Stability analysis of an artificial biomolecular oscillator with non-cooperative regulatory interactions

Oscillators are essential to fuel autonomous behaviours in molecular systems. Artificial oscillators built with programmable biological molecules such as DNA and RNA are generally easy to build and tune, and can serve as timers for biological computation and regulation. We describe a new artificial nucleic acid biochemical reaction network, and we demonstrate its capacity to exhibit oscillatory solutions. This network can be built in vitro using nucleic acids and three bacteriophage enzymes, and has the potential to be implemented in cells. Numerical simulations suggest that oscillations occur in a realistic range of reaction rates and concentrations.     

Constrained Structure of Ancient Chinese Poetry Facilitates Speech Content Grouping

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线性双滞量NDDE振动性的代数判据

本文给出一阶双滞量NDDE对所有参数振动与非振动的充要条件，这些条件用系统诸参数的若干代数式表达，方便于应用验证．     

Diversification of subgenus Calathus (Coleoptera: Carabidae) in the Mediterranean region – glacial refugia and taxon pulses

Aim To investigate the effects of Pleistocene climatic variations on the diversification rate of the subgenus Calathus (Coleoptera: Carabidae), and to estimate the role of vicariance and dispersal for explaining current distributional patterns. Location Western Palaearctic Region, particularly the Mediterranean Basin. Methods Fragments of the mitochondrial cox1–cox2 and the nuclear 28S and EF1α genes were analysed by Bayesian inference. Lineage divergence times were estimated using a Bayesian relaxed molecular clock. Three diversification rate analyses were conducted, namely gamma (γ)‐statistic, birth–death likelihood (BDL) test and survival analyses, in order to test departures from a constant rate model of diversification. A Bayesian approach to dispersal–vicariance analysis was developed to reconstruct the most probable ancestral area of subgenus Calathus and subsequent events of dispersal and colonization. Results A constant rate of speciation events from the late Miocene onwards was found for the subgenus Calathus, whereas recent Pleistocene climatic oscillations played an important role only in shaping intraspecific diversity. Overall diversification patterns for the subgenus are best explained by at least four westward dispersal events from the eastern Mediterranean Basin. Three distinct phylogroups were found for the widely distributed Calathus fuscipes. Incongruence between mitochondrial and nuclear loci was found for a number of species. Main conclusions Diversification analyses suggest either a constant rate of diversification (BDL analysis) or a decrease in diversification rates for the subgenus (survival or γ‐statistics analyses), but not an increase related to the effects of glaciation cycles. Diversification patterns in the subgenus Calathus agree with predictions of the taxon pulse model. From the middle Miocene onwards the Anatolian Peninsula was possibly the main centre of diversification, with successive dispersal events towards the western Mediterranean Basin. Range expansion and secondary contact zones are postulated between members of different phylogroups in C. fuscipes.     

Effects of El Niño Southern Oscillation on avian breeding phenology

Aim

Climate oscillations are known to influence the reproductive phenology of birds. Here, we quantify the effects of cyclic climatic variation, specifically El Niño Southern Oscillation (ENSO), on birds that breed opportunistically. We aim to show how inter‐decadal climate fluctuations influence opportunistic breeding. This knowledge is essential for tracking the phenological responses of birds to climate change.

Location

Temperate and arid Australia.

Methods

We assessed variation in egg‐laying (start, peak, conclusion, length) during the three phases of ENSO (El Niño, La Niña and Neutral) for 64 temperate and 15 arid region species using ~80,000 observations. Linear mixed‐effect models and analysis of variance were used to (1) determine if, on average within each region, egg‐laying dates differed significantly among species between Neutral‐El Niño and Neutral‐La Niña phases, and (2) assess how La Niña and El Niño episodes influence egg‐laying in birds which breed early in the year.

Results

During La Niña phases, which are characterized by mild/wet conditions, most bird species in the temperate and arid regions exhibited longer egg‐laying periods relative to Neutral phases. However, there was substantial variation across species. This effect was strongly seasonal; species breeding in spring experienced the greatest increases in egg‐laying periods during La Niña. Further, we found only small differences in peak egg‐laying dates during Neutral and La Niña in the arid region; suggesting that hot temperatures may constrain breeding regardless of rainfall. The effects of El Niño on breeding phenology were not consistent in the temperate and arid regions and may be confounded by highly mobile species opportunistically moving and breeding with localized rainfall during dry periods.

Main conclusions

In both arid and temperate regions, increased rainfall associated with La Niña phases positively influences avian breeding, and likely recruitment. However, dry El Niño phases may not have the dramatic impacts on breeding phenology that are commonly assumed.

     

Phylogeography of two closely related species of Allium endemic to East Asia: Population evolution in response to climate oscillations

This study investigated the effects of climate oscillations on the evolution of two closely related Allium species, A. neriniflorum and A. tubiflorum. We sequenced three cp DNA (cpDNA) fragments (rps16, rpl32‐trnL, and trnD‐trnT, together approximately 2,500 bp in length) of two closely related Allium species, with samples from 367 individuals in 47 populations distributed across the total range of these species. The interspecific and intraspecific divergence times of the two species were in the Quaternary glaciation. The population divergence was high for the cpDNA variation, suggesting a significant phylogeographic structure (N_ST = 0.844, G_ST = 0.798, p < 0.05). Remarkable ecological differentiation was also revealed by Niche models and statistical analyses. Our results suggest the speciation event of the two species was triggered by violent climatic changes during the Quaternary glaciation.