1,017 research outputs found
Sociobiological Control of Plasmid copy number
Background:
All known mechanisms and genes responsible for the regulation of plasmid replication lie with the plasmid rather than the chromosome. It is possible therefore that there can be copy-up mutants. Copy-up mutants will have within host selective advantage. This would eventually result into instability of bacteria-plasmid association. In spite of this possibility low copy number plasmids appear to exist stably in host populations. We examined this paradox using a computer simulation model.

Model:
Our multilevel selection model assumes a wild type with tightly regulated replication to ensure low copy number. A mutant with slightly relaxed replication regulation can act as a “cheater” or “selfish” plasmid and can enjoy a greater within-host-fitness. However the host of a cheater plasmid has to pay a greater cost. As a result, in host level competition, host cell with low copy number plasmid has a greater fitness. Furthermore, another mutant that has lost the genes required for conjugation was introduced in the model. The non-conjugal mutant was assumed to undergo conjugal transfer in the presence of another conjugal plasmid in the host cell.

Results:
The simulatons showed that if the cost of carrying a plasmid was low, the copy-up mutant could drive the wild type to extinction or very low frequencies. Consequently, another mutant with a higher copy number could invade the first invader. This process could result into an increasing copy number. However above a certain copy number within-host selection was overcompensated by host level selection leading to a rock-paper-scissor (RPS) like situation. The RPS situation allowed the coexistence of high and low copy number plasmids. The non-conjugal “hypercheaters” could further arrest the copy numbers to a substantially lower level.

