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opencc-zeroNov 2020View details →

Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup

Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a Line Weaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Next, we estimate the fraction of time in locked states and number of transcription events prior to locking, which we validate by measurements under Gyrase inhibition. Replacing the gene of interest by one with slower transcription rate decreases the fraction of time in locked states due to PSB. Finally, we combine data from both constructs to infer a range of possible transcription initiation locking kinetics in a chromosomal location, obtainable by tuning the transcription rate. We validate with measurements of transcription activity at different induction levels. This strategy for dissecting transcription initiation locking kinetics due to PSB can contribute to resolve the transcriptional programs of E. coli and in the engineering of synthetic genetic circuits.

Resource pulses influence the spatio-temporal dynamics of a large carnivore population

Resource availability is a key component in animal ecology, yet the manner in which carnivore populations respond to spatial and temporal fluctuations of resources remains unclear. We take a population-level approach to determine how resource pulses, in this case a temporary hyper-abundance of prey, influence the densities and space-use of cheetahs Acinonyx jubatus. The Maasai Mara in Kenya experiences an annual migration of > 1.4 million wildebeest Connochaetes taurinus and large numbers of zebras Equus quagga and Thomson's gazelle Eudorcas thomsonii thereby providing a natural experiment to examine the influence of resource pulses on carnivore movement and densities. To draw inferences on fluctuating cheetah densities and space-use, we collected unstructured search-encounter data during eight sampling sessions, four during and four out of the migration, and analysed these using Bayesian spatially-explicit capture–recapture (SECR) models with sex-specific detection function parameters. Both density and space-use fluctuated seasonally but this varied according to sex. Local cheetah densities increased in areas and during times when prey abundance was highest but this was more pronounced for females than males. In terms of space-use, movements were larger during the migration than out of the migration but this was more pronounced for males than females. These results suggest that males are influenced more by resource distribution whereas females by resource abundance. Overall densities did vary but there was no clear pattern in relation to resource pulses. Understanding the behavioural drivers of population dynamics in relation to resource pulses can provide important insights into ecological processes at multiple ecological levels.

Data for manuscript: Extinction pulse at Eocene–Oligocene boundary drives diversification dynamics of the two Australian temperate floras

The diversification dynamics of the Australian temperate flora remains poorly understood. Here, we investigate whether differences in plant richness in the southwest Australian biodiversity hotspot (SWA) and southeast (SEA) regions of the Australian continent can be attributed to higher net diversification, more time for species accumulation, or both. We assembled dated molecular phylogenies for the 21 most species-rich flowering plant families found across mesic temperate Australia, encompassing both SWA and SEA regions, and applied a series of diversification models to investigate responses across different groups and time scales. We show that the high richness in SWA can be attributed to a higher net rate of lineage diversification and more time for species accumulation. Different pulses of diversification were retrieved in each region. A decrease in diversification rate across major flowering plant lineages at the Eocene–Oligocene boundary (c. 34 Ma) was witnessed in SEA but not in SW A.

Data from: Infection dynamics, dispersal, and adaptation: understanding the lack of recovery in a remnant frog population following a disease outbreak

Emerging infectious diseases can cause dramatic declines in wildlife populations. Sometimes these declines are followed by recovery, but many populations do not recover. Studying differential recovery patterns may yield important information for managing disease-afflicted populations and facilitating population recoveries. In the late1980s, a chytridiomycosis outbreak caused multiple frog species in Australia's Wet Tropics to decline. Populations of some species (e.g., Litoria nannotis) subsequently recovered, while others (e.g., Litoria dayi) did not. We examined the population genetics and current infection status of L. dayi, to test several hypotheses regarding the failure of its populations to recover: 1) a lack of individual dispersal abilities has prevented recolonization of previously occupied locations, 2) a loss of genetic variation has resulted in limited adaptive potential, and 3) L. dayi is currently adapting to chytridiomycosis. We found moderate to hig h levels of gene flow and diversity (Fst range: <0.01–0.15; minor allele frequency: 0.192–0.245), which were similar to previously published levels for recovered L. nannotis populations. This suggests that dispersal ability and genetic diversity do not limit the ability of L dayi to recolonize upland sites. Further, infection intensity and prevalence increased with elevation, suggesting that chytridiomycosis is still limiting the elevational range of L. dayi. Outlier tests comparing infected and uninfected individuals consistently identified 18 markers as putatively under selection, and several of those markers matched genes that were previously implicated in infection. This suggests that L. dayi has genetic variation for genes that affect infection dynamics and may be undergoing adaptation.

