Scheuring I.,Eotvos Lorand University |
Yu D.W.,CAS Kunming Institute of Zoology |
Yu D.W.,University of East Anglia
Ecology Letters | Year: 2012
There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long-term vertical transmission of Pseudonocardia bacteria, which (somehow) evolve new compounds in arms-race fashion against parasites. Alternatively, attines (somehow) selectively recruit multiple, non-coevolved actinobacterial genera from the soil, enabling a 'multi-drug' strategy against parasites. We reconcile the models by showing that when hosts fuel interference competition by providing abundant resources, the interference competition favours the recruitment of antibiotic-producing (and -resistant) bacteria. This partner-choice mechanism is more effective when at least one actinobacterial symbiont is vertically transmitted or has a high immigration rate, as in disease-suppressive soils. © 2012 Blackwell Publishing Ltd/CNRS.
Ma Z.,CAS Kunming Institute of Zoology
Applied Soft Computing Journal | Year: 2012
We set two objectives for this study: one is to emulate chaotic natural populations in GA (Genetic Algorithms) populations by utilizing the Logistic Chaos map model, and the other is to analyze the population fitness distribution by utilizing insect spatial distribution theory. Natural populations are so dynamic that one of the first experimental evidences of Chaos in nature was discovered by a theoretical ecologist, May (1976, Nature, 261,459-467), in his analysis of insect population dynamics. In evolutionary computing, perhaps influenced by the stable or infinite population concepts in population genetics, the status quo of population settings has dominantly been the fixed-size populations. In this paper, we propose to introduce dynamic populations controlled by the Logistic Chaos map model to Genetic Algorithms (GA), and test the hypothesis - whether or not the dynamic populations that emulate chaotic populations in nature will have an advantage over traditional fixed-size populations. The Logistic Chaos map model, arguably the simplest nonlinear dynamics model, has surprisingly rich dynamic behaviors, ranging from exponential, sigmoid growth, periodic oscillations, and aperiodic oscillations, to complete Chaos. What is even more favorable is that, unlike many other population dynamics models, this model can be expressed as a single parameter recursion equation, which makes it very convenient to control the dynamic behaviors and therefore easy to apply to evolutionary computing. The experiments show result values in terms of the fitness evaluations and memory storage requirements. We further conjecture that Chaos may be helpful in breaking neutral space in the fitness landscape, similar to the argument in ecology that Chaos may help the exploration and/or exploitation of environment heterogeneity and therefore enhance a species' survival or fitness. © 2012 Elsevier B.V.
Ding Y.,CAS Kunming Institute of Zoology
PLoS genetics | Year: 2010
Gene duplication is supposed to be the major source for genetic innovations. However, how a new duplicate gene acquires functions by integrating into a pathway and results in adaptively important phenotypes has remained largely unknown. Here, we investigated the biological roles and the underlying molecular mechanism of the young kep1 gene family in the Drosophila melanogaster species subgroup to understand the origin and evolution of new genes with new functions. Sequence and expression analysis demonstrates that one of the new duplicates, nsr (novel spermatogenesis regulator), exhibits positive selection signals and novel subcellular localization pattern. Targeted mutagenesis and whole-transcriptome sequencing analysis provide evidence that nsr is required for male reproduction associated with sperm individualization, coiling, and structural integrity of the sperm axoneme via regulation of several Y chromosome fertility genes post-transcriptionally. The absence of nsr-like expression pattern and the presence of the corresponding cis-regulatory elements of the parental gene kep1 in the pre-duplication species Drosophila yakuba indicate that kep1 might not be ancestrally required for male functions and that nsr possibly has experienced the neofunctionalization process, facilitated by changes of trans-regulatory repertories. These findings not only present a comprehensive picture about the evolution of a new duplicate gene but also show that recently originated duplicate genes can acquire multiple biological roles and establish novel functional pathways by regulating essential genes.
Chen Y.,CAS Kunming Institute of Zoology |
Jiang J.,University of Texas Southwestern Medical Center
Cell Research | Year: 2013
Hedgehog (Hh) signaling plays pivotal roles in embryonic development and adult tissue homeostasis, and its deregulation leads to numerous human disorders including cancer. Binding of Hh to Patched (Ptc), a twelve-transmembrane protein, alleviates its inhibition of Smoothened (Smo), a seven-transmembrane protein related to G-protein-coupled receptors (GPCRs), leading to Smo phosphorylation and activation. Smo acts through intracellular signaling complexes to convert the latent transcription factor Cubitus interruptus (Ci)/Gli from a truncated repressor to a full-length activator, leading to derepression/activation of Hh target genes. Increasing evidence suggests that phosphorylation participates in almost every step in the signal relay from Smo to Ci/Gli, and that differential phosphorylation of several key pathway components may be crucial for translating the Hh morphogen gradient into graded pathway activities. In this review, we focus on the multifaceted roles that phosphorylation plays in Hh signal transduction, and discuss the conservation and difference between Drosophila and mammalian Hh signaling mechanisms. © 2013 IBCB, SIBS, CAS All rights reserved.
Xu L.,CAS Kunming Institute of Zoology
Dong wu xue yan jiu = Zoological research / "Dong wu xue yan jiu" bian ji wei yuan hui bian ji | Year: 2013
Animal models are indispensible in biomedical research and have made tremendous contributions to answer fundamental questions on human biology, disease mechanisms, and to the development of new drugs and diagnostic tools. Due to the limitations of rodent models in translational medicine, tree shrews (Tupaia belangeri chinensis), the closest relative of primates, have attracted increasing attention in modeling human diseases and therapeutic responses. Here we discuss the recent progress in tree shrew biology and the development of tree shrews as human disease models including infectious diseases, metabolic diseases, neurological and psychiatric diseases, and cancers. Meanwhile, the current problems and future perspectives of the tree shrew model are explored.