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ScienceWeek
SCIENCE-WEEK - November 30, 2001 -- Vol. 5 Number 48
An Email Research Digest Published Weekly Since 1997
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Who ever heard a theologian preface his creed,
or a politician conclude his speech with an
estimate of the probable error of his opinion?
-- Bertrand Russell (1872-1970)
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Section 1
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Contents of this Issue (Full reports in Section 2):
1. On Control of Octopus Arms
2. Evolution, Viruses, and Cell-Surface Receptors
3. On Aquaporin Water Channels in Membranes
4. On the Microbiome
5. On Self-Organization of Motors and Microtubules
6. Ecology and Social Network Analysis
7. A Sperm Ion Channel Required for Sperm Motility
8. On Catastrophic Shifts in Ecosystems
9. Problems in NMR Spectroscopy of Biological Macromolecules
10. Behavior of Water in Thin Films
11. On the Moons of Jupiter
12. Plasma Jets in Active Galactic Nuclei
13. PostDoctoral Fellowships Profile: Laboratory of Sampath
Parthasarathy at Emory University, US
14. In Focus: On Russian Science and Bioterrorism
15. From PRAXIS: Bt Corn: Current Risk Assessment
16. This Week in PRAXIS
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Section 2
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1. ON CONTROL OF OCTOPUS ARMS
G. Sumbre et al (Hebrew University Jerusalem, IL) discuss octopus
arm control. The octopus arm can move in any direction, using a
virtually infinite number of degrees of freedom. This high
maneuverability results from the fact that the octopus arm is
almost entirely constructed of densely packed muscle fibers along
its transverse, longitudinal, and oblique axes. The flexible arms
are controlled by an elaborate peripheral nervous system
containing approximately 5 x 10^(7) neurons distributed along
each arm. Only approximately 4 x 10^(5) of these neurons are the
motor neurons which innervate the intrinsic muscles of the arm
and locally control muscle action. This peripheral nervous system
is organized as an axial nerve cord composed of approximately 300
interconnected clusters of nerve cell bodies (ganglia) and two
cerebrobrachial axonal tracts of approximately 30,000 nerve
fibers running dorsally to the ganglia. The axons in the tracts
carry sensory and motor information to and from the highly
developed centralized brain. The authors demonstrate that octopus
arm extensions can be evoked mechanically or electrically in arms
whose connection with the brain has been severed. These
extensions exhibit kinematic features that are almost identical
to normal behavior, which suggests that the basic motor program
for voluntary movement is embedded within the neural circuitry of
the arm itself. The authors suggest that such peripheral motor
programs represent considerable simplification in the motor
control of this highly redundant appendage.
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Science 2001 293:1845
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2. EVOLUTION, VIRUSES, AND CELL-SURFACE RECEPTORS
E. Baranowski et al (Autonomous University of Madrid, ES) discuss
viruses and cell surface receptors. Ever since the first evidence
that animal viruses and bacterial viruses enter cells through
specific receptors, considerable effort has been devoted to the
identification of those structures that mediate cell recognition
by viruses and the transfer of their genetic material into cells.
The picture of how viruses exploit cell-surface macromolecules to
initiate their infectious cycles has become increasingly complex,
with evidence that receptors used by viruses belong to widely
different families of proteins, carbohydrates, or lipids, often
in complex cell surface matrix structures. Some of these
receptors are involved in immune modulation, signaling pathways,
and cell adhesion, but others have no known function. A survey of
different virus groups demonstrates that receptor usage does not
generally show any obvious correlation with apparent virus
phylogeny. The evolution of receptor specificity by viruses has
several implications for viral pathogenesis, host range, virus-
mediated gene targeting, and viral adaptation after ordinary
organ transplantation and cross-species transplantation
(xenotransplantation), as well as for the emergence of viral
diseases. Recent evidence suggests that minimal changes in viral
genomes may trigger a shift in receptor usage for virus entry,
even into the same cell type. A capacity to exploit alternative
entry pathways may reflect the ancient evolutionary origins of
viruses and a possible role as agents of *horizontal gene
transfers among cells.
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Science 2001 292:1102
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... ... *horizontal gene transfers: Biologists recognize two
types of gene transfer from one organism to another: vertical and
horizontal. Vertical gene transfer occurs between parents and
offspring, and horizontal gene transfer is the transfer that may
occur between organisms otherwise. It is in bacteria that
horizontal gene transfer has been studied most extensively,
particularly in the last decade. Three types of horizontal gene
transfer are known: conjugation, transduction, and
transformation. Conjugation is a type of sexual reproduction
exhibited by some bacteria, the process involving the exchange of
genetic material by means of a tube or bridge, the transfer of
DNA occurring either in one direction or in both directions.
Transduction involves the transfer of genetic material from one
bacterium to another with the intermediation of a virus.
Essentially, when the virus infects one bacterium, it often
carries away pieces of that bacterium's genome, and those pieces,
upon the infection of a new bacterium, become incorporated into
the second bacterial genome. Finally, transformation is the
process involving the uptake or incorporation of DNA fragments
(plasmids) by a bacterium, first observed in 1944 by Oswald
Avery.
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3. ON AQUAPORIN WATER CHANNELS IN MEMBRANES
P. Pohl et al (Institute of Molecular Pharmacology Berlin, DE)
discuss aquaporins. Water is the major component of all
biological fluids, and the transport of water across cell
membranes is fundamental to life. In order to withstand varying
environmental and physiological stresses, all organisms must be
able to absorb water, release water, and redistribute water
between tissues with remarkable speed and precision. At the same
time, the transport of water across cell membranes must be
sufficiently selective to prevent the movement of other solutes,
ions, and even protons. The discovery of aquaporin water channels
in 1992 provided a molecular explanation for these cellular
processes. Multiple homologous proteins were soon identified, and
their importance throughout nature is reflected by the existence
of aquaporins in diverse life forms, including vertebrates,
invertebrates, microbials, and plants. Although the aquaporin
AQP1 was found to be selectively permeable to water, other
members of the aquaporin protein family subsequently were found
to have somewhat broader permeability. Thus, the mammalian
aquaporins include a subset of proteins highly selective water
("orthodox aquaporins") and a subset permeable by water plus
glycerol ("aquaglyceroporins"). The authors provide experimental
evidence that an orthodox aquaporin (AqpZ) is permeated by water
but not by charged ions, and they suggest this should permit
direct analyses of proposed electrogenic properties of other
aquaporins.
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Proc. Nat. Acad. Sci. 2001 98:9624
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4. ON THE MICROBIOME
L.V. Hooper and J.I. Gordon (Washington University St. Louis, US)
discuss host-bacterial relationships. From birth to death, humans
are colonized by a vast, complex, and dynamic consortium of
microorganisms that may outnumber the total number of our own
cells. The Nobel laureate Joshua Lederberg has suggested using
the term "microbiome" to describe the collective genome of our
indigenous microbes (microflora), the idea being that a
comprehensive genetic view of the species Homo sapiens as a life-
form should include the genes in our microbiome. Bacteria have
inhabited Earth for at least 2.5 billion years, and as a result,
our evolutionary predecessors have had to adapt to a biosphere
dominated by microbes. However, we have minimal knowledge of how
coevolution with indigenous microorganisms has shaped our genome
and our microbiome as well as our physiology and postnatal
development. For example, the human genome encodes 223 proteins
with significant homology to bacterial but not to eukaryotic
proteins, suggesting that these 223 proteins were acquired
through horizontal transfer of bacterial genes. One potential
outcome of the adaptive coevolution of humans and bacteria is the
development of *commensal relationships, where neither partner is
harmed, or symbiotic relationships, where unique metabolic traits
or other benefits are provided. Our gastrointestinal tract is
colonized by a vast community of symbionts and commensals that
have important effects on immune function, nutrient processing,
and a broad range of other host activities, and the current
genomic revolution offers an unprecedented opportunity to
identify the molecular foundations of these relationships.
