genes was monitored by transmission electron microscopy.
The thin chromatin axis of the transcriptionally active genes
condensed into a thick (20-25 nm) chromatin fiber, which was
recorded as a linear structure, an open loop or a supercoiled
loop. The compacted genes were finally packed into dense clumps
of chromatin. It was proposed that upon repression of RNA
synthesis the BR gene template attains the following consecutive
stages with increasing compaction: transcription loop ----
linear thick fiber ---- open thick fiber loop ---- supercoiled
thick fiber loop ---- dense chromatin. Within the chromatin
blocks, structures that resembled the supercoiled loops were
discerned, suggesting that the final packing of the template
might be accomplished by a close alignment of supercoiled loops.
K. Andersson et al: J Cell Biol 1984 98:1296.
Related Background:
ON CHROMATIN
In the nuclei of all eukaryotic cells, genomic DNA is highly
folded, constrained, and compacted by histone and non-histone
proteins in a dynamic polymer called "chromatin". The distinct
levels of chromatin organization are dependent on the dynamic
higher order structuring of "nucleosomes", which represent the
basic repeating unit of chromatin.
N. Gilbert and J. Allan (University of Edinburgh, UK) discuss
chromatin fibers, the authors making the following points:
1) When fragments of chromatin are isolated from cells and
maintained under ionic conditions comparable to those in the
nucleus, the chromatin fragments are invariably found to be
folded into higher-order fibers. Structural studies on such bulk
material have formed the basis for a variety of models that are
proposed to explain the manner in which chains of nucleosomes
are packaged into the higher-order state. However, the
ubiquitous and uniform character of the higher-order chromatin
fiber suggested by these models tends to mask the fact that the
higher-order chromatin fiber must be an adaptable structure
capable of undergoing dynamic structural transitions. Such
properties are required to facilitate the unfolding processes
presumed to be essential for gene activation and chromosome
replication. On the other hand, the chromatin fiber must also
have the capacity to adopt an inert character required to
maintain genes in a state of sustained repression and to provide
local chromosomal domains with distinctive architectures within
which specific chromosomal structures (e.g., the centromere) can
exist.
2) Despite these expectations, studies on isolated higher-order
chromatin fibers have failed to reveal a diversity of structure
compatible with the diversity of function. For example,
chromatin fibers containing globin gene sequences isolated from
erythroid cells in an activated state have physical properties
equivalent to both bulk and transcriptionally inactive chromatin
fibers. The presence of nucleosome-free hypersensitive sites
disrupts the fiber, but between these distinctive regions the
chromatin appears to be typically folded. Within the cell, the
higher-order chromatin fiber does unfold during transcription,
but maintenance of this state is notably transient because the
inhibition of polymerase activity leads to a rapid reformation
of the folded state. Thus, with regard to structural criteria,
it appears that chromatin fibers containing active gene
sequences cannot be distinguished from bulk or inactive
chromatin fibers once they are removed from the nucleus.
Proc. Nat. Acad. Sci. 2001 98:11949
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7. MATHEMATICAL SOCIOECONOMICS: ON PUBLIC GOODS GAMES
In economic game theory, cooperation between individuals has
been analyzed by some researchers with a model non-zero-sum game
called the "Prisoner's Dilemma". In a typical game, two players
can choose between two moves, either "cooperate" or "defect".
Each player gains when both cooperate, but if only one of them
cooperates, the other one, the defector, will gain more. If both
defect, both lose (or gain very little).
G. Szabo and C. Hauert (Research Institute for Technical Physics
and Materials Science Budapest, HU) discuss public goods games,
the authors making the following points:
1) In behavioral sciences, and more recently in economics, the
evolution of cooperation among unrelated individuals represents
one of the most stunning phenomena [1,2]. The prisoner's dilemma
(PD) has long been established as a paradigm to explain
cooperative behavior through pairwise interactions [3]. While
the PD attracted attention from biologists and social
scientists, most studies in experimental economics focused on
the closely related but more general public goods game (PGG) for
group interactions [4].
