Precise species identification and whole-genome sequencing analysis of Enterobacter cloacae complex causing bloodstream infections in China
Yanbing Li, Ziran Wang, Ge Zhang
et al.
ABSTRACT The Enterobacter cloacae complex (ECC) is one of the major causes of hospital-acquired infections. However, achieving accurate species identification and comprehensive resistance profiling remains difficult in clinical practice, with a limited understanding of species-specific resistance patterns. ECC isolates were collected from patients with bloodstream infections at Peking Union Medical College Hospital between 2015 and 2020. Whole-genome sequencing (WGS) was performed to identify species, analyze antimicrobial resistance genes, and explore genomic variation in serial isolates. Multi-locus sequence typing (MLST) profiles were extracted from the WGS data. Phylogenetic analysis was conducted based on hsp60 sequences. Eleven hsp60 clusters were identified, with cluster VIII being the most prevalent (28/108). Average nucleotide identity (ANI)-based species classification showed Enterobacter hormaechei (31.5%) and Enterobacter xiangfangensis (15.7%) were dominant species. Five clade-cluster pairs (B-VIII, A-VI, G-XI, D-III, R-IX) accounted for 74% of isolates. A total of 90 sequence types (STs) were detected, including 29 novel STs. Resistance gene analysis revealed a high prevalence of blaACT, with distinct distribution patterns observed among different species. Twenty isolates were carbapenem-resistant, with three carrying blaNDM-1/5. Enterobacter roggenkampii was the most common species (5/20) among all carbapenem-resistant isolates, and 83.3% of the isolates showed resistance to both carbapenems and colistin. Comparative genomics of longitudinal isolates from individual patients revealed adaptive single-nucleotide polymorphisms (SNPs) in pco genes. This study provides a detailed genomic characterization of ECC isolates from bloodstream infections, highlighting species diversity, resistance gene distribution, and potential within-host evolution. These insights advocate genome-based surveillance in managing ECC infections and understanding resistance evolution in clinical contexts.IMPORTANCEEnterobacter cloacae complex (ECC) is a major cause of hospital-acquired bloodstream infections, yet species-level identification and resistance profiling remain challenging. As one of the largest whole-genome sequencing (WGS)-based studies of ECC bloodstream isolates in northern China to date, we performed whole-genome sequencing of 108 ECC isolates, revealing high genetic diversity and identifying 29 novel sequence types. We clarified the correspondence between species, clades, and clusters and highlighted Enterobacter roggenkampii as a potential high-risk species linked to carbapenem and colistin resistance. Our findings not only improve the understanding of ECC population structure and resistance evolution in China but also provide valuable genomic data for future epidemiological surveillance and species-level diagnostics.
Spatiotemporal heterogeneity and driving forces of construction carbon emissions in transitional regions: evidence from six provinces in Central China
Yinkai Wei, Wudong Ban
This study explores the spatiotemporal patterns of construction carbon emissions in Central China (Anhui, Shanxi, Jiangxi, Henan, Hunan, Hubei) under China's carbon peak and neutrality goals. Using certified construction data, NPP–VIIRS nighttime light data, energy statistics, and socioeconomic panel data from 2012 to 2025, we examine emission dynamics and spatial heterogeneity. Results show that total emissions reached 1.039 billion tons of CO₂ equivalent, with Shanxi accounting for over 20%. Spatial clustering exhibited a fluctuating downward trend, with High–High clusters in Shanxi and northern Henan, and Low–Low clusters in southern Anhui, western Hubei, and northern Jiangxi. Geodetector results reveal that regional GDP and secondary industry output were dominant drivers, and their interactions with population and technology investment reached a maximum q‑statistic of 0.98. These findings support targeted low-carbon policies for the construction sector in transitional regions.
New femoral evidence from the Afar reveal the early evolution of habitual squatting behaviors in the genus Theropithecus
Laurent Pallas, Laurent Pallas, Laurent Pallas
et al.