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Science 2001 292:1115
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Notes:
... ... *commensal: In general, the term "commensal" refers to a
type of symbiosis in which one party derives benefit while the
other party suffers little or no disadvantage.
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Related Background:
EPIDEMIOLOGY: BACTERIAL POPULATION GENETICS AND DISEASE
Bacteria are classified as "prokaryotes", and the primary
distinguishing characteristics of prokaryotes are their
relatively small size, on the order of 1 micron in diameter, and
the absence of a nuclear membrane. The DNA of almost all bacteria
consists of a circular molecule with a length of approximately 1
millimeter, this comprising the so-called prokaryote
"chromosome". The specialized region of a bacterium that contains
the DNA is called the "nucleoid, and it can be observed with
electron microscopy. Thus, it is not true that subcellular
differentiation, clearly demarcated by membranes in eukaryotes,
is lacking in prokaryotes. Indeed, some prokaryotes form
membrane-bound subcellular structures with specialized function,
e.g., chromophores of photosynthetic bacteria. However, such
prokaryotic structures differ from eukaryotic counterparts in
that the membranes in prokaryotes that surround specialized
regions are extensions of the cell membrane and not separate
membrane entities.
Another distinguishing characteristic of prokaryotes is
their ability to exchange small packets of genetic information.
In many cases, this genetic information is carried on "plasmids",
small and specialized genetic elements that are capable of
replication within at least one prokaryotic cell line. In some
cases, plasmids may be transferred from one cell to another, thus
carrying sets of specialized genetic information through a
bacterial population. Some plasmids have a broad host range that
allows them to convey sets of genes to diverse organisms. Of
particular concern are drug-resistance plasmids that may render
diverse bacteria resistant to antibiotics.
The single circle comprising the bacterial chromosome
contains approximately 4 million base pairs of DNA. Plasmid base
pairs range in number from a few thousand to 100,000. The DNA
genome entities (chromosome and plasmid) that contain genetic
information necessary for their own replication are called
"replicons".
Many bacterial species exhibit a type of association with
large eukaryote species called "commensalism". In such an
association the "commensal" (the bacterium) gains some benefit
(e.g., surplus food), while the other party (the host) suffers no
serious disadvantage. In "mutualism", members of two different
species benefit and neither suffers disadvantage. In
"parasitism", one party gains considerably at the other party's
expense. Certain species of bacteria resident in the human
gastrointestinal tract are examples of mutualism. Other bacterial
species, in the gastrointestinal tract and elsewhere (e.g., in
the nostrils) are examples of commensalism. Many disease states
involve an altered virulence of bacteria once translocated from
the part of the body they normally occupy to some other part. For
example, ordinarily harmless human gastrointestinal bacteria
(e.g., Escherichia coli) transferred from the gastrointestinal
tract to an open wound and/or the blood system can cause serious
infection. In other cases, bacteria that are ordinarily involved
in commensalism or mutualism may undergo mutation into a virulent
strain.
In general, the term "population genetics" refers to the
study of the genetic composition of populations, with one
approach the estimation of gene frequencies and detection of the
selective influences that determine these gene frequencies in
natural populations. A good deal of the work in this field
involves the construction of mathematical models of the influence
of various factors (e.g., selection, population size, mutation)
upon the fixation and loss of linked and unlinked genes.
... ... Marc Lipsitch (Harvard University, US) presents a
commentary on current research in bacterial population genetics
and disease, the author making the following points:
1) The author poses the question: What makes a successful
pathogen? Genetic studies have addressed this question by
focusing on the mechanisms by which pathogens cause disease
(pathogenesis), i.e., how pathogens infect hosts, evade the host
immune system, secrete toxins, and interrupt and co-opt host
signaling pathways. Evolutionary theory suggests that microbes
evolve to a level of virulence that maximizes their transmission
from one host to another. This requires that microbes balance the
benefit of achieving high numbers with the risk of killing or
incapacitating the host and thereby reducing the length of time
available for transmission.
2) The author suggests that although useful in analysis of
some pathogens, this explanation is hard to reconcile with the
life-styles of those infectious agents, particularly commensal
bacteria, that appear to thrive by colonizing their hosts without
producing host disease symptoms, and yet cause severe disease
when they breach the normal barriers of the host and enter the
bloodstream. Commensal bacteria include a diverse range of
microbes that are carried in the gastrointestinal tract, nose, or
throat, or on the skin of their human hosts. These organisms
colonize their hosts without causing symptoms, with symptom-
producing infection a rare, often accidental, and probably "dead-
end" event. How do the genetically and biochemically complex
factors that produce virulence contribute to the evolutionary
success of commensal bacteria?
3) The author suggests that epidemiologists and other
researchers who study how microbes cause disease have been
skeptical about the relevance of evolutionary biology and
population genetics to their disciplines. However, this is
beginning to change as researchers recognize the importance of
pathogen population structure for understanding antimicrobial
resistance, interactions between pathogens and the immune system,
identifying candidate antigens for vaccines, and predicting and
assessing the effectiveness of vaccination programs. Recent work
demonstrates that studies of the population genetics of an
infectious agent can generate hypotheses about microbial
pathogenesis that are both new and experimentally testable.
Recent work also demonstrates that a complete understanding of
the epidemiology and transmission of infectious disease depends
on a clear picture of the population genetics of the causative
organism.
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Science 2001 292:59
ScienceWeek 2001 18 May
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5. ON SELF-ORGANIZATION OF MOTORS AND MICROTUBULES
T. Surrey et al (European Molecular Biology Laboratory
Heidelberg, DE) discuss self-organization in biological cells. A
central question in biology concerns the origin of complex
macroscopic structures. Two fundamentally different mechanisms
can account for the generation of large-scale structures from
random mixtures of small molecules. One mechanism is self-
assembly near thermodynamic equilibrium. A very different
mechanism is self-organization in energy-dissipating systems.
Although they do not reach thermodynamic equilibrium, these
latter systems can reach steady states, with kinetic parameters
influencing or determining the final structures. In eukaryotic
cells, microtubules and their associated motor proteins can be
organized into various large-scale patterns. Using a simplified
experimental system (microtubules and soluble motor complexes)
combined with computer simulations, the authors examined how the
concentrations and kinetic parameters of the motors contribute to
their collective behavior. The authors report they observed self-
organization of generic steady-state structures such as asters,
vortices, and a network of interconnected poles, and that they
identified parameter combinations that determine the generation
of each of these structures. The authors suggest that in general
this approach may be useful for correlating the morphogenetic
phenomena occurring in a biological system with the biophysical
characteristics of its constituents.
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Science 2001 292:1167
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Related Background:
EVIDENCE THAT MICROTUBULE SELF-ORGANIZATION IS GRAVITY DEPENDENT
The structural framework of eukaryotic cells (biological
cells with nuclei and other membrane-bound internal structures),
called the "cytoskeleton", consists of an arrangement of
macromolecular structures: microtubules, intermediate filaments,
and microfilaments. The microtubules are hollow cylinders
approximately 24 nanometers in diameter, many microns in length,
and consist of heterodimers of alpha- and beta-tubulin proteins
plus a variable set of other proteins. They form the scaffolding
of the mitotic spindle (an important structure in cell division),
organize other cytoplasmic structures, and are the structural
core of various organelles involved in cell movement (cilia and
flagella).
Beginning in the early 1960s, the work of S. Inouye provided
evidence that microtubules exist in equilibrium with free
tubulin: microtubule assembly-disassembly is regulated by factors
that influence the equilibrium between polymerized and
nonpolymerized tubulin. In the early 1970s, R. Weisenberg
demonstrated that microtubules assemble spontaneously in cell
extracts that have been warmed to 37 degrees centigrade in the
absence of calcium ions and in the presence of guanosine
triphosphate.
