5,878 research outputs found
Demography-based adaptive network model reproduces the spatial organization of human linguistic groups
The distribution of human linguistic groups presents a number of interesting
and non-trivial patterns. The distributions of the number of speakers per
language and the area each group covers follow log-normal distributions, while
population and area fulfill an allometric relationship. The topology of
networks of spatial contacts between different linguistic groups has been
recently characterized, showing atypical properties of the degree distribution
and clustering, among others. Human demography, spatial conflicts, and the
construction of networks of contacts between linguistic groups are mutually
dependent processes. Here we introduce an adaptive network model that takes all
of them into account and successfully reproduces, using only four model
parameters, not only those features of linguistic groups already described in
the literature, but also correlations between demographic and topological
properties uncovered in this work. Besides their relevance when modeling and
understanding processes related to human biogeography, our adaptive network
model admits a number of generalizations that broaden its scope and make it
suitable to represent interactions between agents based on population dynamics
and competition for space
Neutral networks of genotypes: Evolution behind the curtain
Our understanding of the evolutionary process has gone a long way since the
publication, 150 years ago, of "On the origin of species" by Charles R. Darwin.
The XXth Century witnessed great efforts to embrace replication, mutation, and
selection within the framework of a formal theory, able eventually to predict
the dynamics and fate of evolving populations. However, a large body of
empirical evidence collected over the last decades strongly suggests that some
of the assumptions of those classical models necessitate a deep revision. The
viability of organisms is not dependent on a unique and optimal genotype. The
discovery of huge sets of genotypes (or neutral networks) yielding the same
phenotype --in the last term the same organism--, reveals that, most likely,
very different functional solutions can be found, accessed and fixed in a
population through a low-cost exploration of the space of genomes. The
'evolution behind the curtain' may be the answer to some of the current puzzles
that evolutionary theory faces, like the fast speciation process that is
observed in the fossil record after very long stasis periods.Comment: 7 pages, 7 color figures, uses a modification of pnastwo.cls called
pnastwo-modified.cls (included
Development and field assessment of a quantitative PCR for the detection and enumeration of the noxious bloom-former Anabaena planktonica
Anabaena planktonica is a harmful, bloom-forming freshwater cyanobacterium, which has arrived recently in New Zealand. In the short time since its incursion (<10 yr), A. planktonica has spread rapidly throughout lakes in the North Island. To date, the identification and enumeration of A. planktonica has been undertaken using light microscopy. There is an urgent demand for a highly sensitive and specific quantitative detection method that can be combined with a high sample processing capability in order to increase sampling frequency. In this study, we sequenced 36 cyanobacterial 16S rRNA genes (partial), complete intergenic transcribed spacers (ITS), and 23S rRNA genes (partial) of fresh-water cyanobacteria found in New Zealand. The sequences were used to develop an A. Planktonica specific TaqMan QPCR assay targeting the long ITS1-L and the 5´ terminus of the 23S rRNA gene. The QPCR method was linear (R2 = 0.999) over seven orders of magnitude with a lower end sensitivity of approximately five A. planktonica cells in the presence of exogenous DNA. The quantitative PCR (QPCR) method was used to assess the spatial distribution and seasonal population dynamics of A. planktonica from the Lower Karori Reservoir (Wellington, New Zealand) over a five-month period. The QPCR results were compared directly to microscopic cell counts and found to correlate significantly (95% confidence level) under both bloom and non-bloom conditions. The current QPCR assay will be an invaluable tool for routine monitoring programs and in research investigating environmental factors that regulate the population dynamics and the blooming of A. planktonica
Meso-Nh simulations of the atmospheric flow above the Internal Antarctic Plateau
Mesoscale model such as Meso-Nh have proven to be highly reliable in
reproducing 3D maps of optical turbulence (see Refs. 1, 2, 3, 4) above
mid-latitude astronomical sites. These last years ground-based astronomy has
been looking towards Antarctica. Especially its summits and the Internal
Continental Plateau where the optical turbulence appears to be confined in a
shallow layer close to the icy surface. Preliminary measurements have so far
indicated pretty good value for the seeing above 30-35 m: 0.36" (see Ref. 5)
and 0.27" (see Refs. 6, 7) at Dome C. Site testing campaigns are however
extremely expensive, instruments provide only local measurements and
atmospheric modelling might represent a step ahead towards the search and
selection of astronomical sites thanks to the possibility to reconstruct 3D Cn2
maps over a surface of several kilometers. The Antarctic Plateau represents
therefore an important benchmark test to evaluate the possibility to
discriminate sites on the same plateau. Our group8 has proven that the analyses
from the ECMWF global model do not describe with the required accuracy the
antarctic boundary and surface layer in the plateau. A better description could
be obtained with a mesoscale meteorological model. In this contribution we
present the progress status report of numerical simulations (including the
optical turbulence - Cn2) obtained with Meso-Nh above the internal Antarctic
Plateau. Among the topic attacked: the influence of different configurations of
the model (low and high horizontal resolution), use of the grid-nesting
interactive technique, forecasting of the optical turbulence during some winter
nights.Comment: 12 pages, 4 figures, SPIE 2008 conferenc
Diversity and biosynthetic potential of culturable microbes associated with toxic marine animals
Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus
Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests
Most surveillance programmes for marine invasive species (MIS) require considerable taxonomic expertise, are laborious, and are unable to identify species at larval or juvenile stages. Therefore, marine pests may go undetected at the initial stages of incursions when population densities are low. In this study, we evaluated the ability of the benchtop GS Junior™ 454 pyrosequencing system to detect the presence of MIS in complex sample matrices. An initial in-silico evaluation of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear small subunit ribosomal DNA (SSU) genes, found that multiple primer sets (targeting a ca. 400 base pair region) would be required to obtain species level identification within the COI gene. In contrast a single universal primer set was designed to target the V1–V3 region of SSU, allowing simultaneous PCR amplification of a wide taxonomic range of MIS. To evaluate the limits of detection of this method, artificial contrived communities (10 species from 5 taxonomic groups) were created using varying concentrations of known DNA samples and PCR products. Environmental samples (water and sediment) spiked with one or five 160 hr old Asterias amurensis larvae were also examined. Pyrosequencing was able to recover DNA/PCR products of individual species present at greater than 0.64% abundance from all tested contrived communities. Additionally, single A. amurensis larvae were detected from both water and sediment samples despite the co-occurrence of a large array of environmental eukaryotes, indicating an equivalent sensitivity to quantitative PCR. NGS technology has tremendous potential for the early detection of marine invasive species worldwide
No evidence for a culturable bacterial tetrodotoxin producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida)
Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography—mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely
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