IntroductionThe femoral anatomy of fossil Theropithecus is poorly known, although it provides critical data for inferring squatting behaviors, a characteristic trait of extant Theropithecus gelada.MethodsHere, we describe and provide functional and taxonomic interpretations on two subcomplete femora from the Afar Depression using a combination of traditional morphometrics (bivariate and multivariate) and 2D geometric morphometric combined with multivariate analyses and hierarchical clustering. ResultsThe ca. 3.20 Ma A.L. 206–1 femur is identified as the oldest known and most complete femur of an adult Theropithecus cf. oswaldi darti and shows a morphology similar to that of extant T. gelada. It supports the hypothesis of an early emergence of squatting behaviors in Theropithecus, prior to the onset of dental adaptations related to the grazing diet of the genus. The ca. 2.60 Ma A.L. 94–5 femur is identified as the oldest and most complete femur known of an adult Theropithecus cf. oswaldi oswaldi. Its knee anatomy is distinct from that of T. o. darti but it nonetheless shares with T. gelada and other fossil Theropithecus functional traits related to squatting behaviors. Unexpected convergences with arboreal cercopithecids are observed in Theropithecus brumpti, indicating diversity in the femoral functional anatomy of Theropithecus. DiscussionOverall, our study highlights the future need to link femoral anatomical diversity with postural and locomotor behaviors by combining paleontological data with neontological data including biomechanical data on the squatting and climbing of large extant papionins.
Evolution of mutating pathogens in networked populations
Aviel Ivry, Reuven Cohen, Amikam Patron
Epidemic spreading over populations networks has been an important subject of research for several decades, and especially during the Covid-19 pandemic. Most epidemic outbreaks are likely to create multiple mutations during their spreading over the population. In this paper, we study the evolution of a pathogen which can mutate continuously during the epidemic spreading. We consider pathogens whose mutating parameter is the mortality mean-time, and study the evolution of this parameter over the spreading process. We use analytical methods to compute the dynamic equation of the epidemic and the conditions for it to spread. We also use numerical simulations to study the pathogen flow in this case, and to understand the mutation phenomena. We show that the natural selection leads to less violent pathogens becoming predominant in the population. We discuss a wide range of network structures and show how different effects are manifested in each case. We also applied our theory in the context of the Covid-19 pandemic, using relevant epidemiological data collected for this outbreak. We provided explanations for the variants spreading processes observed throughout this pandemic.
en
q-bio.PE, physics.soc-ph
Twenty years of population dynamics in European beech-oak forest at their rear range margin anticipate changes in its structure and composition
Álvaro Rubio-Cuadrado, Iciar Alberdi, Isabel Cañellas
et al.
There is an increasing interest in restoring degraded forests, which occupy half of the forest areas. Among the forms of restoration, passive restoration, which involves the elimination of degrading factors and the free evolution of natural dynamics by applying minimal or no management, is gaining attention. Natural dynamics is difficult to predict due to the influence of multiple interacting factors such as climatic and edaphic conditions, composition and abundance of species, and the successional character of these species. Here, we study the natural dynamics of a mixed forest located in central Spain, which maintained an open forest structure, due to intensive use, until grazing and cutting were banned in the 1960s. The most frequent woody species in this forest are Fagus sylvatica, Quercus petraea, Quercus pyrenaica, Ilex aquifolium, Sorbus aucuparia, Sorbus aria and Prunus avium, with contrasting shade and drought tolerance. These species are common in temperate European deciduous forest and are found here near their southern distribution limit, except for Q. pyrenaica. In order to analyze forest dynamics and composition, three inventories were carried out in 1994, 2005 and 2015. Our results show that, despite the Mediterranean influence, the natural dynamics of this forest has been mainly determined by different levels of shade tolerance. After the abandonment of grazing and cutting, Q. pyrenaica expanded rapidly due to its lower shade tolerance, whereas after canopy closure and forest densification, shade-tolerant species gained ground, particularly F. sylvatica, despite its lower drought and late-frost tolerance. If the current dynamics continue, F. sylvatica will overtake the rest of the species, which will be relegated to sites with shallow soils and steep slopes. Simultaneously, all the multi-centennial beech trees, which are undergoing a rapid mortality and decline process, will disappear.
