Network communities within and across borders.
Ontology highlight
ABSTRACT:
SUBMITTER: Cerina F
PROVIDER: S-EPMC3971449 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:Background and aimsTwo Phragmites australis taxa are recognized in Europe: P. australis ssp. altissimus, also known as Phragmites isiaca, in the Mediterranean region and P. australis in the temperate region. Another taxonomic group in the Mediterranean is Phragmites frutescens. European genotypes are diverse genetically, cytologically and morphologically, and are related to African, Asiatic and American genotypes. We investigated chloroplast DNA (cpDNA) diversity in Europe and defined the current borders of the European gene pool.MethodologyWe analysed chloroplast variation with parsimony and genetic distance methods, and compared it with that of nuclear amplified fragment length polymorphism and microsatellites. We also investigated the phenological pattern of 188 genotypes collected worldwide in a common garden in Denmark. We assumed that non-flowering genotypes could indicate climatic, geographic and/or reproductive barriers to dispersal and would have been recorded in the genetic pattern as groups genetically isolated from, or within, the European pool.Principal resultsThe European P. australis gene pool extends from North America to the Far East and South Africa. However, African and North American genotypes are differentiating from the European genotypes. Mediterranean P. australis is genetically different from temperate P. australis and shares several similarities with Phragmites mauritianus in Africa and Phragmites karka in Asia. Phragmites frutescens shares the cpDNA sequences with both these tropical species. Two DNA bands can distinguish Mediterranean P. australis from P. frutescens and P. mauritianus and from temperate P. australis, and reveal possible hybrids among these species in the Mediterranean region. Phenological data confirmed possible gene flow within the temperate region of Europe, whereas the Mediterranean genotypes did not set inflorescences in Denmark, suggesting reproductive barriers between temperate and Mediterranean P. australis.ConclusionsEuropean P. australis appears as one of four main Phragmites groups known in the world. Further research is needed to understand the implications of long-distance dispersal at the population level.
| S-EPMC3435523 | biostudies-literature
Project description:Uncovering modular structure in networks is fundamental for systems in biology, physics, and engineering. Community detection identifies candidate modules as hypotheses, which then need to be validated through experiments, such as mutagenesis in a biological laboratory. Only a few communities can typically be validated, and it is thus important to prioritize which communities to select for downstream experimentation. Here we develop CRANK, a mathematically principled approach for prioritizing network communities. CRANK efficiently evaluates robustness and magnitude of structural features of each community and then combines these features into the community prioritization. CRANK can be used with any community detection method. It needs only information provided by the network structure and does not require any additional metadata or labels. However, when available, CRANK can incorporate domain-specific information to further boost performance. Experiments on many large networks show that CRANK effectively prioritizes communities, yielding a nearly 50-fold improvement in community prioritization.
| S-EPMC6026212 | biostudies-literature
Project description:Background and rationaleThe Compassionate Communities movement emphasizes the importance of illness, disability, dying, caregiving, and grief across the lifespan and highlights the communal responsibility of caring for one another. There is a need to recognize and incorporate the needs of diverse communities within this movement and research on dying, caregiving and grief. An important axis of this diversity is related to individuals' sexual orientation and gender identity.MethodsAs part of the early phases of Healthy End of Life Project Ottawa, a Compassionate Communities, community-based, participatory action research project, we held focus groups with older members of lesbian, gay, bisexual, transgender, queer, and two-spirit communities. Nine older lesbian, gay, bisexual, transgender, queer, and two-spirit people participated in the focus groups (mean age = 72 years). Data were analysed using an inductive, reflexive thematic approach.ResultsThrough an iterative analysis process, we identified themes related to lifecourse experiences of trauma, the need for safety within care contexts, the importance of relationships and connection, as well as participants' ability to ask for and receive help. A core tenet of Compassionate Communities involves responding to the needs of diverse communities with respect to aging, end-of-life, and grief. Our findings emphasize the importance of incorporating the voices of diverse sexual and gender identities and promoting health equity within Compassionate Community initiatives.
| S-EPMC8474303 | biostudies-literature
Project description:The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.
| S-EPMC10634713 | biostudies-literature
Project description:We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.
