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91.
《Journal of biological dynamics》2013,7(5):497-514
The synchronous behaviour of interacting communities is studied in this paper. Each community is described by a tritrophic food chain model, and the communities interact through a network with arbitrary topology, composed of patches and migration corridors. The analysis of the local synchronization properties (via the master stability function approach) shows that, if only one species can migrate, the dispersal of the consumer (i.e., the intermediate trophic level) is the most effective mechanism for promoting synchronization. When analysing the effects of the variations of demographic parameters, it is found that factors that stabilize the single community also tend to favour synchronization. Global synchronization is finally analysed by means of the connection graph method, yielding a lower bound on the value of the dispersion rate that guarantees the synchronization of the metacommunity for a given network topology. 相似文献
92.
93.
Baike Wang Ning Li Juan Wang Shaoyong Huang Yaping Tang Shengbao Yang Tao Yang Qiang Wang Qinghui Yu Jie Gao 《Proteomics》2020,20(8)
So far, over 50 spontaneous male sterile mutants of tomato have been described and most of them are categorized as genetic male sterility. To date, the mechanism of tomato genetic male sterility remained unclear. In this study, differential proteomic analysis is performed between genetic male sterile line (2‐517), which carries the male sterility (ms1035) gene, and its wild‐type (VF‐11) using isobaric tags for relative and absolute quantification‐based strategy. A total of 8272 proteins are quantified in the 2–517 and VF‐11 lines at the floral bud and florescence stages. These proteins are involved in different cellular and metabolic processes, which express obvious functional tendencies toward the hydroxylation of the ω‐carbon in fatty acids, the tricarboxylic acid cycle, the glycolytic, and pentose phosphate pathways. Based on the results, a protein network explaining the mechanisms of tomato genetic male sterility is proposed, finding the compromising fat acid metabolism may cause the male sterility. These results are confirmed by parallel reaction monitoring, quantitative Real‐time PCR (qRT‐PCR), and physiological assays. Taken together, these results provide new insights into the metabolic pathway of anther abortion induced by ms1035 and offer useful clues to identify the crucial proteins involved in genetic male sterility in tomato. 相似文献
94.
Leon Wong Yu‐An Huang Zhu‐Hong You Zhan‐Heng Chen Mei‐Yuan Cao 《Journal of cellular and molecular medicine》2020,24(1):79-87
LncRNA and miRNA are key molecules in mechanism of competing endogenous RNAs(ceRNA), and their interactions have been discovered with important roles in gene regulation. As supplementary to the identification of lncRNA‐miRNA interactions from CLIP‐seq experiments, in silico prediction can select the most potential candidates for experimental validation. Although developing computational tool for predicting lncRNA‐miRNA interaction is of great importance for deciphering the ceRNA mechanism, little effort has been made towards this direction. In this paper, we propose an approach based on linear neighbour representation to predict lncRNA‐miRNA interactions (LNRLMI). Specifically, we first constructed a bipartite network by combining the known interaction network and similarities based on expression profiles of lncRNAs and miRNAs. Based on such a data integration, linear neighbour representation method was introduced to construct a prediction model. To evaluate the prediction performance of the proposed model, k‐fold cross validations were implemented. As a result, LNRLMI yielded the average AUCs of 0.8475 ± 0.0032, 0.8960 ± 0.0015 and 0.9069 ± 0.0014 on 2‐fold, 5‐fold and 10‐fold cross validation, respectively. A series of comparison experiments with other methods were also conducted, and the results showed that our method was feasible and effective to predict lncRNA‐miRNA interactions via a combination of different types of useful side information. It is anticipated that LNRLMI could be a useful tool for predicting non‐coding RNA regulation network that lncRNA and miRNA are involved in. 相似文献
95.
96.
Hai‐Dong Li Linfang Tang Chenxi Jia Marcel Holyoak Jochen Fründ Xiaoqun Huang Zhishu Xiao 《Ecology letters》2020,23(8):1252-1262
Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species’ functional roles in bird–plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird–plant interactions involving birds feeding only on‐the‐tree or both on and under‐the‐tree (shared) had a higher centrality and contributed more to metanetwork organisation than interactions involving birds feeding only under‐the‐tree. Moreover, bird–plant interactions associated with large‐seeded plants disproportionately contributed to metanetwork organisation and centrality. Consequently, on‐the‐tree and shared birds contributed more to metanetwork organisation whereas under‐the‐tree birds were more involved in local processes. We would expect that species’ roles in the metanetwork will translate into different conservation values for maintaining functioning of seed‐dispersal networks. 相似文献
97.
Anna I. Roberts Sam G. B. Roberts 《Biological reviews of the Cambridge Philosophical Society》2020,95(1):51-73
Mammals living in more complex social groups typically have large brains for their body size and many researchers have proposed that the primary driver of the increase in brain size through primate and hominin evolution was the selection pressures associated with sociality. Many mammals, and especially primates, use flexible signals that show a high degree of voluntary control and these signals may play an important role in forming and maintaining social relationships between group members. However, the specific role that cognitive skills play in this complex communication, and how in turn this relates to sociality, is still unclear. The hypothesis for the communicative roots of complex sociality and cognition posits that cognitive demands behind the communication needed to form and maintain bonded social relationships in complex social settings drives the link between brain size and sociality. We review the evidence in support of this hypothesis and why key features of cognitively complex communication such as intentionality and referentiality should be more effective in forming and maintaining bonded relationships as compared with less cognitively complex communication. Exploring the link between cognition, communication and sociality provides insights into how increasing flexibility in communication can facilitate the emergence of social systems characterised by bonded social relationships, such as those found in non‐human primates and humans. To move the field forward and carry out both within‐ and among‐species comparisons, we advocate the use of social network analysis, which provides a novel way to describe and compare social structure. Using this approach can lead to a new, systematic way of examining social and communicative complexity across species, something that is lacking in current comparative studies of social structure. 相似文献
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99.
Piyush Parkhey Aadil Keshaw Ram Batul Diwan J. Satya Eswari 《Preparative biochemistry & biotechnology》2020,50(8):768-780
AbstractThe present study demonstrates a comparative analysis between the artificial neural network (ANN) and response surface methodology (RSM) as optimization tools for pretreatment and enzymatic hydrolysis of lignocellulosic rice straw. The efficacy for both the processes, that is, pretreatment and enzymatic hydrolysis was evaluated using correlation coefficient (R2) & mean squared error (MSE). The values of R2 obtained by ANN after training, validation, and testing were 1, 0.9005, and 0.997 for pretreatment and 0.962, 0.923, and 0.9941 for enzymatic saccharification, respectively. On the other hand, the R2 values obtained with RSM were 0.9965 for cellulose recovery and 0.9994 for saccharification efficiency. Thus, ANN and RSM together successfully identify the substantial process conditions for rice straw pretreatment and enzymatic saccharification. The percentage of error for ANN and RSM were 0.009 and 0.01 for cellulose recovery and for 0.004 and 0.005 for saccharification efficiency, respectively, which showed the authority of ANN in exemplifying the non-linear behavior of the system. 相似文献
100.
Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ). 相似文献