Carnivores’ contributions to people in Europe
Sofía Palacios-Pacheco, Berta Martín-López, Mónica Expósito-Granados
et al.
Human-carnivore relations in Europe have varied throughout history. Because of recent conservation efforts and passive rewilding, carnivore populations are recovering, which translates into more interactions with humans. Thus, unraveling these interactions as well as the multiple contributions carnivores provide to people is crucial to their conservation. We examined the literature conducted in Europe since 2000 and used the nature’s contributions to people (NCP) framework to identify factors that have shaped human-carnivore relations. To do so, we examined the state of scientific knowledge and relationships among types of NCP from carnivores, countries, and carnivore species; and between NCP, actors, and management actions. Results indicated that research has been oriented toward large carnivore species and their detrimental contributions to people. Further, the effectiveness of carnivore management strategies has only been evaluated and monitored in a limited set of all the research. To balance any negative views on carnivores, we suggest that the recognition of the duality of carnivores, as providers of both beneficial and detrimental contributions, should be included in EU conservation policies.
Biology (General), Ecology
Palaeoenvironments and hominin evolutionary dynamics in southeast Asia
Anne-Marie Bacon, Nicolas Bourgon, Elise Dufour
et al.
Abstract Secure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164–131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of early Homo sapiens from Tam Pà Ling Cave (46–43 ka), Laos, it appears that only our species was able to exploit rainforest resources.
Effect of Inoculation on the Mechanical Properties of AZ91
C. Rapiejko, D. Mikusek, K. Kubiak
et al.
The effect of Ca element on the microstructure evolution of the AZ91 magnesium alloy was investigated in this research. The magne-sium-aluminium alloy AZ91 was inoculated with the Emgesal® Flux 5 to refine its microstructure and also improve its microstructure. Six different concentrations of the Emgesal® Flux 5 content were tested, ranging from 0.1 to 0.6% wt., and compared to the baseline of the AZ91 alloy without inoculation. Melted metal was poured into a preheated metallic mould. Samples to test were achieved after turning treatment. Formed microstructure was assessed using an optical microscope. The microstructure was refined for every tested samples. Me-chanical properties such as tensile strength, elongation, Brinell hardness, Vickers microhardness, abrasion resistance and adhesive resistance were tested on the inoculated samples and compared to the non-inoculated AZ91. Introducing an Emgesal®Flux 5 inoculant caused a change in the tensile strength, elongation, Brinell hard-ness, Vickers microhardness, abrasive wear resistance as well as adhesive wear resistance in each examined concentration.
Role of second phases in the corrosion resistance and cerium conversion coating treatment of as-extruded Mg–8Al–4Ca magnesium alloy
Chang-Yang Hsieh, Shih-Yen Huang, Yu-Ren Chu
et al.
The presence of a second phase in the Mg–8Al–4Ca (at. %) alloy plays a significant role on both its corrosion behavior and the chemical conversion coating processes. Using scanning Kelvin probe force microscopy (SKPFM), a lower Volta-potential of the second phase present on the surface has been measured. The β-Al-Ca phase has a higher electrochemical activity than the α-Mg matrix and may act as the micro-galvanic anode in a local electrochemical corrosion process. Transmission electron microscopy (TEM) examinations reveal that the β-Al-Ca phase is more susceptible to corrosion than the α-Mg matrix in an aqueous solution, and its higher activity and higher corrosion rate accelerate the hydrogen evolution rate on the α-Mg matrix in the cerium (Ce) conversion coating process. It's also been discovered that by immersing the bare Mg–Al–Ca alloy in deionized (DI) water, the β-Al-Ca phase, exposed on the surface, can be dissolved and converted in situ into aluminum hydroxide (Al(OH)3), and the Ce conversion coating can be deposited via replacement reactions in the subsequent conversion coating process. A thicker Ce coating with smaller blisters has then been produced on the DI-treated Ce-coated Mg specimen; it indeed improves the corrosion resistance.