opencc-zeroAug 2021View details →

Taxon pulse dynamics, episodic dispersal, and host colonization across Beringia drive diversification of a holarctic tapeworm assemblage

Aim: We test the predictions of the Stockholm Paradigm, a synthesis of eco-evolutionary theory explaining the nature of faunal assembly, host range and parasite diversification. Faunal diversification and assembly, manifested in patterns of host colonization, co-adaptation and parasite speciation, is predicted to emerge as a consequence of alternating episodes of ecological disruption and stability. Specifically, for a diverse cestode genus (Arostrilepis), we evaluate the number and direction of Pleistocene dispersal events across Beringia, the number and relative timing of host colonization events, and the relationship between host and parasite biogeographic histories and associations through time. Location: Beringia and adjacent temperate to arctic biomes in North America and Eurasia. Taxon: Arostrilepis (Cyclophyllidea: Hymenolepididae) and its rodent hosts. Methods: Multi-locus phylogenetic reconstruction and biogeographic ancestral range estimation. Results: Arostrilepis lineages crossed Beringia eastward into North America a minimum of four times and westward into Asia twice in association with temporally disjunct geographic expansions of three major tribes of cricetid rodents (Arvicolini, Myodini, Lemmini). Inferences of ancestral host associations support at least nine instances of host-colonization involving shifts from one rodent tribe or family to another. Several previously unrecognized lineages of Arostrilepis are revealed. Main conclusions: Consistent with expectations of the Stockholm Paradigm, episodes of intercontinental dispersal were both frequent in the history of Arostrilepis and preceded a majority of inferred host-colonization events. Events of historical geographic expansion created numerous opportunities for development of novel host-parasite associations through ecological fitting, as parasites tracked historically conserved resources available across diverse host taxa. Beringia played a major role in shaping rodent/parasite assemblages by mediating dispersal between the northern continents during glacial episodes of the Pleistocene, rather than by serving as a zone of refugial isolation.

Self-stabilizing Byzantine-resilient communication in dynamic networks (video)

Full video presentation of the paper: Self-stabilizing Byzantine-resilient communication in dynamic networks. Appears in Session 1 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020 <a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>

Dynamic Byzantine Reliable Broadcast

Full video presentation of the paper: Dynamic Byzantine Reliable Broadcast. Appears in Session 1 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020 <a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>

Dynamics of soliton self-injection locking in optical microresonators

<pre>The code and data used to produce the plots within the paper entitled "Dynamics of soliton self-injection locking in optical microresonators." </pre>

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data

This upload contains data and all the scripts required to reproduce the results of the artice entitled "Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data". Code is located within Code.zip . It contains scripts in R and Bash and launchers. Some of the scripts require data files contained within Data.zip. Data is located within Data.zip , such as the sequences, the inferred phylogeny and the Beast XML file.

Data used in: "Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird"

Data for: Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird doi: 10.1098/rspb.2020.2653 Diana E. Bowler, Mikkel A. J. Kvasnes, Hans C. Pedersen, Brett K. Sandercock, Erlend B. Nilsen Questions to: diana.e.bowler@gmail.com or erlend.nilsen@nina.no

Radio-tracking reveals insight into survival and dynamic habitat selection of fledgling Cerulean Warblers

The Cerulean Warbler is a declining Nearctic-Neotropical migrant species of concern that breeds in hardwood forests of the eastern United States and Canada. While much knowledge has been gained about the nesting period of this canopy species, little is known about the post-fledging period. During the 2014 and 2015 breeding seasons, after locating and monitoring nests within a matrix of habitat conditions created by various forest management strategies in NW Pennsylvania, USA, we captured fledglings and used radio telemetry to estimate survival, track movements, and examine habitat selection during their dependent stage. Mortality occurred in 10 of 20 fledglings (50%) during this period, with 8 deaths occurring within three days post-fledging. Most birds left the parental territory within a week of fledging and the maximum distance moved from the nest after 5 d was 462 m; after 14 d it was 1.3 km; and after 24 d it was, somewhat unexpectedly, 4.4 km. Fledglings used a diversity of habitat and management types, including clear-cut patches, 25-yr-old regenerating clear-cuts, shelterwood cuts, and mature undisturbed forest. Over the entire tracking period (up to 35 d), fledglings selected for habitats with greater midstory cover, lower basal area, and lesser sapling cover (when compared with paired, random locations). However, lesser sapling cover may also be correlated with decreased survival for birds that come down from the canopy immediately upon fledging. Our results suggest that a diversity of management types, including some quite different from those that produce habitat typically selected by adults, and maintaining large blocks of contiguous forest would benefit fledgling Cerulean Warblers.

Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses

Transposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in twenty-six genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The twenty-six genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.

Imaging elastodynamic and hydraulic properties of in-situ fractured rock: An experimental investigation exploring effects of dynamic stressing and shearing

We describe laboratory experiments to elucidate the relationship between nonlinear elasticity and permeability evolution in fractured media subjected to local stress perturbations. This study is part of an effort to image fluid pathways and fracture properties using active-source acoustic monitoring during fluid injection and shear of rough fractures. Experiments were conducted with L-shaped samples of Westerly granite fractured in-situ under tri-axial conditions with deionized water subsequently circulated through the resulting fractures. After in-situ fracturing, we separately imposed oscillations of the applied normal stress and pore pressure with amplitudes ranging from 0.2 to 1 MPa and frequencies from 0.1 to 40 Hz. During these dynamic perturbations an array of piezoelectric transducers continuously transmitted ultrasonic pulses across the fracture to monitor the evolving  elastic response. We interpret the resulting evolution of elastic wave properties in the context of elastic nonlinearity and relate the estimated nonlinearity parameters to the relative change in permeability of the fractured media. Fracture roughness is then altered in-situ by shearing, with the generation of breccia and wear products. We document the evolution of permeability and fracture contact stiffness as a function of dynamic stressing and shear offset and discuss our findings in relation to fractures in Earth's crust.

Data from: Carbon flux and forest dynamics: increased deadwood decomposition in tropical rainforest tree-fall gaps

This study was carried out within an area of lowland, old growth dipterocarp rainforest in the Maliau Basin Conservation Area, Sabah, Malaysia (4° 44' 35" to 55" N and 116° 58' 10" to 30" E; mean annual rainfall 2838 mm ± 93 mm). On the 20th of July 2017, there was a storm at the study site, which generated winds speeds of 8.4 m/s (Fig. S1). These were among the strongest winds normally experienced in inland forests of the region, which placed extreme sheer stress on trees. Consequently, a large number of trees fell within the same 24-hour period in the study location. Ten tree-fall gaps (mean length: 32 m ± 2.8, mean width: 24.5 m ± 3; see table S1 for gap characteristics) created during this event were selected for use in this investigation, along with ten adjacent closed canopy sites, located 20 m from the edge of each gap. We took 10 hemispherical photos in each gap and closed canopy sites to quantity canopy openness at each location.

opencc-by-4.0Jan 2021View details →

Dynamic Characteristics of Lightning Channel Radial Expansion

The original datas of  manuscript entitled“Dynamic Characteristics of Lightning Channel Radial Expansion”.

DragonDrop: passive dynamics and control strategies of aerial righting in the dragonfly

Dragonflies perform dramatic aerial manoeuvres when hunting prey or chasing rivals but glide leisurely with wings virtually fixed. This makes dragonflies a great system to explore how to minimize the trade-off between manoeuvrability and stability. We challenged the dragonfly by dropping it from selected inverted attitudes and digitised the 6-degrees-of-freedom aerial recovery kinematics via custom motion capture techniques. From these kinematic data we then performed rigid-body inverse dynamics to reconstruct the forces and torques involved in the righting behaviour. We found that inverted dragonflies typically recover themselves with the shortest rotation from the initial body inclination. Additionally, they exhibited a strong tendency to pitch up with their head leading out of the manoeuvre. Surprisingly, anaesthetised dragonflies could also complete the aerial righting. Such passive righting disappears in recently dead dragonflies but can be partially recovered by waxing their wings to mimic the wing posture of the anesthetised dragonflies. Our inverse dynamics model and wind tunnel experiments support the idea that certain wing postures readily provide stability and may explain the dragonfly's rotational preference. This work demonstrates for the first time that aerodynamically stable body configuration exists in gliding insects, and an active insect can leverage this passive stability as needed.

opencc-by-4.0Jan 2021View details →

Static and Dynamic Monolith Migration

A data set of two monolith systems and evaluation of their migration to a microservices architecture

Data for: Pendulum-based measurements reveal impact dynamics at the scale of a trap-jaw ant