In general, under appropriate conditions, microtubules
spontaneously assemble when a solution containing purified
tubulin protein and guanosine triphosphate is warmed from 7
degrees centigrade to 36 degrees centigrade. In the laboratory,
following the spontaneous assembly of tubulin heterodimers into
microtubules, the microtubules further spontaneously organize
into superstructures, striped or circular macroscopic patterns
that can be detected with suitable polarization optics. These
macroscopic patterns are formed as a connected final self-
organization following tubulin polymerization into microtubules.
According to J. Taboy et al (1990), these macroscopic microtubule
patterns are evidence of a self-organizing system behaving
according to "reaction-diffusion mechanisms".
In general, in theoretical chemistry, a "reaction-diffusion
system" involves the coupling between a chemical reaction and
molecular diffusion, with the coupling modifying the rate of the
reaction. In a reaction-diffusion system, according to theory,
nonlinear dynamic processes may result in the appearance of
density fluctuations. One important aspect of such systems is
that the theoretical nonlinear equations that describe them are
not "well-behaved": solutions to the equations can be extremely
sensitive to small perturbations. For example, I. Prigogine and
his co-workers demonstrated theoretically 20 years ago that in a
reaction-diffusion system, the interaction of density
fluctuations with gravity results in a small directional
transport term in the equation describing the system, a term that
can destabilize the equilibrium state and push the system into
the formation of macroscopic patterns.
To anticipate the crux of this report, an account of an
experiment startling in its simplicity and profound in its
implications for studies of biological macromolecular structures,
there is now evidence that microtubules do not spontaneously
self-organize into macroscopic patterns in vitro in the absence
of gravity.
... ... C. Papaseit et al (3 authors at Commissariat a l'Energie
Atomique Grenoble, FR) present a study of the gravity-dependence
of microtubule self-organization, the authors making the
following points:
1) The authors point out that experiments in space have
furnished evidence that various cellular processes, such as
growth rates, signaling pathways, and gene expression are
modified when cells are placed under conditions of
weightlessness. At the present time, there is no coherent
explanation for these observations, and neither is it known which
biomolecules are involved. No cellular component has been
identified as having a sufficiently large density difference with
the surrounding medium that the force exerted on it by gravity is
larger than the forces involved with random thermal motions, and
biochemical reactions are generally considered as being
independent of gravity. But one possible mechanism by which
gravity may intervene in biochemical processes is a mechanism
theoretically apparent in reaction-diffusion systems. Reaction-
diffusion mechanisms can lead to the progressive appearance of a
macroscopically self-organized state from an initially homogenous
solution, and it has been calculated that gravity can play a
significant role in this process.
2) In the experiments of the authors, to investigate the
dependence of self-organization on gravity, microtubules were
assembled under low-gravity conditions produced during space
flight. Contrary to the samples formed on an in-flight 1 x g
centrifuge, the samples prepared in microgravity showed almost no
self-organization and were locally disordered. The experiments
were carried out during the space flight of a MAXUS sounding
rocket of the European Space Agency. The flight provided
approximately 13 minutes of low gravity [2 x 10^(-4)g] before the
payload fell back to Earth to be recovered.
3) The authors suggest the results demonstrate how a very
simple biological system, initially comprised of only tubulin and
guanosine triphosphate, is capable of behaving as a gravi-
receptor. In the present case, gravity apparently triggers the
self-organizing process, the gravity direction breaking the
symmetry of the initially homogeneous state and leading to the
emergence of form and pattern. Such processes, the authors
suggest, may have played a role in the development of life on
Earth. Other external factors, such as magnetic and electric
fields, or shearing, could have the same effect. Processes of
this type could form a general class of mechanism by which weak
environmental factors are transduced by biological systems. The
authors suggest the results presented demonstrate that gravity
substantially modifies microtubule self-organization by way of
its participation in a reaction-diffusion process. Gravity can
thus intervene in a fundamental cellular process and may
indirectly affect other cellular processes that in their turn
depend on microtubule self-organization.
4) The authors point out that in humans weightlessness
depresses the immune system, reduces bone mass, and leads to
various changes associated with aging. These and other effects
are believed to arise at a cellular level, and many experiments
point to an involvement of the intracellular cytoskeleton.
Researchers have observed modifications in cytoskeletal
organization, and recent results on human immune system cells
(lymphocyte cells) cultured in space show a disorganized
microtubule network compared with ground control experiments. The
authors suggest this observation, which is consistent with their
results, raises the possibility that reaction-diffusion processes
form an underlying mechanism for the dependence of cellular
function on gravity. The authors suggest that if this is the
case, then it would also mean that microtubule reaction-diffusion
processes occur in living cells and may lead to new insights into
the physical-chemical processes controlling the organization of
the cytoskeleton.
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Proc. Nat. Acad. Sci. 2000 97:8364
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Related Background:
EVIDENCE FOR SELF-ORGANIZATION OF CELL MICROTUBULES
Biologists who study cells with the light microscope are always
presented with a panoply of striking visible events in time, the
cell movements, particularly those inside the cell, and
especially those involved in cell division. Our understanding of
what is happening at the molecular level to produce these
movements is far from complete, but we do know much more than we
did a decade ago. Several cell "motor" protein molecules called
kinesins have been identified. The microtubules, along which the
cell motors appear to move, are thin hollow protein cylinders
found in eukaryote cells and are assembled from globular monomers
of the protein "tubulin". Asters, classical structures, are
spherical arrays of microtubules that occur during cell division.
Now F. J. Nedelec et al (Princeton University, US; E.S. Physique
et Chimie, Paris FR) report that dynamic asters can be obtained
from in vitro solutions of tubulin and cell motors, with a
variety of self-organizing structures resulting from varying
concentrations. By studying this process in the constrained
geometry of micro-fabricated glass chambers, the same final
structure can apparently be attained through different assembly
pathways.
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Nature 1997 18 Sep
ScienceWeek 1997 3 Oct
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6. ECOLOGY AND SOCIAL NETWORK ANALYSIS
S.M. McMahon et al (University of Tennessee Knoxville, US)
discuss ecology and social network analysis. For the past 30
years, a subdiscipline of the social sciences known as "social
network analysis" has developed structural models to analyze
human interactions. In social network analysis, discrete
mathematics and statistics are combined with the emerging
epistemology of complex systems to explore processes and
phenomena as diverse as the diffusion of information through an
organization, the adoption of innovations in society, and the
spread of infectious disease in a population. Researchers working
on social network analysis draw upon many disciplines: sociology,
anthropology, psychology, geography, mathematics, statistics, and
computer science. Like social network analysis, analyses of
trophic structure in ecological communities and of energy flow
and nutrient transfer through ecosystems incur the problem of how
to conceptualize and test interactions within these complex
systems. The striking similarities between social networks and
biological communities suggest that there exist constraining or
structuring forces common to both. Social and ecological networks
also share the need to reduce the elements and interactions of
the network to an order simple enough to analyze, yet complex
enough to reflect reality. In general, most of the difficult
problems modern society faces arrive in the form of complex
structures such as economies, ecosystems, and societies, and
interactions among social scientists and biologists and the
integration of their techniques and insights may prove crucial to
developing a new understanding of how these complex systems
behave.