Mining engineering. Metallurgy
Long-term N addition reduced the diversity of arbuscular mycorrhizal fungi and understory herbs of a Korean pine plantation in northern China
Wei Wang, Yuhan Feng, Ruotong Wu
et al.
With the development of agriculture and industry, the increase in nitrogen (N) deposition has caused widespread concern among scientists. Although emission reduction policies have slowed N releases in Europe and North America, the threat to biodiversity cannot be ignored. Arbuscular mycorrhizal (AM) fungi play an important role in the establishment and maintenance of plant communities in forest ecosystems, and both their distribution and diversity have vital ecological functions. Therefore, we analyzed the effects of long-term N addition on AM fungi and understory herbaceous plants in a Korean pine plantation in northern China. The soil properties, community structure, and diversity of AM fungi and understory herbaceous plants were detected at different concentrations of NH4NO3 (0, 20, 40, 80 kg N ha−1 year−1) after 7 years. The results showed that long-term N deposition decreased soil pH, increased soil ammonium content, and caused significant fluctuations in P elements. N deposition improved the stability of soil aggregates by increasing the content of glomalin-related soil protein (GRSP) and changed the AM fungal community composition. The Glomus genus was more adaptable to the acidic soil treated with the highest N concentration. The species of AM fungi, understory herbaceous plants, and the biomass of fine roots were decreased under long-term N deposition. The fine root biomass was reduced by 78.6% in the highest N concentration treatment. In summary, we concluded that long-term N deposition could alter soil pH, the distribution of N, P elements, and the soil aggregate fractions, and reduce AM fungal and understory herb diversity. The importance of AM fungi in maintaining forest ecosystem diversity was verified under long-term N deposition.
A Chondritic Solar Neighborhood
Isabella L. Trierweiler, Alexandra E. Doyle, Edward D. Young
A persistent question in exoplanet demographics is whether exoplanetary systems form from similar compositional building blocks to our own. Polluted white dwarf stars offer a unique way to address this question, as they provide measurements of the bulk compositions of exoplanetary material. We present a statistical analysis of the rocks polluting oxygen-bearing white dwarfs and compare their compositions to rocks in the solar system. We find that the majority of the extrasolar rocks are consistent with the composition of typical chondrites. Measurement uncertainties prevent distinguishing between chondrites and bulk Earth but do permit detecting the differences between chondritic compositions and basaltic or continental crust. We find no evidence of crust among the polluted white dwarfs. We show that the chondritic nature of extrasolar rocks is also supported by the compositions of local stars. While galactic chemical evolution results in variations in the relative abundances of rock-forming elements spatially and temporally on galaxy-wide scales, the current sample of polluted white dwarfs are sufficiently young and close to Earth that they are not affected by this process. We conclude that exotic compositions are not required to explain the majority of observed rock types around polluted white dwarfs and that variations between exoplanetary compositions in the stellar neighborhood are generally not due to significant differences in the initial composition of protoplanetary disks. Nonetheless, there is evidence from stellar observations that planets formed in the first several billion years in the Galaxy have lower metal core fractions compared with Earth on average.
The context-specificity of virulence evolution revealed through evolutionary invasion analysis
Sudam Surasinghe, Ketty Kabengele, Paul E. Turner
et al.
Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict how the relationship between virulence (the harm to hosts caused by an infection) and transmission will evolve in certain virus-host contexts. In this study, we invoke evolutionary invasion analysis -- a method used to identify the evolution of uninvadable strategies in dynamical systems -- to examine how the virulence-transmission dichotomy can evolve in models of virus infections defined by different natural histories. We reveal that peculiar ecologies drive different evolved relationships between virulence and transmission. Specifically, we discover patterns of virulence evolution between epidemics of various kinds (SARS-CoV-2 and hepatitis C virus) and that varying definitions of virulence alter our predictions for how viruses will evolve. We discuss the findings in light of contemporary conversations in the public health sector around the possibility of predicting virus evolution and in more extensive theoretical discussions involving virulence evolution in emerging infectious diseases.
