Arik Kershenbaum  Daniel T. Blumstein  Marie A. Roch  Çağlar Akçay  Gregory Backus  Mark A. Bee  Kirsten Bohn  Yan Cao  Gerald Carter  Cristiane Cäsar  Michael Coen  Stacy L. DeRuiter  Laurance Doyle  Shimon Edelman  Ramon Ferrer‐i‐Cancho  Todd M. Freeberg  Ellen C. Garland  Morgan Gustison  Heidi E. Harley  Chloé Huetz  Melissa Hughes  Julia Hyland Bruno  Amiyaal Ilany  Dezhe Z. Jin  Michael Johnson  Chenghui Ju  Jeremy Karnowski  Bernard Lohr  Marta B. Manser  Brenda McCowan  Eduardo Mercado III  Peter M. Narins  Alex Piel  Megan Rice  Roberta Salmi  Kazutoshi Sasahara  Laela Sayigh  Yu Shiu  Charles Taylor  Edgar E. Vallejo  Sara Waller  Veronica Zamora‐Gutierrez 《Biological reviews of the Cambridge Philosophical Society》2016,91(1):13-52

Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well‐known example of birdsong, other animals such as insects, amphibians, and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise – let alone understand – the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near‐future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning, quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, ‘Analysing vocal sequences in animals’. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field, across taxa and across disciplines. We also provide a tutorial‐style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.  相似文献   

    

Xiaofei Chen  Qing Li  Hexin Tan  Xin Dong  Ying Xiao  Langdong Chen  Wansheng Chen 《Plant biotechnology journal》2016,14(12):2217-2227

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《Ecological Indicators》2016

Although changes to interspecific relationships can significantly alter the composition of insect assemblages, they are often ignored when assessing impacts of environmental change. Long-term ground beetle data were used in this study to analyse ecological networks from three habitats at two sites in Scotland. A Bayesian Network inference algorithm was used to reveal interspecific relationships. The significance and strength of relationships between species (nodes) were estimated along with other network properties. Links were identified as positive relationships if co-occurrences of beetles correlated positively, and as negatives relationships if there was a negative correlation between the occurrences of the species. Most of the species had few links and only 10% of the nodes were connected with several links. Calathus fuscipes, a common carabid in the samples, was the most connected, with nine links to other species. More interspecific relationships were found to be positive than negative, with 48 and 23 links, respectively. The modular structure of the network was assessed and eight separate sub-networks were found. Habitat preferences of the species were clearly represented in the structure of the sets of those five sub-networks containing more than one species and were in line with the findings of the indicator species analysis. In our study, we showed that generated Bayesian networks can model interspecific relationships between carabid species. Due to the relative ease of the collection of field data and the high information content of the results, this method could be incorporated into everyday ecological analysis.  相似文献   

    

Dongwang Zheng  Xiaoyan Yang  Donglai Sheng  Dongliang Yu  Guoqing Liang  Luming Guo  Mei Xu  Xu Hu  Daqiang He  Yang Yang  Yuying Wang 《Genesis (New York, N.Y. : 2000)》2016,54(10):534-541

Pou4f2 acts as a key node in the comprehensive and step‐wise gene regulatory network (GRN) and regulates the development of retinal ganglion cells (RGCs). Accordingly, deletion of Pou4f2 results in RGC axon defects and apoptosis. To investigate the GRN involved in RGC regeneration, we generated a mouse line with a POU4F2‐green fluorescent protein (GFP) fusion protein expressed in RGCs. Co‐localization of POU4F2 and GFP in the retina and brain of Pou4f2‐GFP/+ heterozygote mice was confirmed using immunofluorescence analysis. Compared with those in wild‐type mice, the expression patterns of POU4F2 and POU4F1 and the co‐expression patterns of ISL1 and POU4F2 were unaffected in Pou4f2‐GFP/GFP homozygote mice. Moreover, the quantification of RGCs showed no significant difference between Pou4f2‐GFP/GFP homozygote and wild‐type mice. These results demonstrated that the development of RGCs in Pou4f2‐GFP/GFP homozygote mice was the same as in wild‐type mice. Thus, the present Pou4f2‐GFP knock‐in mouse line is a useful tool for further studies on the differentiation and regeneration of RGCs.  相似文献   

    

Cheng-Wei Li 《Cell cycle (Georgetown, Tex.)》2016,15(19):2593-2607

Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest.

Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.  相似文献   

    

Rampal S. Etienne  Gregory S. Gilbert  Shixiao Yu 《Ecology and evolution》2016,6(23):8412-8422

Recent studies have detected phylogenetic signals in pathogen–host networks for both soil‐borne and leaf‐infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next‐generation high‐throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host–fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant–fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant–fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.  相似文献   

    

Tim Kroon  Johny Pires  Valerie J. Dassen  Janna A. Berkhout  Javier Emperador Melero  Aish G. Nadadhur  Mihai Alevra  Ruud F. Toonen  Vivi M. Heine  Huibert D. Mansvelder  Rhiannon M. Meredith 《Developmental neurobiology》2016,76(4):357-374

Developing networks in the immature nervous system and in cellular cultures are characterized by waves of synchronous activity in restricted clusters of cells. Synchronized activity in immature networks is proposed to regulate many different developmental processes, from neuron growth and cell migration, to the refinement of synapses, topographic maps, and the mature composition of ion channels. These emergent activity patterns are not present in all cells simultaneously within the network and more immature “silent” cells, potentially correlated with the presence of silent synapses, are prominent in different networks during early developmental periods. Many current network analyses for detection of synchronous cellular activity utilize activity‐based pixel correlations to identify cellular‐based regions of interest (ROIs) and coincident cell activity. However, using activity‐based correlations, these methods first underestimate or ignore the inactive silent cells within the developing network and second, are difficult to apply within cell‐dense regions commonly found in developing brain networks. In addition, previous methods may ignore ROIs within a network that shows transient activity patterns comprising both inactive and active periods. We developed analysis software to semi‐automatically detect cells within developing neuronal networks that were imaged using calcium‐sensitive reporter dyes. Using an iterative threshold, modulation of activity was tracked within individual cells across the network. The distribution pattern of both inactive and active, including synchronous cells, could be determined based on distance measures to neighboring cells and according to different anatomical layers. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 357–374, 2016  相似文献   

    

Heather E. Golden  Heather A. Sander  Charles R. Lane  Chang Zhao  Katie Price  Ellen D'Amico  Jay R. Christensen 《Ecohydrology》2016,9(1):21-38

Geographically isolated wetlands (GIWs) are characterized as ‘isolated’ because they are embedded by uplands, though they potentially exhibit a gradient of hydrologic, biological, or chemical connections to other surface waters. In fact, recent field studies have begun to elucidate that GIWs exhibit varying degrees of hydrologic connectivity. In this study, we examine the influence of GIWs on streamflow, a potential indicator of GIW hydrologic connectivity with surface waters. We assess annual and seasonal spatially based statistical relationships between GIW characteristics (e.g. volume and extent) and streamflow across a dense network of subbasins using a hybrid modeling approach. Our method involves the Spatial Stream Network (SSN) model, which considers spatial autocorrelation of model covariates explicitly, and the Soil and Water Assessment Tool (SWAT), which predicts streamflow across a network of 579 subbasins in the lower Neuse River Basin, North Carolina, USA. Our study results suggest that GIWs, to some extent, influence streamflow. The further GIWs are from a stream, the greater their capacity to increase streamflow due to the physiographic setting, hypothesized transit times, and sequencing of watershed hydrologic connectivity in the study area. However, as the combined extent of GIWs and non‐GIWs increases in subbasins, seasonal and annual streamflow decreases. Results also suggest that other landscape indicators of watershed‐scale hydrology can, in aggregate with GIWs and non‐GIWs, explain variations in seasonal and annual simulated streamflow. Our study findings begin to elucidate the aggregate influence of GIWs on streamflow, providing insights for future decision‐making on GIW protection and management. Copyright © 2015 John Wiley & Sons, Ltd.  相似文献   

    

Andrew Schneider  Delasa Aghamirzaie  Haitham Elmarakeby  Arati N. Poudel  Abraham J. Koo  Lenwood S. Heath  Ruth Grene  Eva Collakova 《The Plant journal : for cell and molecular biology》2016,85(2):305-319

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Marco Moretto  Alberto Ferrarini  Paola Tononi  Brian Farneti  Nicola Busatto  Urska Vrhovsek  Alessandra dal Molin  Carla Avanzato  Franco Biasioli  Luca Cappellin  Matthias Scholz  Riccardo Velasco  Livio Trainotti  Massimo Delledonne  Fabrizio Costa 《The Plant journal : for cell and molecular biology》2016,88(6):963-975

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