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Science 2001 293:1604
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7. A SPERM ION CHANNEL REQUIRED FOR SPERM MOTILITY
D. Ren et al (Harvard University, US) discuss discovery of a new
sperm ion channel. Male sperm and female eggs interact
reciprocally in mammalian fertilization. To reach the site of
fertilization, sperm must travel long distances and become primed
for fertilization of the eggs through *capacitation and other
processes. Once they arrive at the surface of the egg, sperm
interact with the egg's extracellular matrix glycoproteins, which
include the *zona pellucida proteins. Sperm release acidic
material during the *acrosome reaction, a signaling event that
presumably involves the opening of calcium ion channels and the
influx of calcium ions into the sperm heads. Calcium and cyclic
nucleotides have crucial roles in mammalian fertilization, but
the molecules comprising the calcium ion-permeation pathway in
sperm motility are poorly understood. The authors describe an
apparent sperm cation channel, called "CatSper", whose amino-acid
sequence most closely resembles a single 6-transmembrane-spanning
repeat of the voltage-dependent calcium ion channel 4-repeat
structure. CatSper is located specifically in the principal piece
of the sperm tail. Targeted disruption of the gene of the CatSper
protein results in male sterility in otherwise normal mice. Sperm
motility is decreased markedly in CatSper mice, and CatSper sperm
are unable to fertilize intact eggs. In addition, the cyclic-AMP-
induced calcium ion influx is abolished in the sperm of mutant
mice. The authors suggest that CatSper is thus vital to cyclic
AMP-mediated calcium ion influx in sperm, sperm motility, and
fertilization, and that the gene represents an excellent target
for non-hormonal contraceptives for both men and women.
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Nature 2001 413:603
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Notes:
... ... *capacitation: Although sperm undergo maturation in the
testes, in humans they are unable to fertilize an oocyte until
they have been in the female reproductive tract approximately 10
hours. The term "capacitation" refers to the functional changes
that sperm undergo in the female reproductive tract that allow
the sperm to fertilize an oocyte. Among the functional changes
are permeabilization of the acrosome membrane, followed by
release of various enzymes necessary for penetration of the
oocyte.
... ... *zona pellucida: A gelatinous glycoprotein layer, one of
the layers surrounding the oocyte.
... ... *acrosome reaction: The acrosome is a dense granule at
the head of the sperm cell, the granule containing various
enzymes (hyaluronidase and proteases) that aid penetration of the
oocyte. In general, the term "acrosome reaction" refers to the
activation of sperm by egg jelly, the details of the process
varying according to species.
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8. ON CATASTROPHIC SHIFTS IN ECOSYSTEMS
M. Scheffer et al (Wageningen University, NL) discuss sudden
shifts in ecosystems. The notion that ecosystems may switch
abruptly to a contrasting alternative stable state emerged from
work on theoretical models, and although this provided an
inspiring search image for ecologists, the first experimental
examples that were proposed were criticized strongly. Indeed, it
seemed easier to demonstrate shifts between alternative stable
states in models than in the real world. In particular,
unraveling the mechanisms governing the behavior of spatially
extensive ecosystems is notoriously difficult, because it
requires the interfacing of phenomena that occur on very
different scales of space, time, and ecological organization.
Nonetheless, recent studies have provided a strong case for the
existence of alternative stability domains in various important
ecosystems. In summary, all ecosystems are exposed to gradual
changes in climate, nutrient loading, habitat fragmentation, or
biotic exploitation. Nature is usually assumed to respond to
gradual change in a smooth way. However, studies on lakes, coral
reefs, oceans, forests, and arid lands have shown that smooth
change can be interrupted by sudden drastic switches to a
contrasting state. Although diverse events can trigger such
shifts, recent studies demonstrate that a loss of resilience
usually paves the way for a switch to an alternative state. This
suggests that strategies for sustainable management of such
ecosystems should focus on maintaining resilience.
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Nature 2001 413:591
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9. PROBLEMS IN NMR SPECTROSCOPY OF BIOLOGICAL MACROMOLECULES
Z. Serber et al (University of California San Francisco, US)
discuss problems in current NMR spectroscopy techniques applied
to biological macromolecules. Of all the methods currently
available for obtaining high resolution structures of biological
macromolecules, nuclear magnetic resonance (NMR) is the only
method that can provide this information in solution under near-
physiological conditions. However, NMR structures are still
determined in vitro, and often buffer conditions are not selected
for their closest match to the natural environment of the protein
but to optimize experimental parameters such as solubility and
sensitivity or to minimize NMR buffer signals that could
interfere with measurements. A recent survey of buffer conditions
used for NMR structure determinations demonstrated that 27
percent of all structures were determined in unbuffered (or auto-
buffered) solutions, 50 percent in phosphate buffer, 10 percent
in acetate buffer, and 9 percent in TRIS buffer. Depending on the
natural host cell and the exact cellular compartment, these NMR
buffer conditions can be substantially different from the natural
environment of a protein and may influence its structure and
dynamics. Furthermore, interactions with other cellular
macromolecules and post-translational modifications can alter the
conformation of the protein. The authors demonstrate that NMR
observation of the conformations and dynamics of proteins in the
bacterial cytoplasm is possible, making NMR a new high-resolution
tool for studying proteins in vivo.
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J. Am. Chem. Soc. 2001 123:8895
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10. BEHAVIOR OF WATER IN THIN FILMS
U. Raviv et al (Weizmann Institute of Science, IL) discuss the
fluidity of water confined to subnanometer films. The fluidity of
water in confined geometries is relevant to processes ranging
from tribology to protein folding, and the molecular mobility of
water in pores and slits has been extensively studied using a
variety of approaches. Studies in which liquid flow is measured
directly suggest that the viscosity of aqueous electrolytes
confined to films of thickness greater than approximately 2 to 3
nanometers remains close to that in the bulk, and this behavior
is similar to that of non-associative organic liquids confined to
films thicker than approximately 7 to 8 molecular layers. The
authors report they observe that the effective viscosity of water
remains within a factor of 3 of its bulk value, even when it is
confined to films in the thickness range (3.5 +- 1) to (0.0 +-
0.4) nanometers. This contrasts markedly with the behavior of
organic solvents, whose viscosity diverges when confined to films
thinner than approximately 5 to 8 molecular layers. The authors
attribute this difference to the fundamentally different
mechanisms of solidification in the two cases. For non-
associative liquids, confinement promotes solidification by
suppressing translational freedom of the molecules. However, in
the case of water, confinement seems primarily to suppress the
formation of the highly directional hydrogen-bonded networks
associated with freezing.
-----------
Nature 2001 413:51
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
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Related Background:
PHYSICAL CHEMISTRY: A NEW MODEL OF LIQUID WATER
A prominent consideration in the minds of biologists who
work at the level of cells and molecules is that water is the
most prevalent chemical substance in all biological systems, and
that interactions of water with other biological molecules,
particularly with biological macromolecules, are not clearly
defined but are probably of considerable significance.
Of importance in understanding the role of water, not only
in biological interactions, but also in all solute-solute
interactions in aqueous systems, is the unique structure of water
produced by the short-term and long-term interactions of water
molecules with other water molecules, these interactions caused
primarily by a) hydrogen bonding, and b) polar interactions due
to electrostatic asymmetry.
Contemporary "molecular dynamics simulations", which are
extrapolations of statistical mechanics and which originate in
the work of Alder and Wainright in the 1960s, are computer
simulations of molecular systems typically involving hundreds or
sometimes thousands of idealized particles interacting with
physically realistic potentials. Such molecular dynamics
simulations can provide time-dependent properties of a liquid,
but most commonly they are used to produce a set of
configurations and forces which can be averaged to give
equilibrium properties of the system.
... ... J. Higo et al (5 authors at 2 installations, JP) present
a new model of liquid water, the authors making the following
points:
1) The authors point out that in order to understand the
dynamics of solute molecules and biomolecules functioning in
aqueous solutions, it is important to describe the cooperative
motions of solvent water molecules. Although molecular dynamics
analyses have focused on the statistical laws of motions of water
molecules, and on the collective dynamics of hydrogen-bond
network rearrangements, a clear theoretical picture of these
complex motions has not yet been obtained.
2) The authors point out that the study of the structure and
dynamics of the liquid state must involve both cooperative
motions of molecules and random motions of individual molecules.