On fractional-order symmetric oscillator with offset-boosting control
Changjin Xu, Mati ur Rahman, Dumitru Baleanu
This article analyzes the dynamical evolution of a three-dimensional symmetric oscillator with a fractional Caputo operator. The dynamical properties of the considered model such as equilibria and its stability are also presented. The existence results and uniqueness of solutions for the suggested model are analyzed using the tools from fixed point theory. The symmetric oscillator is analyzed numerically and graphically with various fractional orders. It is observed that the fractional operator has a significant impact on the evolution of the oscillator dynamics showing that the system has a limit-cycle attractor. Offset-boosting control phenomena in the system are also studied with different orders and parameters.
Impact of Timanian thrust systems on the late Neoproterozoic–Phanerozoic tectonic evolution of the Barents Sea and Svalbard
J.-B. P. Koehl, J.-B. P. Koehl, J.-B. P. Koehl
et al.
<p>The Svalbard Archipelago consists of three basement terranes that record a
complex Neoproterozoic–Phanerozoic tectonic history, including four
contractional events (Grenvillian, Caledonian, Ellesmerian, and Eurekan) and
two episodes of collapse- to rift-related extension (Devonian–Carboniferous
and late Cenozoic). Previous studies suggest that these three terranes likely
accreted during the early to mid-Paleozoic Caledonian and Ellesmerian
orogenies. Yet recent geochronological analyses show that the northwestern
and southwestern terranes of Svalbard both record an episode of amphibolite
(–eclogite) facies metamorphism in the latest Neoproterozoic, which may
relate to the 650–550 <span class="inline-formula">Ma</span> Timanian Orogeny identified in northwestern
Russia, northern Norway, and the Russian Barents Sea. However, discrete
Timanian structures have yet to be identified in Svalbard and the Norwegian
Barents Sea. Through analysis of seismic reflection, as well as regional
gravimetric and magnetic data, this study demonstrates the presence of
continuous thrust
systems that are several kilometers thick, NNE-dipping, deeply buried, and extend thousands of kilometers from northwestern Russia to
northeastern Norway, the northern Norwegian Barents Sea, and the Svalbard
Archipelago. The consistency in orientation and geometry, as well as apparent
linkage between these thrust systems and those recognized as part of the
Timanian Orogeny in northwestern Russia and Novaya Zemlya, suggests that the
mapped structures are likely Timanian. If correct, these findings would
imply that Svalbard's three basement terranes and the Barents Sea were
accreted onto northern Norway during the Timanian Orogeny and should hence
be attached to Baltica and northwestern Russia in future
Neoproterozoic–early Paleozoic plate tectonics reconstructions. In the
Phanerozoic, the study suggests that the interpreted Timanian thrust systems
represent major preexisting zones of weakness that were reactivated,
folded, and overprinted by (i.e., controlled the formation of new) brittle
faults during later tectonic events. These faults are still active at
present and can be linked to folding and offset of the seafloor.</p>
Historical surveys reveal a long‐term decline in muskrat populations
Carrie Sadowski, Jeff Bowman
Abstract The muskrat (Ondatra zibethicus) is an iconic species in Canada, valued for both its fur and its integral role in wetland ecosystems, and widely regarded for its perseverance. However, the resilience of this semiaquatic mammal seems to be in question now as increasing evidence points to widespread population declines. Recent analyses of harvest data across North America suggest a reduction in their numbers, but this has not been widely corroborated by population surveys. In this study we replicated historic muskrat house count surveys at two large Great Lakes coastal wetlands and present confirmation that declines in muskrat harvest correspond to actual declines in muskrat abundance. At the Point Pelee National Park marsh and the Matchedash Bay‐Gray Marsh wetland we found that mean muskrat house counts declined by 93% and 91% respectively between historic surveys 40–50 yrs ago and contemporary surveys over the past 7 yrs. The factors responsible for these dramatic declines remain unclear but there may be a relationship with changes in the habitat quality of these wetlands that have occurred over the same time frame. Not only is the loss of muskrats an issue for the resulting loss of the wetland ecosystem services they provide, but it may be an indication of broader marsh ecosystem degradation. As such, a scarcity of muskrats should be considered a red flag for the state of biodiversity in our wetlands. Continued surveys and ongoing research are needed to shed more light on the current status of muskrat populations and their marsh habitats across their native range.