2) In typical PGG experiments, an experimenter endows, for
example, four players with $10 each. The players then have the
opportunity to invest part or all of their money into a common
pool. The players know that the total amount in the pool is
doubled and equally divided among all participants irrespective
of their contributions. If everybody cooperates and contributes
their money, each player ends up with $20. However, every player
faces the temptation to defect and to free ride on the other
players' contributions by withholding their money. Obviously,
defection represents the dominating strategy leading to the
"rational" equilibrium where no one increases the initial
capital. Such strategical behavior prescribed to homo
oeconomicus is frequently at odds with experimental findings [5]
and led to the decline of this rationality concept as an
approach to behavior analysis.
3) Note that for pairwise encounters with a fixed investment
amount, the PGG reduces to the PD. PGG interactions are abundant
in animal and human societies. Consider, for example, predator
inspection behavior, alarm calls, and group defense, as well as
health insurance, public transportation, or environmental
issues, to name only a few. Recently it was demonstrated that
voluntary participation in such public enterprises may provide
an escape hatch out of economic stalemate and results in a
substantial and persistent willingness to cooperate even in
sizable groups, in the absence of repeated interactions, under
full anonymity, and without secondary mechanisms such as
punishment or reward.
4) In summary: The authors present a simple yet effective
mechanism promoting cooperation under full anonymity by allowing
for voluntary participation in public goods games. This natural
extension leads to "rock-scissors-paper"-type cyclic dominance
of the three strategies, cooperate, defect, and loner. In
spatial settings with players arranged on a regular lattice,
this results in interesting dynamical properties and intriguing
spatiotemporal patterns. In particular, variations of the value
of the public good leads to transitions between one-, two-, and
three-strategy states which either are in the class of directed
percolation or show interesting analogies to Ising-type models.
Although volunteering is incapable of stabilizing cooperation,
it apparently efficiently prevents successful spreading of
selfish behavior.
References (abridged):
1. J. von Neumann and 0. Morgenstem, Theory of Games and
Economic Behaviour (Princeton University Press, Princeton, 1944).
2. J. Maynard Smith and E. Szathmary, The Major Transitions in
Evolution (W. H. Freeman & Co., Oxford, 1995).
3. R. Axelrod and W.D. Hamilton, Science 211, 1390 (1981).
4. The Handbook of Experimental Economics, edited by J. H. Kagel
and A.E. Roth (Princeton University Press, Princeton, 1995).
5. E. Fehr and S. Gachter, Nature (London) 415, 137 (2002).
Phys. Rev. Lett. 2002 89:118101
Related Background:
ECONOMICS: ON PREDICTING RATIONAL BEHAVIOR
D.P. Foster and H.P. Young (University of Pennsylvania, US)
discuss the prediction of rational behavior. A foundational
assumption in economics is that people are rational: they choose
optimal plans of action given their predictions about future
states of the world. In games of strategy, this means that each
player's strategy should be optimal given his or her prediction
of the opponent's strategies. The authors demonstrate that there
is an inherent tension between rationality and prediction when
players are uncertain about their opponent's payoff functions.
Specifically, there are games in which it is impossible for
perfectly rational players to learn to predict the future
behavior of their opponents (even approximately) no matter what
learning rule they use. The reason is that in trying to predict
the next-period behavior of an opponent, a rational player must
take an action this period that the opponent can observe. This
observation may cause the opponent to alter the next-period
behavior, thus invalidating the first player's prediction. The
resulting feedback loop has the property that a positive
fraction of the time the predicted probability of some action
next period differs substantially from the actual probability
with which the action is going to occur. The authors conclude
that there are strategic situations in which it is impossible in
principle for perfectly rational agents to learn to predict the
future behavior of other perfectly rational agents based solely
on their observed actions.
Proc. Nat. Acad. Sci. 2001 98:12848
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8. ON CLASSICAL VS. QUANTUM CHAOS
Y.S. Weinstein et al (Massachusetts Institute of Technology, US)
discuss classical vs. quantum chaos, the authors making the
following points:
1) Chaos is a phenomenon in which nonlinear dynamical systems
exhibit heightened sensitivity to small perturbations [1-5]. The
study of chaos is computationally intensive. When direct
experiments are not available, computers can be used to simulate
chaotic dynamics and to calculate the effect of perturbations.
