468 research outputs found
Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database
Background
The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of bacterial taxa in relation to defined habitats and contexts.
Results
In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution of each of the 24 phyla of the bacteria superkingdom and of the Archaea. Over two and a half million records are filtered in their cross-association with each of 48 sets of keywords, defined to cover natural or artificial habitats, interactions with plant, animal or human hosts, and physical-chemical conditions. The results are processed showing: (a) how the different descriptors enrich or deplete the proportions at which the phyla occur in the total database; (b) in which order of abundance do the different keywords score for each phylum (preferred habitats or conditions), and to which extent are phyla clustered to few descriptors (specific) or spread across many (cosmopolitan); (c) which keywords individuate the communities ranking highest for diversity and evenness.
Conclusions
A number of cues emerge from the results, contributing to sharpen the picture on the functional systematic diversity of prokaryotes. Suggestions are given for a future automated service dedicated to refining and updating such kind of analyses via public bioinformatic engines
Detecting early signs of the 2007-2008 crisis in the world trade
Since 2007, several contributions have tried to identify early-warning
signals of the financial crisis. However, the vast majority of analyses has
focused on financial systems and little theoretical work has been done on the
economic counterpart. In the present paper we fill this gap and employ the
theoretical tools of network theory to shed light on the response of world
trade to the financial crisis of 2007 and the economic recession of 2008-2009.
We have explored the evolution of the bipartite World Trade Web (WTW) across
the years 1995-2010, monitoring the behavior of the system both before and
after 2007. Our analysis shows early structural changes in the WTW topology:
since 2003, the WTW becomes increasingly compatible with the picture of a
network where correlations between countries and products are progressively
lost. Moreover, the WTW structural modification can be considered as concluded
in 2010, after a seemingly stationary phase of three years. We have also
refined our analysis by considering specific subsets of countries and products:
the most statistically significant early-warning signals are provided by the
most volatile macrosectors, especially when measured on developing countries,
suggesting the emerging economies as being the most sensitive ones to the
global economic cycles.Comment: 18 pages, 9 figure
Randomizing bipartite networks: the case of the World Trade Web
Within the last fifteen years, network theory has been successfully applied
both to natural sciences and to socioeconomic disciplines. In particular,
bipartite networks have been recognized to provide a particularly insightful
representation of many systems, ranging from mutualistic networks in ecology to
trade networks in economy, whence the need of a pattern detection-oriented
analysis in order to identify statistically-significant structural properties.
Such an analysis rests upon the definition of suitable null models, i.e. upon
the choice of the portion of network structure to be preserved while
randomizing everything else. However, quite surprisingly, little work has been
done so far to define null models for real bipartite networks. The aim of the
present work is to fill this gap, extending a recently-proposed method to
randomize monopartite networks to bipartite networks. While the proposed
formalism is perfectly general, we apply our method to the binary, undirected,
bipartite representation of the World Trade Web, comparing the observed values
of a number of structural quantities of interest with the expected ones,
calculated via our randomization procedure. Interestingly, the behavior of the
World Trade Web in this new representation is strongly different from the
monopartite analogue, showing highly non-trivial patterns of self-organization.Comment: 22 pages, 13 figure
Hierarchical organization of functional connectivity in the mouse brain: a complex network approach
This paper represents a contribution to the study of the brain functional
connectivity from the perspective of complex networks theory. More
specifically, we apply graph theoretical analyses to provide evidence of the
modular structure of the mouse brain and to shed light on its hierarchical
organization. We propose a novel percolation analysis and we apply our approach
to the analysis of a resting-state functional MRI data set from 41 mice. This
approach reveals a robust hierarchical structure of modules persistent across
different subjects. Importantly, we test this approach against a statistical
benchmark (or null model) which constrains only the distributions of empirical
correlations. Our results unambiguously show that the hierarchical character of
the mouse brain modular structure is not trivially encoded into this
lower-order constraint. Finally, we investigate the modular structure of the
mouse brain by computing the Minimal Spanning Forest, a technique that
identifies subnetworks characterized by the strongest internal correlations.
This approach represents a faster alternative to other community detection
methods and provides a means to rank modules on the basis of the strength of
their internal edges.Comment: 11 pages, 9 figure
Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes
Abstract The culturable bacteria from root nodules of Sulla coronaria growing in spontaneous conditions in Sardinia were characterized. This plant's peculiarity is to represent a legume still found in both wild and cropped statuses. We tested whether culturable bacteria would differ from those commonly isolated from its field-cropped varieties, to date exclusively represented by Rhizobium sullae. 63 isolates from 60 surface-sterilized nodules were analyzed by ARDRA and 16S rDNA sequencing. The official nitrogen-fixing symbiont Rhizobium sullae was found only in 25 nodules out of 60. The remaining nodules did not yield culturable rhizobia but a number of different endophytic genera including Pseudomonas sp. (17 nodules), Microbacterium sp. (15 nodules), Pantoea agglomerans (5 nodules). The situation appears therefore a hybrid between what is commonly observed in other Mediterranean legumes occurring only in wild status (featuring non-culturable rhizobia and arrays of culturable endophytes within nodules), as opposed to cropped legumes (endowed with fully culturable rhizobia and minimal endophytic occurrence). These findings, within a species bridging the ecology between native and cropped conditions, suggest insights on the relative importance of endophytic co-occupancy vs. true N-fixing symbiont culturability within nodules. The latter trait thus appears to accompany the domestication path of plants with a main trade-off of renouncing to interactions with a diversity of endophytic co-invaders; the relationships with those being critical in the non-cropped status. In fact, endophytes are known to promote plant growth in harsh conditions, which can be particularly stressful in the Mediterranean due to drought, highly calcareous soils, and pathogens outbreaks
Inferring monopartite projections of bipartite networks: an entropy-based approach
Bipartite networks are currently regarded as providing a major insight into
the organization of many real-world systems, unveiling the mechanisms driving
the interactions occurring between distinct groups of nodes. One of the most
important issues encountered when modeling bipartite networks is devising a way
to obtain a (monopartite) projection on the layer of interest, which preserves
as much as possible the information encoded into the original bipartite
structure. In the present paper we propose an algorithm to obtain
statistically-validated projections of bipartite networks, according to which
any two nodes sharing a statistically-significant number of neighbors are
linked. Since assessing the statistical significance of nodes similarity
requires a proper statistical benchmark, here we consider a set of four null
models, defined within the exponential random graph framework. Our algorithm
outputs a matrix of link-specific p-values, from which a validated projection
is straightforwardly obtainable, upon running a multiple hypothesis testing
procedure. Finally, we test our method on an economic network (i.e. the
countries-products World Trade Web representation) and a social network (i.e.