Cooperativity of motions of water molecules is manifested in the
observed correlation between orientations of neighboring
molecules. On the other hand, each water molecule rapidly
translates and rotates with a 5 to 10 picosecond timescale, which
produces rapid randomization of orientations.
3) The authors propose a framework to describe the two
aspects of water molecule behavior in a unified way, the
framework involving the introduction of a new quantity, "site-
dipole field". The "site dipole" is defined at each spatial
position by the averaged orientation of water molecules that pass
through that position. Although each water molecule randomly
moves and quickly passes through each spatial site, it is
expected that the site-dipole field shows a coherent pattern
because of cooperativity among water molecules. Such coherent
patterns in bulk water should be perturbed by the presence of
solute molecules and give rise to a characteristic site-dipole
structure around solute molecules. The authors demonstrate that
such coherent patterns indeed exist and that the structural
ordering of site dipoles provides a perspective for the
understanding of hydration of biomolecules.
4) The authors report their simulations reveal the presence
of large vortex-like structures of more than 10 angstroms in
size, with such coherent patterns persisting more than 300
picoseconds, although the orientational memory of individual
molecules is quickly lost. A 1 nanosecond molecular dynamics
simulation of systems consisting of two amino acids shows that
the fluctuations of site-dipole field of solvent are pinned
around the amino acids, resulting in a stable dipole bridge
between side chains of amino acids. The dipole bridge forms even
for a side-chain separation of 14 angstroms, which corresponds to
5 layers of water molecules. The formation of the dipole bridge
is sensitive to the side-chain orientations, and thereby suggests
an explanation for specificity in solvent-mediated interactions
between biomolecules.
-----------
Proc. Nat. Acad. Sci. 2001 98:5961
SW 2001 13 Jul
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
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Related Background:
PHYSICAL CHEMISTRY: ON THE STRUCTURE OF WATER
Water is the most abundant compound on the surface of the
Earth and the principle constituent of all living organisms. The
oceans alone contain 1.4 x 10^(24) grams, or approximately 3.2 x
10^(7) cubic miles of water. Another 0.8 x 10^(24) grams of water
is held within the rocks of the Earth's crust in the form of
water of hydration. The human body is approximately 65 percent
water by weight, with some tissues (e.g., brain and lung)
composed of nearly 80 percent water.
The experiments of Henry Cavendish (1731-1810) and Antoine
Lavoisier (1743-1794) in the 1780s established that water is
composed of hydrogen and oxygen. Although the careful data of
Cavendish was sufficient to prove that two volumes of hydrogen
combine with one volume of oxygen, he did not point this out, and
it was left to Joseph-Louis Gay-Lussac (1778-1850) and Friedrich
Humboldt (1769-1859) to make this discovery in 1805. In 1842,
Jean Dumas (1800-1884) found that the ratio of the combining
weights of hydrogen and oxygen in water is very nearly 2 to 16.
Although water is the most familiar of liquids, it is also a
liquid of peculiar properties. Perhaps the best-known peculiarity
of water is its density maximum at 4 degrees centigrade (at
atmospheric pressure); cooling or heating water from this
temperature reduces its density. An equally striking anomaly is
that as the density of water is increased, water molecules
diffuse more rapidly, but only up to a point known as the
"diffusivity maximum". At higher densities, the diffusivity
decreases with increasing density, similar to what is observed
with normal liquids.
... ... J.R. Errington and P.G. Debenedetti (Princeton
University, US) present a report on the relationship between the
structure of liquid water and its anomalies, the authors making
the following points:
1) The authors point out that in contrast to crystalline
solids, for which a precise framework exists for describing
structure, quantifying structural order in liquids and *glasses
has proved more difficult because even though such systems
possess *short-range order, they lack *long-range crystalline
order. Some progress has been made using model systems of hard
spheres, but it remains difficult to describe accurately liquids
such as water, where directional attractions (hydrogen bonds)
combine with short-range repulsions to determine the relative
orientation of neighboring molecules as well as their
instantaneous separation. This difficulty is particularly
relevant when discussing the anomalous kinetic and thermodynamic
properties of water, which have long been interpreted
qualitatively in terms of underlying structural causes.
2) The authors introduce two measures of order in water: a)
the "translational order parameter" measures the tendency of
pairs of molecules to adopt preferential separations; this
parameter vanishes for an ideal gas, and is large for a crystal.
b) the "orientational order parameter" measures the extent to
which a molecule and its four nearest neighbors adopt a
tetrahedral arrangement, such as exists in hexagonal ice; this
parameter vanishes for an ideal gas, and equals 1 in a perfectly
tetrahedral arrangement.
3) The authors report they have attempted to gain a
quantitative understanding of the structure-property
relationships of water through the study of translational and
orientational order in a model of water. Using *molecular
dynamics simulations, they identify a structurally anomalous
region -- bounded by loci of maximum orientational order (at low
densities) and minimum translational order (at high densities) --
in which order decreases on compression, and where orientational
and translational order are strongly coupled. This region
encloses the entire range of temperature and densities for which
the anomalous diffusivity and thermal expansion coefficient of
water are observed, and enables a quantification of the degree of
structural order required for these anomalies to occur. The
authors also find that these structural, kinetic, and
thermodynamic anomalies constitute a cascade: they occur
consecutively as the degree of order is increased.
4) The authors summarize: "The physical picture that emerges
from this work is the following: In liquid water there occurs a
cascade of anomalies. Structural anomalies, whereby order
decreases upon compression, occur over the broadest range of
densities and temperatures. Diffusive anomalies, whereby the
diffusion coefficient of water increases by compression, occur
entirely inside the region of structural anomalies. Thermodynamic
anomalies, whereby the density decreases upon cooling at constant
pressure, occur entirely inside the region of diffusive
anomalies. All anomalous states share the topological property
that orientational and translational order are strongly coupled."
... ... In a commentary on this work, Srikanth Sastry (Jawaharlal
Nehru Center for Advanced Scientific Research Bangalore, IN)
states: "Errington and Debenedetti's observations raise
interesting questions and open a new line of investigation. The
characterization of structural anomaly in terms of the strong
coupling between translational order and orientational order may
help to identify precise conditions necessary for anomalous
behavior. But at present it isn't clear why this observed
relationship and the nested pattern of structural, dynamic, and
thermodynamic anomalies hold, and whether we should expect to
find them in other liquids as well."
-----------
Nature 2001 409:300,318
-----------
Notes:
... ... *glasses: In this context, the term "glass" refers to an
amorphous solid whose atoms form a random network.
... ... *short-range order: A solid is crystalline if it has
long-range order: once the positions of an atom and its neighbors
are known at one point, the place of each atom is known precisely
throughout the crystal. Most liquids lack long-range order,
although many liquids have short-range order. In this context,
"short range" is defined as the first- or second-nearest
neighbors of a water molecule. However, at distances many
molecules away, the positions of the molecules become
uncorrelated. Fluids such as water have short-range order but
lack long-range order.
... ... *long-range crystalline order: See previous note.
... ... *molecular dynamics simulations: This study was based on
constant temperature and density molecular dynamics simulations
of 256 interacting particles.
-----------
ScienceWeek 2001 9 Feb
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
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Related Background:
ON WATER AND THE STRUCTURES OF BIOLOGICAL MOLECULES
... ... M. Gerstein and M. Levitt present a review of some
aspects of the physical chemistry of water and an account of
their own computer simulations of biological macromolecules in
aqueous solutions. The authors make the following points: 1) At
the present time it is possible to model proteins and their
associated water molecules on a desktop computer in a few days.
Researchers have now simulated the aqueous structures of more
than 50 proteins and nucleic acids. 2) A single water molecule
has an essentially tetrahedral geometry, with an oxygen atom at
the center of the tetrahedron, hydrogen atoms at 2 of the 4
corners, and clouds of negative charges at the other 2 corners.