Small organisms can produce powerful, sub-millisecond impacts by moving tiny structures at high accelerations. We developed and validated a pendulum device to measure the impact energetics of microgram-sized trap-jaw ant mandibles accelerated against targets at 105 m s-2. Trap-jaw ants (Odontomachus brunneus; 19 individuals; 212 strikes) were suspended on one pendulum and struck swappable targets that were either attached to an opposing pendulum or fixed in place. Mean post-impact kinetic energy (energy from strike converted to pendulum motion) was higher with a stiff target (21.0-21.5 µJ) than a compliant target (6.4-6.5 µJ). Target mobility had relatively little influence. Mean contact duration of strikes against stiff targets was shorter (3.9-4.5 ms) than against compliant targets (6.2-7.9 ms). Shorter contact duration was correlated with higher post-impact kinetic energy. These findings contextualize and provide an energetic explanation for the diverse, natural uses of trap-jaw ant strikes such as impaling prey, launching away threats, and performing mandible-powered jumps. The strong effect of target material on energetic exchange suggests material interactions as an avenue for tuning performance of small, high acceleration impacts. Our device offers a foundation for novel research into the ecomechanics and evolution of tiny biological impacts and their application in synthetic systems.

Dynamic feedbacks among tree functional traits, termite populations and deadwood turnover

1. Changes in the composition of plant functional traits may affect ecosystem processes through influencing trophic interactions. Bottom-up control by plant species through food availability to animals may vary with time. However, such dynamics and their consequences for deadwood turnover are poorly known for detrital food webs. 2. We introduce a dynamic conceptual model of the feedback of (deadwood-feeding) termite populations, tree functional traits and deadwood decomposition. We hypothesized that tree functional diversity (in terms of a wood resource economic spectrum, WES) supports the sustenance of termite populations via complementary food supplied through time, as deadwood varies in traits both initially between species and because of different decomposition rates. Simultaneously, the consumption of deadwood by termites was hypothesized to sustain deadwood turnover in a functionally diverse forest by the same temporal mechanism of changing wood quality of multiple species over time. 3. We tested our hypothesis through an 18-month termite-exclusion decomposition experiment by incubating coarse (i.e., 5 cm diameter) deadwood of 34 woody species in two subtropical forests in East China. One site still sustained a healthy population of pangolins as the keystone termite predator, while another had lost its pangolins due to hunting and illegal wildlife trade. 4. The results supported our hypothesis: in the first 12 months, termites amplified the positive linear relationship between % wood mass loss and initial wood quality (WES). In contrast, between 12 and 18 months, termite-mediated consumption, and associated wood mass loss, showed a humpback relation with the initial WES. This shift in termite preference of deadwood species along the WES indicated complementary food availability to termites through time. 5. Synthesis. Our findings imply that tree functional composition, through variation in deadwood quality through decomposition time, can help to sustain termite populations and thereby forest carbon turnover. Future studies need to test whether and how our conceptual model may apply to other detrital systems and food webs. In general, food web research would benefit from a stronger focus on temporal patterns for better understanding the interactions of basal resource functional traits and consumers on ecosystem functions.

Temporal dynamics and biocontrol potential of a hyperparasite on coffee leaf rust across a landscape in Arabica coffee's native range

Agroforestry systems can provide habitats for rich biodiversity including multitrophic interactions, which presents opportunities to develop natural pest control. Shade coffee systems in several coffee-growing areas of the world host such unique habitats where pests and their natural enemies interact. One of the major global challenges for coffee production, coffee leaf rust caused by the fungal pathogen Hemileia vastatrix is attacked by the fungal hyperparasite, Lecanicillium lecanii. However, we lack insights in the dynamics and biocontrol potential of the hyperparasite on coffee leaf rust from landscapes in Arabica coffee's native range. To understand the temporal dynamics across landscapes and environmental drivers of the rust and hyperparasite, and the potential for biocontrol of the rust by the hyperparasite, we studied the rust and hyperparasite during the dry and wet seasons for three consecutive years at 60 sites across a gradient of coffee management in southwestern Ethiopia. We found that coffee leaf rust was more severe during the dry season, whereas the hyperparasite was more severe during the wet season in two out of three years. The rust growth rate from the wet to the dry season transition was negatively related to the hyperparasite index during the wet season, implying a potential top-down control. Coffee leaf rust was generally more severe at lower altitudes in the dry season, whereas the hyperparasite was more severe at high altitude. The rust incidence increased with management intensity, while the hyperparasite was more common under less intensive management. This study could be interesting in that it represents a landscape where Arabica coffee originated and the rust and hyperparasite might have a long co-evolutionary history. Our findings highlight the potential of the hyperparasite to suppress the rust's growth rate from the wet to dry season transition when the rust severity could otherwise be at its peak. We show that less intensively managed landscapes with dense shade levels are likely to increase hyperparasite abundance and result in an improved top-down control of the rust. However, more detailed knowledge is needed on the interaction of these species to assess its importance for reducing rust induced yield losses or the risk of rust outbreaks.