MovieLens, collecting the users' ratings of a list of movies). In both cases
non-trivial communities are detected: while projecting the World Trade Web on
the countries layer reveals modules of similarly-industrialized nations,
projecting it on the products layer allows communities characterized by an
increasing level of complexity to be detected; in the second case, projecting
MovieLens on the films layer allows clusters of movies whose affinity cannot be
fully accounted for by genre similarity to be individuated.Comment: 16 pages, 9 figure
Identification of ferredoxin II as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
BACKGROUND: Legumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. Calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. Regulation of intracellular free Ca(2+) concentration, which is a fundamental prerequisite for any Ca(2+)-based signalling system, is accomplished by complex mechanisms including Ca(2+) binding proteins acting as Ca(2+) buffers. In this work we investigated the occurrence of Ca(2+) binding proteins in Mesorhizobium loti, the specific symbiotic partner of the model legume Lotus japonicus. RESULTS: A soluble, low molecular weight protein was found to share several biochemical features with the eukaryotic Ca(2+)-binding proteins calsequestrin and calreticulin, such as Stains-all blue staining on SDS-PAGE, an acidic isoelectric point and a Ca(2+)-dependent shift of electrophoretic mobility. The protein was purified to homogeneity by an ammonium sulfate precipitation procedure followed by anion-exchange chromatography on DEAE-Cellulose and electroendosmotic preparative electrophoresis. The Ca(2+) binding ability of the M. loti protein was demonstrated by (45)Ca(2+)-overlay assays. ESI-Q-TOF MS/MS analyses of the peptides generated after digestion with either trypsin or endoproteinase AspN identified the rhizobial protein as ferredoxin II and confirmed the presence of Ca(2+) adducts. CONCLUSIONS: The present data indicate that ferredoxin II is a major Ca(2+) binding protein in M. loti that may participate in Ca(2+) homeostasis and suggest an evolutionarily ancient origin for protein-based Ca(2+) regulatory systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-015-0352-5) contains supplementary material, which is available to authorized users
Network reconstruction via density sampling
Reconstructing weighted networks from partial information is necessary in many important circumstances, e.g. for a correct estimation of systemic risk. It has been shown that, in order to achieve an accurate reconstruction, it is crucial to reliably replicate the empirical degree sequence, which is however unknown in many realistic situations. More recently, it has been found that the knowledge of the degree sequence can be replaced by the knowledge of the strength sequence, which is typically accessible, complemented by that of the total number of links, thus considerably relaxing the observational requirements. Here we further relax these requirements and devise a procedure valid when even the the total number of links is unavailable. We assume that, apart from the heterogeneity induced by the degree sequence itself, the network is homogeneous, so that its (global) link density can be estimated by sampling subsets of nodes with representative density. We show that the best way of sampling nodes is the random selection scheme, any other procedure being biased towards unrealistically large, or small, link densities. We then introduce our core technique for reconstructing both the topology and the link weights of the unknown network in detail. When tested on real economic and financial data sets, our method achieves a remarkable accuracy and is very robust with respect to the sampled subsets, thus representing a reliable practical tool whenever the available topological information is restricted to small portions of nodes
Estimating topological properties of weighted networks from limited information
A problem typically encountered when studying complex systems is the limitedness of the information available on their topology, which hinders our understanding of their structure and of the dynamical processes taking place on them. A paramount example is provided by financial networks, whose data are privacy protected: Banks publicly disclose only their aggregate exposure towards other banks, keeping individual exposures towards each single bank secret. Yet, the estimation of systemic risk strongly depends on the detailed structure of the interbank network. The resulting challenge is that of using aggregate information to statistically reconstruct a network and correctly predict its higher-order properties. Standard approaches either generate unrealistically dense networks, or fail to reproduce the observed topology by assigning homogeneous link weights. Here, we develop a reconstruction method, based on statistical mechanics concepts, that makes use of the empirical link density in a highly nontrivial way. Technically, our approach consists in the preliminary estimation of node degrees from empirical node strengths and link density, followed by a maximum-entropy inference based on a combination of empirical strengths and estimated degrees. Our method is successfully tested on the international trade network and the interbank money market, and represents a valuable tool for gaining insights on privacy-protected or partially accessible systems
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