Reflecting the tetrahedral geometry of water, each molecule in
liquid water often forms 4 hydrogen bonds: 2 hydrogen bonds
between its hydrogens and the oxygen atoms of 2 other water
molecules, and 2 hydrogen bonds between its oxygen atom and the
hydrogens of other water molecules. The necessity of maintaining
a tetrahedral hydrogen-bonded structure gives water an "open"
loosely packed structure compared with that of most other liquids
[*Note #1]. 3) Present computer simulations are able to reproduce
quantitatively many of the bulk properties of water, such as its
average structure, rate of diffusion, and *heat of vaporization.
4) Biological molecules such as proteins and DNA contain both
hydrophilic and hydrophobic parts arranged in long chains. The 3-
dimensional structures of these molecules are determined by the
way these chains fold into more compact arrangements in which
hydrophilic groups are on the surface where they can interact
with water and hydrophobic groups are buried in the interior away
from water. These local macromolecule solubility considerations
were formulated in 1959 by Walter Kauzman as a "hydrophobic
effect" crucial for protein folding. 4) There are 3 types of
water molecules that must be considered in a computer model of a
biological molecule in aqueous solution: a) the ordered water
surrounding and strongly interacting with the macromolecule; b)
the bulk water beyond the ordered water; and, c) any water
molecules that may be buried within the macromolecule. 5)
Computer simulations of DNA in water have revealed that water
molecules are able to interact with nearly every part of the
double helix of DNA, including the nucleotide base pairs that
constitute the genetic code. In contrast, water is not able to
penetrate deeply into the structure of proteins, whose
hydrophobic regions are arranged on the inside into a close-
fitting core [*Note #2].
-----------
Scientific American 1998 November
-----------
Notes:
... ... *Note #1: In hydrated crystal structures, water molecules
generally donate two hydrogen bonds but may accept either one or
two. When water molecules are 3-coordinated (rather than 4-
coordinated as discussed by the authors in their review), the
geometry can be planar or pyramidal. But examples are known of
coordination as low as 2 and as large as 7.
... ... *heat of vaporization: The quantity of energy required to
evaporate 1 mole (or a unit mass) of a liquid at constant
pressure and temperature.
... ... *Note #2: Concerning the interaction of water molecules
with biological molecules, water molecules hydrogen-bonded to the
functional groups of biological molecules are apparently linked
in chains into extended networks, and some researchers have
suggested the *polarizability of these networks provides a
mechanism for long-range recognition between biological molecules
in aqueous solution.
... ... *polarizability: The electric dipole moment induced in a
system (such as an atom or molecule) by an electric field of unit
strength.
-----------
ScienceWeek 2001 13 Nov
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
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11. ON THE MOONS OF JUPITER
David J. Stevenson (California Institute of Technology, US)
discusses Jupiter and its moons. There are many similarities
between the Jovian system (Jupiter plus its moons) and our Solar
System. Both systems are extremely regular. Bodies orbit in a
nearly common plane -- Jupiter's equatorial plane for the
Galilean satellites (the moons discovered by Galileo: Io, Europa,
Ganymede, and Callisto), and the Sun's ecliptic plane for the
Solar System. In both cases, bodies orbit in a prograde sense
(anti-clockwise when viewed from above), with orbits spaced in
approximate geometric progression. The total mass of Jupiter's
satellites is approximately the same as that of Mars and probably
approximately 1 percent of the heavy-element mass (everything
except hydrogen and helium) inside Jupiter. This is a similar
ratio to the heavy-element distribution in our Solar System,
where the Sun contains approximately 10 Jupiter masses and the
planetary system tens of Earth masses of heavy elements. Yet
there are also striking differences between the Jovian system and
the Solar System. The Solar System is spread out relative to the
size of the Sun, with even the Sun-hugging Earth over 200 solar
radii away, whereas the most distant Galilean satellite,
Callisto, is less than 30 Jupiter radii from Jupiter. The
compactness of the Jupiter system undoubtedly arises from the
limited size of the region in which Jupiter is gravitationally
dominant over the Sun.
-----------
Science 2001 294:72
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12. PLASMA JETS IN ACTIVE GALACTIC NUCLEI
A.P. Lobanov and J.A. Zensus (Max Planck Institute for Radio
Astronomy Bonn, DE) discuss plasma jets in active galactic
nuclei. One of the most intriguing features observed in active
galactic nuclei is highly collimated and relativistic plasma
outflows (jets) that originate in the immediate vicinity of the
center of activity and propagate at distances of up to several
megaparsecs (1 parsec = 3.26 light years). Observations of jets
in active galactic nuclei probe the behavior of extremely
relativistic matter in the Universe and provide a unique and
remote "laboratory" for studying the most powerful cosmic
phenomena such as supermassive black holes and extragalactic
accretion disks. The quasar 3C273 is one of the closest and most
luminous and best studied active galactic nuclei, with a
prominent relativistic outflow observed in the x-ray, optical,
and radio wave bands. The relativistic jet observed in this
quasar is one-sided, with no signs of emission on the counterjet
side at dynamic ranges of up to 16,000:1. This is evidence for
strong relativistic boosting in an intrinsically double-sided
outflow powered by an accretion disk around a black hole. The
enhanced emission features (jet components) identified in the jet
on scales of up to approximately 20 milli-arc seconds are moving
at apparent speeds exceeding the speed of light by factors of 5
to 8. These jet components may result from the flares observed in
this quasar in the optical and radio wavelengths and also reflect
the precession of the jet axis. The structure and kinematics of
such outflows are typically explained in terms of shock waves and
Kelvin-Helmholtz instability.
-----------
Science 2001 294:128
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
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Related Background:
ACTIVE GALACTIC NUCLEI
Some galaxies are known to have very "active" central regions
from which enormous amounts of energy are emitted each second,
and it is believed that these "active galactic nuclei" are
probably powered by accretion of matter into a supermassive black
hole of 10^(6) to 10^(9) solar-masses. Astronomers have recently
discovered that many active galactic nuclei eject clouds of
ionized gas with velocities of up to 10 percent of the speed of
light over a wide range of angles, in contrast to the previously
known collimated jets. These mass outflows are considered to be
intriguing because they provide information about the dynamical
forces (such as radiation and wind pressure) near an active
supermassive black hole. D. Michael Crenshaw points out that a
greater understanding of mass outflow from active galactic nuclei
will come through comparison between observations and dynamical
models, which have grown in sophistication over the past few
years. "It also remains to be shown how matter reaches the active
nucleus in order to fuel the central engine. The UV and x-ray
observations have found no evidence for infalling matter."
-----------
Science 2001 292:1500
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
-------------------
Related Background:
ON ACTIVE GALACTIC NUCLEI
The term "active galactic nucleus" refers to the central regions
of certain galaxies, regions in which considerable energy is
generated by processes apparently other than those operating in
ordinary stars. It is currently believed the energy may result
from the accretion of material onto a massive *black hole
situated at the core of the galaxy. ... ... Andrew C. Fabian
(Cambridge University, UK) presents a short account of current
views in this field, the author making the following points:
1) Active galactic nuclei involve the most powerful steady
sources of luminosity in the Universe. They range from the nuclei
of some nearby galaxies emitting approximately 10^(40) *erg/sec
to distant *quasars emitting more than 10^(47) erg/sec. The
emission is spread widely across the electromagnetic spectrum,
often peaking in the ultraviolet, but with significant luminosity
in the x-ray and infrared bands. The emission is spatially
unresolved except in the radio band, where there is sometimes
evidence for collimated outflows at *relativistic speeds. The
power output of active galactic nuclei are often variable on time
scales of years and sometimes on time scales of days, hours, or
even minutes.
