369 research outputs found
Food web topology and nested keystone species complexes
Important species may be in critically central network positions in ecological interaction networks. Beyond quantifying
which one is the most central species in a food web, a multi-node approach can identify the key sets of the most central
n species as well. However, for sets of different size n, these structural keystone species complexes may differ in their
composition. If larger sets contain smaller sets, higher nestedness may be a proxy for predictive ecology and efficient
management of ecosystems. On the contrary, lower nestedness makes the identification of keystones more complicated.
Our question here is how the topology of a network can influence nestedness as an architectural constraint. Here, we
study the role of keystone species complexes in 27 real food webs and quantify their nestedness. After quantifying their
topology properties, we determine their keystones species complexes, calculate their nestedness and statistically analyze
the relationship between topological indices and nestedness. A better understanding of the cores of ecosystems is crucial
for efficient conservation efforts and to know which networks will have more nested keystone species complexes would
be a great help for prioritizing species that could preserve the ecosystem’s structural integrity
Molecular dynamics recipes for genome research
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect
SOCIAL DEATH AS CYBER DEATH: INTERPERSONAL OSTRACISM ONLINE
openRicerca bibliografica volta ad identificare ed analizzare fattori individuali, sociali ed Intergruppi che predispongono all’iniziazione e perpetrazione di comportamenti volti allo sviluppo di forme di ostracismo informatico, attraverso canali digitali quali social network
RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts
The physiology and behavior of living organisms are featured by time-related variations driven by molecular clockworks that arose during evolution stochastically and heterogeneously. Over the years, several high-throughput experiments were performed to evaluate time-dependent gene expression in different cell types across several species and experimental conditions. Here, these were retrieved, manually curated, and analyzed by two software packages, BioCycle and MetaCycle, to infer circadian or ultradian transcripts across different species. These transcripts were stored in RhythmicDB and made publically available
Fusion channels of non-Abelian anyons from angular-momentum and density-profile measurements
We present a method to characterize non-Abelian anyons that is based only on
static measurements and that does not rely on any form of interference. For
geometries where the anyonic statistics can be revealed by rigid rotations of
the anyons, we link this property to the angular momentum of the initial state.
We test our method on the paradigmatic example of the Moore-Read state, that is
known to support excitations with non-Abelian statistics of Ising type. As an
example, we reveal the presence of different fusion channels for two such
excitations, a defining feature of non-Abelian anyons. This is obtained by
measuring density-profile properties, like the mean square radius of the system
or the depletion generated by the anyons. Our study paves the way to novel
methods for characterizing non-Abelian anyons, both in the experimental and
theoretical domains.Comment: 6+10 pages, 2+3 figures -- revised text and Supp. Mat. -- to be
published in Phys. Rev. Let
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics
Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components
Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes
Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves. Discrete stochastic simulation of molecular kinetics potentially oers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described by simple mass action chemistry. Moreover, modelling every individual molecular interac- tion in the cell is probably unnecessary and currently impractical. Simulation is a form of computer aided analysis, relying on human inter- pretation to derive meaning. To improve eciency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version [Sean Sedwards and Tommaso Mazza, Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes, Bioinformatics, 15 October 2007; 23: 2800 - 2802] is available online at: http://bioinformatics.oxfordjournals.org/ [doi:10.1093/bioinformatics/btm416]
Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer
Alterations in the balance of mRNA and microRNA (miRNA) expression profiles contribute to the onset and development of colorectal cancer. The regulatory functions of individual miRNA-gene pairs are widely acknowledged, but group effects are largely unexplored. We performed an integrative analysis of mRNA–miRNA and miRNA–miRNA interactions using high-throughput mRNA and miRNA expression profiles obtained from matched specimens of human colorectal cancer tissue and adjacent non- tumorous mucosa. This investigation resulted in a hypernetwork-based model, whose functional back- bone was fulfilled by tight micro-societies of miR- NAs. These proved to modulate several genes that are known to control a set of significantly enriched cancer-enhancer and cancer-protection biological processes, and that an array of upstream regulatory analyses demonstrated to be dependent on miR-145, a cell cycle and MAPK signalling cascade master regulator. In conclusion, we reveal miRNA-gene clusters and gene families with close functional relationships and highlight the role of miR-145 as potent upstream regulator of a complex RNA–RNA crosstalk, which
mechanistically modulates several signalling path- ways and regulatory circuits that when deranged are relevant to the changes occurring in colorectal carcinogenesis
Statistical Model Checking of Membrane Systems with Peripheral Proteins: Quantifying the Role of Estrogen in Cellular Mitosis and DNA Damage
MicroRNA co-expression networks exhibit increased complexity in pancreatic ductal compared to Vater’s papilla adenocarcinoma
iRNA expression abnormalities in adenocarcinoma arising from pancreatic ductal system (PDAC) and Vater’s papilla (PVAC) could be associated with distinctive pathologic features and clinical cancer behaviours. Our previous miRNA expression profiling data on PDAC (n=9) and PVAC (n=4) were revaluated to define differences/ similarities in miRNA expression patterns. Afterwards, in order to uncover target genes and core signalling pathways regulated by specific miRNAs in these two tumour entities, miRNA interaction networks were wired for each tumour entity, and experimentally validated target genes underwent pathways enrichment analysis.
One hundred and one miRNAs were altered, mainly over-expressed, in PDAC samples. Twenty-six miRNAs were deregulated in PVAC samples, where more miRNAs were down-expressed in tumours compared to normal tissues. Four miRNAs were significantly altered in both subgroups of patients, while 27 miRNAs were differentially expressed between PDAC and PVAC.
Although miRNA interaction networks were more complex and dense in PDAC than in PVAC, pathways enrichment analysis uncovered a functional overlapping between PDAC and PVAC. However, shared signalling events were influenced by different miRNA and/or genes in the two tumour entities.
Overall, specific miRNA expression patterns were involved in the regulation of a limited core signalling pathways in the biology landscape of PDAC and PVAC
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