Conclusions:
These sociobiological interactions might explain the stability of copy numbers better than molecular mechanisms of replication regulation alone
An Over-Massive Black Hole in the Compact Lenticular Galaxy NGC1277
All massive galaxies likely have supermassive black holes at their centers,
and the masses of the black holes are known to correlate with properties of the
host galaxy bulge component. Several explanations have been proposed for the
existence of these locally-established empirical relationships; they include
the non-causal, statistical process of galaxy-galaxy merging, direct feedback
between the black hole and its host galaxy, or galaxy-galaxy merging and the
subsequent violent relaxation and dissipation. The empirical scaling relations
are thus important for distinguishing between various theoretical models of
galaxy evolution, and they further form the basis for all black hole mass
measurements at large distances. In particular, observations have shown that
the mass of the black hole is typically 0.1% of the stellar bulge mass of the
galaxy. The small galaxy NGC4486B currently has the largest published fraction
of its mass in a black hole at 11%. Here we report observations of the stellar
kinematics of NGC 1277, which is a compact, disky galaxy with a mass of 1.2 x
10^11 Msun. From the data, we determine that the mass of the central black hole
is 1.7 x 10^10 Msun, or 59% its bulge mass. Five other compact galaxies have
properties similar to NGC 1277 and therefore may also contain over-sized black
holes. It is not yet known if these galaxies represent a tail of a
distribution, or if disk-dominated galaxies fail to follow the normal black
hole mass scaling relations.Comment: 7 pages. 6 figures. Nature. Animation at
http://www.mpia.de/~bosch/blackholes.htm
Individualization as driving force of clustering phenomena in humans
One of the most intriguing dynamics in biological systems is the emergence of
clustering, the self-organization into separated agglomerations of individuals.
Several theories have been developed to explain clustering in, for instance,
multi-cellular organisms, ant colonies, bee hives, flocks of birds, schools of
fish, and animal herds. A persistent puzzle, however, is clustering of opinions
in human populations. The puzzle is particularly pressing if opinions vary
continuously, such as the degree to which citizens are in favor of or against a
vaccination program. Existing opinion formation models suggest that
"monoculture" is unavoidable in the long run, unless subsets of the population
are perfectly separated from each other. Yet, social diversity is a robust
empirical phenomenon, although perfect separation is hardly possible in an
increasingly connected world. Considering randomness did not overcome the
theoretical shortcomings so far. Small perturbations of individual opinions
trigger social influence cascades that inevitably lead to monoculture, while
larger noise disrupts opinion clusters and results in rampant individualism
without any social structure. Our solution of the puzzle builds on recent
empirical research, combining the integrative tendencies of social influence
with the disintegrative effects of individualization. A key element of the new
computational model is an adaptive kind of noise. We conduct simulation
experiments to demonstrate that with this kind of noise, a third phase besides
individualism and monoculture becomes possible, characterized by the formation
of metastable clusters with diversity between and consensus within clusters.
When clusters are small, individualization tendencies are too weak to prohibit
a fusion of clusters. When clusters grow too large, however, individualization
increases in strength, which promotes their splitting.Comment: 12 pages, 4 figure
Viral population estimation using pyrosequencing
The diversity of virus populations within single infected hosts presents a
major difficulty for the natural immune response as well as for vaccine design
and antiviral drug therapy. Recently developed pyrophosphate based sequencing
technologies (pyrosequencing) can be used for quantifying this diversity by
ultra-deep sequencing of virus samples. We present computational methods for
the analysis of such sequence data and apply these techniques to pyrosequencing
data obtained from HIV populations within patients harboring drug resistant
virus strains. Our main result is the estimation of the population structure of
the sample from the pyrosequencing reads. This inference is based on a
statistical approach to error correction, followed by a combinatorial algorithm
for constructing a minimal set of haplotypes that explain the data. Using this
set of explaining haplotypes, we apply a statistical model to infer the
frequencies of the haplotypes in the population via an EM algorithm. We
demonstrate that pyrosequencing reads allow for effective population
reconstruction by extensive simulations and by comparison to 165 sequences
obtained directly from clonal sequencing of four independent, diverse HIV
populations. Thus, pyrosequencing can be used for cost-effective estimation of
the structure of virus populations, promising new insights into viral
evolutionary dynamics and disease control strategies.Comment: 23 pages, 13 figure
The Galactic Center Black Hole Laboratory
The super-massive 4 million solar mass black hole Sagittarius~A* (SgrA*)
shows flare emission from the millimeter to the X-ray domain. A detailed
analysis of the infrared light curves allows us to address the accretion
phenomenon in a statistical way. The analysis shows that the near-infrared
flare amplitudes are dominated by a single state power law, with the low states
in SgrA* limited by confusion through the unresolved stellar background. There
are several dusty objects in the immediate vicinity of SgrA*. The source G2/DSO
is one of them. Its nature is unclear. It may be comparable to similar stellar
dusty sources in the region or may consist predominantly of gas and dust. In
this case a particularly enhanced accretion activity onto SgrA* may be expected
in the near future. Here the interpretation of recent data and ongoing
observations are discussed.Comment: 30 pages - 7 figures - accepted for publication by Springer's
"Fundamental Theories of Physics" series; summarizing GC contributions of 2
conferences: 'Equations of Motion in Relativistic Gravity' at the
Physikzentrum Bad Honnef, Bad Honnef, Germany, (Feb. 17-23, 2013) and the
COST MP0905 'The Galactic Center Black Hole Laboratory' Granada, Spain (Nov.
19 - 22, 2013
Wet Granular Materials
Most studies on granular physics have focused on dry granular media, with no
liquids between the grains. However, in geology and many real world
applications (e.g., food processing, pharmaceuticals, ceramics, civil
engineering, constructions, and many industrial applications), liquid is
present between the grains. This produces inter-grain cohesion and drastically
modifies the mechanical properties of the granular media (e.g., the surface
angle can be larger than 90 degrees). Here we present a review of the
mechanical properties of wet granular media, with particular emphasis on the
effect of cohesion. We also list several open problems that might motivate
future studies in this exciting but mostly unexplored field.Comment: review article, accepted for publication in Advances in Physics;
tex-style change
A multicentre phase II study of cisplatin and gemcitabine for malignant mesothelioma
Our previous phase II study of cisplatin and gemcitabine in malignant mesothelioma showed a 47.6% (95% CI 26.2–69.0%) response rate with symptom improvement in responding patients. Here we confirm these findings in a multicentre setting, and assess the effect of this treatment on quality of life and pulmonary function. Fifty-three patients with pleural malignant mesothelioma received cisplatin 100 mg m−2 i.v. day 1 and gemcitabine 1000 mg m−2 i.v. days 1, 8, and 15 of a 28 day cycle for a maximum of six cycles. Quality of life and pulmonary function were assessed at each cycle. The best response achieved in 52 assessable patients was: partial response, 17 (33%, 95% CI 20–46%); stable disease, 31 (60%); and progressive disease, four (8%). The median time to disease progression was 6.4 months, median survival from start of treatment 11.2 months, and median survival from diagnosis 17.3 months. Vital capacity and global quality of life remained stable in all patients and improved significantly in responding patients. Major toxicities were haematological, limiting the mean relative dose intensity of gemcitabine to 75%. This schedule of cisplatin and gemcitabine is active in malignant mesothelioma in a multicentre setting. Investigation of alternative scheduling is needed to decrease haematological toxicity and increase the relative dose intensity of gemcitabine whilst maintaining response rate and quality of life
An unusually massive stellar black hole in the Galaxy
Here we report a measurement of the orbital period and mass function of GRS
1915+105 which allow us to deduce a mass of 14 +- 4 solar masses for its black
hole. This large mass provides a challenge for black hole formation scenarios
in binaries, since black holes with masses above 5-7 solar masses are hard to
explain. Also, the mass estimate allows us to understand the unique X-ray
variability of GRS 1915+105 as being due to instabilities of a
radiation-pressure dominated disk radiating near the Eddington limit. Finally,
several models are constrained which relate observable X-ray properties to the
spin of black holes in microquasars. Once further calibrated, these relations
may soon turn into a valuable tool to study relativistic effects in strong
gravitational fields.Comment: appeared in Nature 414, p. 522 (Nov. 29, 2001
Theory of disk accretion onto supermassive black holes
Accretion onto supermassive black holes produces both the dramatic phenomena
associated with active galactic nuclei and the underwhelming displays seen in
the Galactic Center and most other nearby galaxies. I review selected aspects
of the current theoretical understanding of black hole accretion, emphasizing
the role of magnetohydrodynamic turbulence and gravitational instabilities in
driving the actual accretion and the importance of the efficacy of cooling in
determining the structure and observational appearance of the accretion flow.
Ongoing investigations into the dynamics of the plunging region, the origin of
variability in the accretion process, and the evolution of warped, twisted, or
eccentric disks are summarized.Comment: Mostly introductory review, to appear in "Supermassive black holes in
the distant Universe", ed. A.J. Barger, Kluwer Academic Publishers, in pres
Variation in helper effort among cooperatively breeding bird species is consistent with Hamilton's Rule.
Investment by helpers in cooperative breeding systems is extremely variable among species, but this variation is currently unexplained. Inclusive fitness theory predicts that, all else being equal, cooperative investment should correlate positively with the relatedness of helpers to the recipients of their care. We test this prediction in a comparative analysis of helper investment in 36 cooperatively breeding bird species. We show that species-specific helper contributions to cooperative brood care increase as the mean relatedness between helpers and recipients increases. Helper contributions are also related to the sex ratio of helpers, but neither group size nor the proportion of nests with helpers influence helper effort. Our findings support the hypothesis that variation in helping behaviour among cooperatively breeding birds is consistent with Hamilton's rule, indicating a key role for kin selection in the evolution of cooperative investment in social birds
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