2) An upper limit to the dimensions of active galactic
nuclei can be estimated from theoretical considerations. The
principle of causality (in general, in this context, that an
effect cannot precede its cause) implies that the variation
period of an object whose radiation emission varies in time must
be greater than the time for light to cross that object. Observed
emission variability, therefore, provides an upper bound to the
diameter of an active galactic nucleus.
3) High luminosities imply high masses whose gravity can
combat the radiation pressure that would otherwise blow the
object apart (in other words, the luminosity must be less than
the *Eddington limit). Active galactic nuclei therefore are of
very high mass density, and considering their apparent relatively
small dimensions and high mass density, it has long been assumed
that each active galactic nucleus consists of a massive black
hole, of approximately 10^(8) solar-mass or more, the black-hole
mass accreting gas and dust at the center of the galaxy. The
gravitational energy liberated during accretion onto a black hole
is estimated to be approximately 10 percent of the rest mass
energy of that accreting matter, and is the most efficient mass-
energy conversion process known involving normal matter. The
efficiency is at least an order of magnitude greater than that of
stellar nuclear burning, which releases at most 0.7 percent of
mass-energy.
3) The current view is that the accreting matter of the
black hole of an active galactic nucleus probably has some
angular momentum, which causes the accreting matter to orbit the
black hole and, through dissipation of energy, flatten to form a
disk within which *magnetic viscosity transfers the angular
momentum outward and the mass inward. Unless the accretion rate
is either high or very low, it is likely that the gravitational
energy liberated is radiated locally, much of it as thermal
radiation from the surface of the disk, peaking in the UV as
expected. Some energy, however, is probably stored temporarily in
magnetic fields before being released in flares, which make the
x-ray emission particularly variable.
-----------
Proc. Nat. Acad. Sci. 1999 96:4749
-----------
Notes:
... ... *black hole: If the terminal stages of star death leave a
remnant star mass greater than 3 solar masses, the ultimate
gravitational collapse will produce a *black hole, a relativistic
singularity. A black hole is a localized region of space from
which neither matter nor radiation can escape. The "trapping"
occurs because the requisite escape velocity, which can be
calculated from the relevant equations, exceeds the velocity of
light and is therefore unattainable. Another view of a black hole
is that it is a mass that has collapsed to such a small volume
that its gravity prevents the escape of all radiation. Space and
time essentially have no meaning in a black hole. The boundary of
the black hole is called the "event horizon", because any event
within the boundary is invisible outside, the invisibility
resulting from the fact that no radiation can escape to be
detected. The radius of the black hole depends upon how much
matter has fallen into the region; it is called the "Schwarzchild
radius", and it is usually a few kilometers. However, massive
black holes are possible and, in addition to providing the
engines for active galactic nuclei, as described above, are also
thought to be the source of quasars (quasi-stellar objects),
which are extremely luminous sources radiating energy over the
entire spectrum from x-rays to radio waves, and which are
apparently the oldest and most distant objects in the universe.
If quasars indeed involve black holes, the radiation is from
material just outside the black hole, and not from anything
within it. Nothing inside a black hole can get out of it.
... ... *erg: The work done by a force of 1 dyne acting through a
distance of 1 centimeter. 1 joule = 10^(7) erg. 1 kilocal = 4.2 x
10^(10) erg.
... ... *quasars: (quasi-stellar objects) Extremely luminous
sources radiating energy over the entire spectrum from x-rays to
radio waves, and which are apparently among oldest and most
distant objects in the universe.
... ... *relativistic speeds: In general, speeds approaching the
speed of light. At such velocities, the mass of an object becomes
significantly greater than its rest mass.
... ... *Eddington limit: The theoretical upper limit to the
luminosity of a star of given mass, at which limit the outward
force of radiation just balances the inward force of gravity.
Stars with a greater luminosity would be blown apart by their own
radiation. Named after A.S. Eddington (1882-1944).
... ... *magnetic viscosity: In this context (plasma physics),
the term "magnetic viscosity" refers to an effect, possessed by a
magnetic field in the absence of sizable mechanical forces or
electric fields, of damping motions of a conducting fluid
perpendicular to the field, the effect similar to the effect of
ordinary viscosity. (The "conducting fluid" in this context is
the "plasma" of ionized gases.)
-----------
ScienceWeek 1999 16 Jul
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13. POSTDOCTORAL FELLOWSHIPS PROFILE:
Laboratory of Sampath Parthasarathy at Emory University, US
-----------------------------------------------------------
Department: Gynecology and Obstetrics
General research areas: lipid peroxidation, antioxidants,
atherosclerosis, exercise, endometriosis, gyn/ob cancer,
fertilization, angiogenesis, redox-regulation of gene
expression, dietary oxidized lipids, nutrition of oxidized
lipids.
Head of this laboratory: Sampath Parthasarathy, PhD.
Specific research problems: dietary oxidized lipids,
endometriosis, gyn/ob cancer, exercise and atherosclerosis.
Previous research experience and degrees required: immuno-
histochemistry, basic molecular biology, cell culture.
Usual starting stipend: $28,000 and up.
Special requirements: Minorities are encouraged.
Approximate number of people currently working in this
laboratory (faculty, staff, students, postdocs): 15, consisting
of postdocs from 7 different countries.
Contact for more information: Email: spartha@emory.edu
Other information: Handling of mice, transgenic animal
generation, hands on experience in molecular biological
techniques or immunohistochemistry essential. Good English
language communication skills absolutely necessary.
-----------
Sampath Parthasarathy, Ph.D., McCord-Cross Professor of
Gynecology and Obstetrics and Professor of Medicine, Emory
University, Atlanta, GA 30322.
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14. IN FOCUS: ON RUSSIAN SCIENCE AND BIOTERRORISM
"The Russian Nobel Prize winner of 2000, Zhores Alfyorov,
academician and director of the Ioffe Physical-Technical
Institute in St. Petersburg, appealed to Putin personally to
improve funding for Russian science. 'With Vladimir
Vladimirovich's [Putin's] help there will be a new impulse from
politics in science and cutting-edge technologies,' Alfyorov said
after a meeting with Putin. I am not sure that after this meeting
Russian science will be properly funded, but I am positive that
the security service structures in charge of science will be.
Unfortunately, Alfyorov belongs to the Communist faction in the
Russian Duma and, therefore, apparently believes in the Soviet
system of organization of science, including KGB/FSB control. The
financial crisis of Russian science could be potentially
dangerous in two ways. First, Russian nuclear, chemical, and
biological warfare technology could be sold or smuggled to such
countries as Iran and Iraq, despite American programs to help
former Soviet military scientists to destroy stockpiles of these
substances. Terrorism is an additional problem. Thus, enriched
uranium has already been smuggled out of the former Soviet Union
by the Russian Mafia. Although the threat of chemical and
biological terrorist attacks is not high (there have been 71
actual attacks from 1900 until May 1999, with 123 fatalities and
3774 injuries), such substances from the Soviet past as cyanide
were among the tools used. In one case within the United States,
even *Mairanovsky's beloved ricin was prepared for assassination
attacks. In 1991, four members of the Minnesota Patriots Council
acquired ricin for use in a plot to assassinate Internal Revenue
Service officials, a US deputy marshal, and local law enforcement
officers. The FBI arrested the terrorists before the attacks were
carried out. However, many modern agents such as VX nerve gas,
anthrax, salmonella bacteria, and the HIV virus were also among
international terrorists' tools. Second, in violation of
international agreements, work on chemical and biological weapons
in Russia might be intensified because the state funding for
military technology will be increased. The law on state secrets
can be easily used to cover up such research."
-----------
Notes:
... ... *Mairanovsky's beloved ricin: Grigory Mairanovsky (1899-
1964) was a biochemist and poison expert who headed various
secret laboratories sponsored by the NKVD and KGB, and who is
alleged to have experimented with poisons on prisoners condemned
to death. After falling out of favor with the authorities,
Maironovsky himself spent 10 years in prison (1951 to 1961).