| S-EPMC6046413 | biostudies-literature
Project description:BackgroundThe residents of remote areas mostly depend on folk knowledge of medicinal plants to cure different ailments. The present study was carried out to document and analyze traditional use regarding the medicinal plants among communities residing in Koh-e-Safaid Range northern Pakistani-Afghan border.MethodsA purposive sampling method was used for the selection of informants, and information regarding the ethnomedicinal use of plants was collected through semi-structured interviews. The collected data was analyzed through quantitative indices viz. relative frequency citation, use value, and family use value. The conservation status of medicinal plants was enumerated with the help of International Union for Conservation of Nature Red List Categories and Criteria (2001). Plant samples were deposited at the Herbarium of Botany Department, University of Peshawar for future reference.ResultsOne hundred eight informants including 72 male and 36 female were interviewed. The informants provided information about 92 plants species used in the treatment of 53 ailments. The informant reported maximum number of species used for the treatment of diabetes (16 species), followed by carminatives (12 species), laxatives (11 species), antiseptics (11 species), for cough (10 species), to treat hepatitis (9 species), for curing diarrhea (7 species), and to cure ulcers (7 species), etc. Decoction (37 species, i.e., 40%) was the common method of recipe preparation. Most familiar medicinal plants were Withania coagulans, Caralluma tuberculata, and Artemisia absinthium with relative frequency (0.96), (0.90), and (0.86), respectively. The relative importance of Withania coagulans was highest (1.63) followed by Artemisia absinthium (1.34), Caralluma tuberculata (1.20), Cassia fistula (1.10), Thymus linearis (1.06), etc. This study allows identification of novel uses of plants. Abies pindrow, Artemisia scoparia, Nannorrhops ritchiana, Salvia reflexa, and Vincetoxicum cardiostephanum have not been reported previously for their medicinal importance. The study also highlights many medicinal plants used to treat chronic metabolic conditions in patients with diabetes.ConclusionsThe folk knowledge of medicinal plants species of Koh-e-Safaid Range was unexplored. We, for the first time, conducted this quantitative study in the area to document medicinal plants uses, to preserve traditional knowledge, and also to motivate the local residents against the vanishing wealth of traditional knowledge of medicinal flora. The vast use of medicinal plants reported shows the significance of traditional herbal preparations among tribal people of the area for their health care. Knowledge about the medicinal use of plants is rapidly disappearing in the area as a new generation is unwilling to take interest in medicinal plant use, and the knowledgeable persons keep their knowledge a secret. Thus, the indigenous use of plants needs conservational strategies and further investigation for better utilization of natural resources.
| S-EPMC5922303 | biostudies-literature
Project description:One of the mandates of the International Union of Immunological Societies (IUIS) is to promote immunological education to young scientists across the globe, including a large focus on those from low and low-to-middle income countries (LIC and LMIC). It strives to achieve this goal through the Education Committee (EDU), which is one of ten committees of the IUIS. To this end, EDU organizes three to four one-week courses per year in close cooperation with regional immunological societies and local organizers. Initially, the focus has been on Africa, addressing the most relevant topics and health issues facing specific countries or regions in the continent. The idea was then extended to Latin America and now also includes courses in Asia. The faculty of all courses is a blend of international and local/regional experts also known for their teaching expertise. The courses are highly interactive, and include "meet-the-speakers" sessions, poster walks, and sessions on grant or PhD project writing, and on practical aspects of becoming a successful scientist. Importantly, all the IUIS-EDU courses use a combination of pre- and during-course on-line learning followed by consolidation of knowledge in a collegial setting. This "flipped" classroom approach ensures that participants have acquired the basic knowledge needed to optimize their participation in the course. Immunopaedia is the IUIS-endorsed immunology learning site used for this purpose. All faculty members are requested to contribute material related to their specific topic while students must learn the on-line material before coming in person to the course. All course participants have free access to all Immunopaedia material indefinitely. The implementation of regional immunology courses targeted to local health issues in areas of the world where PhD students, post-doctoral, and early career scientists often do not have access to open on-line resources and contact with renowned experts in the field has proven to be highly successful. The long-term impact of this structured educational program is already visible through the large number of young scientists who are now connected via Immunopaedia and who are forming networks in regions where there had been very little contact before and building new Immunological Societies.
| S-EPMC6724660 | biostudies-literature
Project description:A prominent feature of complex networks is the appearance of communities, also known as modular structures. Specifically, communities are groups of nodes that are densely connected among each other but connect sparsely with others. However, detecting communities in networks is so far a major challenge, in particular, when networks evolve in time. Here, we propose a change in the community detection approach. It underlies in defining an intrinsic dynamic for the nodes of the network as interacting particles (based on diffusive equations of motion and on the topological properties of the network) that results in a fast convergence of the particle system into clustered patterns. The resulting patterns correspond to the communities of the network. Since our detection of communities is constructed from a dynamical process, it is able to analyse time-varying networks straightforwardly. Moreover, for static networks, our numerical experiments show that our approach achieves similar results as the methodologies currently recognized as the most efficient ones. Also, since our approach defines an N-body problem, it allows for efficient numerical implementations using parallel computations that increase its speed performance.
| S-EPMC4860646 | biostudies-literature
Project description:To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.
| S-EPMC3240966 | biostudies-literature
Project description:The release of antibiotics (AB) into the environment poses several threats for human health due to potential development of AB-resistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance) in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold. These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of the effects of AB in aquatic ecosystems.
| S-EPMC4077313 | biostudies-literature