But when the chaotic system is quantum mechanical, simulating
its dynamics on a classical computer is notoriously difficult:
the computational complexity of the calculation rises
exponentially with the number of degrees of freedom of the
simulated quantum chaotic system and with the accuracy to which
the simulation is to take place [4]. If one can simulate quantum
chaos on a quantum computer, by contrast, the computational
complexity rises only as a small polynomial in the number of
degrees of freedom and in the accuracy. Consequently, quantum
computation represents a potentially powerful technique for
investigating quantum chaos.
2) Small perturbations to the initial state of a classical
chaotic system typically lead to large changes in behavior. Two
states that are initially close are driven apart at a rate
governed by the positive Lyapunov exponents [1] of the chaotic
dynamics. By contrast, quantum dynamics, whether regular or
chaotic, preserves the overlap between quantum states and does
not drive them apart. Nonetheless, quantum chaos can be
characterized by the sensitivity of the time evolution of states
to small changes in the Hamiltonian that governs the chaotic
dynamics.
3) In summary: The term "baker's map" refers to a specific
algebraic mapping formalism that has recently been found useful
in the analysis of chaotic systems. The authors report on the
experimental implementation of the quantum baker's map via a
three bit nuclear magnetic resonance quantum information
processor. The experiments tested the sensitivity of the quantum
chaotic map to perturbations. In the first experiment, the map
was iterated forward and then backward to provide benchmarks for
intrinsic errors and decoherence. In the second set of
experiments, the least significant qubit was perturbed in
between the iterations to test the sensitivity of the quantum
chaotic map to controlled perturbations. The authors suggest
these experiments can be used to investigate existing
theoretical predictions for quantum chaotic dynamics.
References (abridged):
1. A.J. Lichtenberg and M. A. Lieberman, Regular and Chaotic
Dynamics (Springer-Verlag, Berlin, 1992).
2. M.V. Berry, Proc. R. Soc. London A 413, 183 (1987).
3. M.V. Berry, in New Trends in Nuclear Collective Dynamics,
edited by Y. Abe, H. Horiuchi, and K. Matsuyanagi (Springer,
Berlin, 1992), p. 183.
4. F. Haake, Quantum Signatures of Chaos (Springer, New York,
1991).
5. F. Haake, M. Kus, and R. Scharf, Z. Phys. B 65, 381 (1987).
Phys. Rev. Lett. 2002 89:157902
Related Background:
ON CHAOTIC SYSTEMS
Andreas Albrecht (University of California Davis, US) discusses
chaotic systems. Chaotic behavior is well understood from a
classical perspective, and is typically discussed in the context
of a mathematical "phase space" in which there are dimensions
for both position (x) and momentum (p). A particle at a given
instant can be specified as a point in classical phase space,
and the time development of the particle describes a curve or
trajectory in phase space. In chaotic systems, particles that
start out in virtually identical states (i.e., at very close
points in phase space) rapidly evolve into completely different
states (i.e., distant parts of phase space). Because nothing is
ever measured with absolute precision, one can never
realistically talk about "points" in phase space. Instead, every
point (x,p) in phase space is typically assigned a probability
P(x,p). For a well-specified particle, this probability peaks
sharply at a localized point in phase space. For an ordinary
classical object, such as a single billiard ball, a phase-space
probability distribution that starts out sharply peaked will
remain peaked over time; a small uncertainty in the starting
point results in a similar small degree of ignorance at a later
time. Chaotic systems are dramatically different. A sharply
peaked initial distribution gets torn apart by the chaotic
evolution, as neighboring phase-space trajectories rapidly head
off in different directions. A small amount of ignorance at the
beginning rapidly translates into huge uncertainties later on,
as the distribution becomes highly delocalized.