OG-SPACE: Optimized Stochastic Simulation of Spatial Models of Cancer Evolution
Fabrizio Angaroni, Marco Antoniotti, Alex Graudenzi
Algorithmic strategies for the spatio-temporal simulation of multi-cellular systems are crucial to generate synthetic datasets for bioinformatics tools benchmarking, as well as to investigate experimental hypotheses on real-world systems in a variety of in-silico scenarios. In particular, efficient algorithms are needed to overcome the harsh trade-off between scalability and expressivity, which typically limits our capability to produce realistic simulations, especially in the context of cancer evolution. We introduce the Optimized Gillespie algorithm for simulating Stochastic sPAtial models of Cancer Evolution (OG-SPACE), a computational framework for the simulation of the spatio-temporal evolution of cancer subpopulations and of the experimental procedures of both bulk andsingle-cell sequencing. OG-SPACE relies on an evolution of the Gillespie algorithm optimized to deal with large numbers of cells and is designed tohandle a variety of birth-death processes and interaction rules on arbitrary lattices. As output OG-SPACE returns: the visual snapshots of the spatial configuration of the system over time, the phylogeny of the (sampled) cells, the mutational tree, the variant allele frequency spectrum (for bulk experiments) and the cell genotypes (for single-cell experiments).OG-SPACE is freely available at:https://github.com/BIMIB-DISCo/OG-SPACE
en
q-bio.PE, physics.bio-ph
Antigenic waves of virus-immune co-evolution
Jacopo Marchi, Michael Lässig, Aleksandra M. Walczak
et al.
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses even further away. Quantitatively understanding how these dynamics result in observed patterns of rapid pathogen and immune adaptation is instrumental to epidemiological and evolutionary forecasting. Here we present a mathematical theory of co-evolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections. We show the emergence of an antigenic wave that is pushed forward and canalized by cross-reactivity. We obtain analytical results for shape, speed, and angular diffusion of the wave. In particular, we show that viral-immune co-evolution generates a new emergent timescale, the persistence time of the wave's direction in antigenic space, which can be much longer than the coalescence time of the viral population. We compare these dynamics to the observed antigenic turnover of influenza strains, and we discuss how the dimensionality of antigenic space impacts on the predictability of the evolutionary dynamics. Our results provide a concrete and tractable framework to describe pathogen-host co-evolution.
Fast Minimization of Fixed Polarity Reed-Muller Expressions
Zhenxue He, Limin Xiao, Zhisheng Huo
et al.
Logic minimization has recently attracted significant attention because in many applications it is important to have a compact representation as possible. In this paper, we propose a fast minimization algorithm (FMA) of fixed polarity Reed-Muller expressions (FPRMs). The main idea behind the FMA is to search the minimum FPRM with the fewest products by using the proposed binary differential evolution algorithm (BDE). The BDE can efficiently maintain population diversity and achieve a better tradeoff between the exploration and exploitation capabilities by use of proposed binary random mutation operator and improved selection operator. The experimental results on 24 MCNC benchmark circuits demonstrate that the FMA outperforms the genetic algorithm-based and simulated annealing genetic algorithm-based FPRMs minimization algorithms in terms of accuracy of solutions and solving efficiency. To the best of our knowledge, we are the first to use differential evolution algorithm to minimize FPRMs. The FMA can be extended to derive a minimum mixed polarity Reed-Muller expression.