After release from prison, he headed a small biochemical
laboratory near the city of Baku. Ricin is a highly toxic lectin
and hemagglutinin occurring in the seeds (castor beans) of the
castor oil plant Ricinus communis. If eaten, ricin acts as a
violent irritant and may be fatal. Biochemically, ricin acts by
inactivating ribosomes. Purified ricin has been alleged to have
been an agent used in various political assassinations. Lectins
are a class of glycoproteins that agglutinate cells. A
hemagglutinin is any agglutinin of red blood cells.
-----------
Vadim J. Birstein: _The Perversion of Knowledge: The True Story
of Soviet Science_
(Westview Press, Boulder, CO (US) 2001, p.303)
http://www.amazon.com/exec/obidos/ASIN/0813339073/scienceweek
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SCIENCE-WEEK 30 Nov 2001 http://scienceweek.com
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15. FROM PRAXIS: Bt CORN: CURRENT RISK ASSESSMENT
A.R. Zangerl et al (University of Illinois Urbana Champaign, US)
discuss Bt corn. The term "Bt corn" refers to the corn species
Zea mays genetically engineered to express genes from the soil
bacterium Bacillus thuringiensis that encode several insecticidal
proteins. Bt corn is the most widely grown transgenic crop plant
in the US. The principal target species for Bt corn is the
European corn borer Ostrinia nubilalis, one of the most damaging
insect pests of corn in North America, with losses resulting from
corn borer damage and costs of control exceeding $1 billion
annually in the US. In addition to direct damage, corn borer
damage results in corn vulnerable to infection by fungi that can
produce toxins harmful to humans if ingested.
... ... M.K. Sears et al (University of Guelph, CA) discuss the
impact of Bt corn pollen on monarch butterfly populations. A
collaborative research effort by scientists in several states and
in Canada has produced information to develop a formal risk
assessment of the impact of Bt corn on monarch butterfly (Danaus
plexippus) populations. Information was sought on the acute toxic
effects of Bt corn pollen and the degree to which monarch larvae
would be exposed to toxic amounts of Bt pollen on its host plant,
the common milkweed, Asclepias syriaca, found in and around
cornfields. Expression of Cry proteins, the active genetically
engineered toxicant found in Bt corn tissues, differed among
hybrids, and especially so in the concentrations found in pollen
of different events. In most commercial hybrids, Bt expression in
pollen is low, and laboratory and field studies show no acute
toxic effects at any pollen density that would be encountered in
the field. Other factors mitigating exposure of larvae include
the variable and limited overlap between pollen shed and larval
activity periods, the fact that only a portion of the monarch
population utilizes milkweed stands in and near cornfields, and
the current adoption rate of Bt corn at 19 percent of North-
American corn-growing areas. The authors conclude that the 2-year
study suggests that the impact of Bt corn pollen from current
commercial hybrids on monarch butterfly populations is
negligible.
-----------
Proc. Nat. Acad. Sci. 2001 98:11908,11937
-----------
PRAXIS 26 Nov 2001 http://scienceweek.com/praxis
-------------------
Related Background:
SCIENCE POLICY: ON GENETIC MODIFICATION OF CROPS
Genetic modification of crops continues to be a controversial
subject, and it is likely to remain so in the near future. The
journal _The Biochemist_, the official organ of The Biochemical
Society (UK), recently devoted a full issue to consideration of
genetic modifications of organisms in the context of
biotechnology, with 7 articles covering a wide range of
viewpoints. Jules Pretty (University of Essex, UK) presents a
review of genetic modification of crops, the author making the
following points:
1) Genetic modification involves the transfer of specific
genes to new host organisms, so that these hosts can perform new
functions not previously possible with their standard genome. The
technology has the potential to revolutionize both the medical-
health and food-agriculture industries, and to change the lives
of billions of people. Associated with both medical and
agricultural applications, however, are growing concerns over
possible environmental and health consequences.
2) In general, biotechnology involves molecular alterations
in living or almost-living systems. The technology has a long
history, dating back to the development 4000 years ago by
Egyptians and Sumerians of fermentation, bread making, brewing,
and cheese making. Modern biotechnology (genetic modification),
by contrast, involves the transfer of DNA from one organism to
another, thus allowing the recipient to express traits or
characteristics normally associated only with the donor. As these
transfers or mixes do not occur in nature, the scope for genetic
modification is far greater than in conventional animal or plant
breeding.
3) The biotechnology industry is now the fastest-growing
sector associated with both the health and food systems. There
are approximately 1500 to 2000 biotechnology companies in the US,
and a further 200 in Europe, the majority of which are concerned
with the production of new drugs and other medical applications.
In the food and farming sector, 6 international conglomerates now
dominate the market: Monsanto, Novartis, AgrEvo, Dupont,
AstraZeneca, and Dow. These entities have apparently already
invested US$8 billion in technology development. Monsanto alone
spent US$730 million on biotechnology research during 1997.
Several companies now dominate the seed market: 10 companies now
account for 30 percent of the global US$23 billion commercial
seed trade, including Pioneer Hi-Bred (US$1.7 billion), Monsanto
(US$1.32 billion), and Novartis (US$0.93 billion).
4) The expansion in the cultivation of genetically modified
crops has been very rapid in recent years. In 1994, there were no
genetically modified crops grown commercially on farms anywhere
in the world. By 1998, some 29 million hectares (1 hectare = 2.47
acres) of genetically modified crops were cultivated in the US,
Australia, Argentina, Canada, and Mexico, up from 12 million
hectares in 1997. In 1998, genetically modified crops were sown
on a quarter of all cotton-growing areas in the US, 43 percent of
soya (up from 14 percent in 1997), and 20 percent of maize (up
from 1 percent in 1996). In China, 650,000 farmers planted
Monsanto's Bollgard cotton in 1998, rising to approximately 1
million farmers in 1999.
5) The first genetically engineered products eaten by humans
were cheese and tomatoes. Genetically modified bacteria were
first used to produce an alternative enzyme to calf chymosin, so
as to make vegetarian cheese. Then, in 1995, tomatoes with their
softening gene "switched-off", allowing them to ripen on the vine
until they reach full flavor and color without rotting, were
introduced on the market as tomato paste. However, the greatest
growth has been in crops containing one of two traits:
... ... a) Herbicide tolerance, mainly in soya, oilseed rape
(canola), and sugar beet, which allows the application of broad-
spectrum herbicides to the standing crop without causing it
damage, but killing all the weeds.
... ... b) Insect resistance via Bacillus thuringiensis (Bt) gene
expression, mainly in maize and cotton, with a bacillus
insecticide toxin expressed by all cells of the plant, thus
killing herbivorous pests and theoretically reducing the need to
supply conventional pesticides.
In 1998, 71 percent of the world's commercial genetically
modified crops were herbicide-tolerant, 28 percent were Bt crops,
and 1 percent were a combination of both (not counting virus-
resistant crops in China).
-----------
The Biochemist October 1999
ScienceWeek 1999 31 Dec 99
-----------
PRAXIS 26 Nov 2001 http://scienceweek.com/praxis
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
16. THIS WEEK IN PRAXIS (26 Nov 2001):
--------------------------------------------
1. Submicron Metallic Barcodes
2. On Pi-Conjugated Materials
3. On Chemical Fluid Deposition
4. On Applications of Dendrimers
5. A Liquid-Crystal Method for Measurement of Chemical Exposure
6. On Spherical Colloids
7. Heart Tissue Regeneration in Adult Mice
8. Health Insurance and Health Decline in Late Middle Age
9. On Vaccines
10. Bt Corn: Current Risk Assessment
11. Antibiotic Resistant Salmonella in Retail Ground Meats
12. On the Molecular Basis of Drug Addiction
For information about PRAXIS, see:
http://www.scienceweek.com/praxis
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