Nature 2001 412:687
Related Background:
THEORETICAL PHYSICS: CHAOS AND NONLINEAR DYNAMICS
In general, a nonlinear dynamical system is a system described
by time-dependent differential equations such that the rates of
change of one or more dependent variables of the system depend
in a nonlinear fashion on the variables themselves. Certain
nonlinear dynamical systems, some of which are of great
scientific interest, exhibit "chaotic dynamics". In this
context, the term "chaos" refers to unpredictable behavior
arising in a system that obeys deterministic laws but exhibits
unpredictability. The essential idea is that in certain systems
small perturbations may produce a cascade of larger
perturbations, so that eventually the behavior of such systems
cannot be predicted from prior states no matter if the systems
appear simple and obey deterministic laws. Examples of chaotic
nonlinear dynamical systems are the weather and populations of
organisms, and instances of chaotic dynamics have now been
documented in most scientific disciplines. Because the
differential equations for many nonlinear systems are often
intractable (i.e., no explicit quantitative solutions are
possible), a focus of theoretical research on nonlinear systems
has been on analysis of the qualitative behavior of such
systems, in particular on analysis of the "phase space" and
"trajectories" in the phase spaces of such systems. The idea is
essentially as follows: If the state of a system depends upon N
variables, the instantaneous state of the system can be viewed
as a point (phase point) in an N-dimensional space (phase space;
system hyperspace), and as the state of the system changes, its
phase point can be viewed as describing a trajectory in its
phase space. Qualitative analysis of the possible families of
solutions of nonlinear differential equations can provide
information about such phase space trajectories, and there are
certain real systems for which qualitative analysis of the phase
space trajectories of the system has revealed significant
properties of the system otherwise difficult to delineate.
J.P. Gollub and M.C. Cross (2 installations, US) present a
commentary on recent research on chaotic nonlinear dynamics, the
authors making the following points:
1) The techniques of nonlinear dynamics are well-developed, but
the impact of this field has been largely confined to phenomena
in which there are only a few important time-dependent
quantities. Unfortunately, this excludes a vast range of
important problems in which the behavior of one point in space
can be quite different (though statistically similar) to that at
another location. A particular example is convective behavior.
2) The traditional approach to studying nonlinear dynamical
behavior is to plot the dynamical variables of the system as a
multidimensional phase space graph indicating how the behavior
changes over time. For example, a simplified model of the Solar
System consisting of the Sun and 9 planets would require a phase
space with as many as 60 dimensions (3 position and 3 momentum
coordinates for each body). In the case of a convecting fluid, a
complete description of the flow pattern requires knowledge of
the velocity and temperature at a very large number of
locations, so the number of dimensions of the phase plot are
enormous (from thousands to millions, depending on the desired
spatial resolution). As a result, the methods of nonlinear
dynamics are cumbersome and progress has been slow, even though
many interesting examples of spatiotemporal chaos have been
explored both experimentally and numerically.
3) Recent research (D.A. Egolf et al: Nature 404:733 2000)
involving numerical studies of an accepted model of thermal
convection indicates that the origin of unpredictable motion in
chaotic thermal convective systems, at least in one particular
form of spatiotemporal chaos, lies in what occurs in small
regions of space and over short time-scales. These local changes
in the organization of the flow affect the surrounding regions
in such a way that the entire future evolution is affected. The
authors state: "This is something akin to Ed Lorenz's famous
remark [E.N. Lorenz: J. Atmos. Sci. 20:130 1963] that the
localized flapping of a butterfly's wings might change the
weather dramatically over the entire world a few weeks later."
Although such sensitivity to localized fluctuations has never
been confirmed as the source of the unpredictability of the
weather, it is apparently the origin of chaotic dynamics in
thermal convection.
4) The authors conclude: "The methods used by Egolf et al should
apply to many other forms of chaos in spatially extended systems
(physical, chemical, and biological) for which reliable model
equations are available, so that the key processes leading to
the complex dynamics can be identified. Applications to areas as
diverse as cardiology and atmospheric dynamics might be expected
eventually. Moreover, it is not unreasonable to imagine that
insight into the processes leading to unpredictability will also
lead to progress in modifying or controlling the dynamics of
these systems."
Nature 13 Apr 2000 404:710
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