Electrical engineering. Electronics. Nuclear engineering
Nature of selection varies on different domains of IFI16-like PYHIN genes in ruminants
Sushil Kumar, Jatinder Singh Chera, Ashutosh Vats
et al.
Abstract Background ALRs (AIM2-like Receptors) are germline encoded PRRs that belong to PYHIN gene family of cytokines, which are having signature N-terminal PYD (Pyrin, PAAD or DAPIN) domain and C-terminal HIN-200 (hematopoietic, interferon-inducible nuclear protein with 200 amino acid repeat) domain joined by a linker region. The positively charged HIN-200 domain senses and binds with negatively charged phosphate groups of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) purely through electrostatic attractions. On the other hand, PYD domain interacts homotypically with a PYD domain of other mediators to pass the signals to effector molecules downwards the pathways for inflammatory responses. There is remarkable inter-specific diversity in the numbers of functional PYHIN genes e.g. one in cow, five in human, thirteen in mice etc., while there is a unique loss of PYHIN genes in the bat genomes which was revealed by Ahn et al. (2016) by studying genomes of ten different bat species belonging to sub-orders yinpterochiroptera and yangochiroptera. The conflicts between host and pathogen interfaces are compared with “Red queen’s arms race” which is also described as binding seeking dynamics and binding avoidance dynamics. As a result of this never-ending rivalry, eukaryotes developed PRRs as antiviral mechanism while viruses developed counter mechanisms to evade host immune defense. The PYHIN receptors are directly engaged with pathogenic molecules, so these should have evolved under the influence of selection pressures. In the current study, we investigated the nature of selection pressure on different domain types of IFI16-like (IFI16-L) PYHIN genes in ruminants. Results Three transcript variants of the IFI16-like gene were found in PBMCs of ruminant animals-water buffalo, zebu cattle, goat, and sheep. The IFI16-like gene has one N-terminal PYD domain and one C-terminal HIN-200 domain, separated by an inter-domain linker region. HIN domain and inter-domain region are positively selected while the PYD domain is under the influence of purifying selection. Conclusion Herein, we conclude that the nature of selection pressure varies on different parts (PYD domain, HIN domain, and inter-domain linker region) of IFI16-like PYHIN genes in the ruminants. This data can be useful to predict the molecular determinants of pathogen interactions.
Predator-Prey Interactions and Eavesdropping in Vibrational Communication Networks
Meta Virant-Doberlet, Anka Kuhelj, Jernej Polajnar
et al.
Due to human perceptional bias in favor of air-borne sounds, substrate-borne vibrational signaling has been traditionally regarded as a highly specialized, inherently short-range and, consequently, a private communication channel, free from eavesdropping by sexual competitors and predators. In this review, we synthesize current knowledge pertinent to the view that most animals live in a rich vibratory world, where vibrational information is available to unintended receivers. In recent years, we realized that vibrational signaling is one of the oldest and taxonomically most widespread forms of communication by mechanical waves and that receptors detecting substrate vibrations are ubiquitous. In nature, substrate vibrations are reliable source of information readily available to all members of the animal community able to detect them. Viewing vibrational communication in more relevant ecological context reveals that animals relying on substrate vibrations live in complex communication networks. Long evolutionary history of this communication channel is reflected in varied and sophisticated predator-prey interactions guided by substrate-borne vibrations. Eavesdropping and exploitation of vibrational signals used in sexual communication have been so far largely neglected; however, existing studies show that generalist arthropod predators can intercept such signals emitted by insects to obtain information about prey availability and use that information when making foraging decisions. Moreover, males which advertise themselves for longer periods than females and with vibrational signals of higher amplitude face higher predation risk. It is likely that eavesdropping and exploitation of vibrational signals are major drivers in the evolution taking place in the vibratory world and we believe that studies of interspecific interactions guided by substrate vibrations will, in the future, offer numerous opportunities to unravel mechanisms that are central to understanding behavior in general.