Intraspecies Interactions Research Articles

Symmetry Oscillations in Strongly Interacting One-Dimensional Mixtures.

Multicomponent quantum mixtures in one dimension can be characterized by their symmetry under particle exchange. For a strongly interacting Bose-Bose mixture, we show that the time evolution of the momentum distribution from an initially symmetry-mixed state is quasiconstant for a SU(2) symmetry conserving Hamiltonian, while it displays large oscillations in time for the symmetry-breaking case where inter- and intraspecies interactions are different. Using the property that the momentum distribution operator at strong interactions commutes with the class-sum operator, the latter acting as a symmetry witness, we show that the momentum distribution oscillations correspond to symmetry oscillations, with a mechanism analogous to neutrino flavor oscillations.

Engineering impurity Bell states through coupling with a quantum bath

We theoretically demonstrate the feasibility of creating Bell states in multicomponent ultracold atomic gases by solely using the ability to control the interparticle interactions via Feshbach resonances. For this we consider two distinguishable impurities immersed in an atomic background cloud of a few bosons, with the entire system being confined in a one-dimensional harmonic trap. By analyzing the numerically obtained ground states we demonstrate that the two impurities can form spatially entangled bipolaron states due to mediated interactions from the bosonic bath. Our analysis is based on calculating the correlations between the two impurities in a two-mode basis, which is experimentally accessible by measuring the particle positions in the left or right sides of the trap. While interspecies interactions are crucial in order to create the strongly entangled impurity states, they can also inhibit correlations depending on the ordering of the impurities and three-body impurity-bath correlations. We show how these drawbacks can be mitigated by manipulating the properties of the bath, namely its size, mass, and intraspecies interactions, allowing one to create impurity Bell states over a wide range of impurity-impurity interactions. Published by the American Physical Society 2024

Empirical evidence of resource dependent evolution of payoff matrices in Saccharomyces cerevisiae populations.

In evolutionary game theory, a relative comparison of the cost and benefit associated with obtaining a resource, called payoff, is used as an indicator of fitness of an organism. Payoffs of different strategies, quantitatively represented as payoff matrices, are used to understand complex inter-species and intra-species interactions like cooperation, mutualism, and altruism. Payoff matrices, however, are usually treated as invariant with time - largely due to the absence of any empirical data quantifying their evolution. In this paper, we present empirical evidence of three types of resource-dependent changes in the payoff matrices of evolving Saccharomyces cerevisiae populations. We show that depending on the carbon source and participating genotypes, N-player games could collapse, be born, or be maintained. Our results highlight the need to consider the dynamic nature of payoff matrices while making even short-term predictions about population interactions and dynamics.

Effect of intraspecies interactions on Pseudomonas aeruginosa biofilm formation and gene expression

Pseudomonas aeruginosa is a common pathogen of acute and chronic infections that can increase risk to burned patients and those with chronic wounds, especially when forming biofilms. These complex ecosystems are formed by several bacteria that communicate, cooperate, and compete with each other. To enhance its survival capacity in such a competitive environment, P. aeruginosa produces secondary metabolites with a range of biological activities, among other factors. Here, we evaluated how such bioactive molecules mediate intraspecies interactions to modulate P. aeruginosa biofilm formation. An overall decrease in biofilm formation on the surface of stainless steel coupons was observed for both dual-strain and single-strain biofilms formed in the presence of secondary metabolites extracted from other P. aeruginosa strains. Modulation of biofilm formation by these metabolites during P. aeruginosa intraspecies interactions suggests a role for these molecules in strain competition. The most likely mechanism by which it occurs might be modulation of iron uptake. Among the genes analyzed, those related to import (tonB1) and biosynthesis (pvdS) of the siderophore pyoverdine were the most downregulated during exposure to the metabolite extracts. Exploring P. aeruginosa intraspecies interactions during biofilm formation might be an interesting approach to understand its lifestyle better and, thus, the mechanisms involved in the species’ biofilm formation.

Quantum soliton-trains of strongly correlated impurities in Bose-Einstein condensates

Strongly correlated impurities immersed in a Bose-Einstein condensate (BEC) can form a periodic structure of tightly localized single atoms due to competing inter and intraspecies interactions, leading to a self-organized pinned state. In this work, we show numerically that the impurities in the self-pinned state form a soliton-train, as a consequence of a BEC-mediated attractive self-interaction and ordering due to the exclusion principle. The dynamics of the impurities possess the characteristics of bright matter-wave soliton trains as often seen in classical fields; however, in the few impurities cases, the detailed nature of collisions is determined by their quantum statistics. Published by the American Physical Society 2024

Spontaneous symmetry breaking of cooperation between species.

In mutualistic associations, two species cooperate by exchanging goods or services with members of another species for their mutual benefit. At the same time, competition for reproduction primarily continues with members of their own species. In intra-species interactions, the prisoner's dilemma is the leading mathematical metaphor to study the evolution of cooperation. Here we consider inter-species interactions in the spatial prisoner's dilemma, where members of each species reside on one lattice layer. Cooperators provide benefits to neighbouring members of the other species at a cost to themselves. Hence, interactions occur across layers but competition remains within layers. We show that rich and complex dynamics unfold when varying the cost-to-benefit ratio of cooperation, r. Four distinct dynamical domains emerge that are separated by critical phase transitions, each characterized by diverging fluctuations in the frequency of cooperation: (i) for large r cooperation is too costly and defection dominates; (ii) for lower r cooperators survive at equal frequencies in both species; (iii) lowering r further results in an intriguing, spontaneous symmetry breaking of cooperation between species with increasing asymmetry for decreasing r; (iv) finally, for small r, bursts of mutual defection appear that increase in size with decreasing r and eventually drive the populations into absorbing states. Typically, one species is cooperating and the other defecting and hence establish perfect asymmetry. Intriguingly and despite the symmetrical model set-up, natural selection can nevertheless favour the spontaneous emergence of asymmetric evolutionary outcomes where, on average, one species exploits the other in a dynamical equilibrium.

Intraspecies interactions of Streptococcus mutans impact biofilm architecture and virulence determinants in childhood dental caries.

Early childhood dental caries (ECC) is the most common chronic disease among children, especially among low socioeconomic populations. Streptococcus mutans is most frequently associated with initiation of ECC. Although many studies report children with multiple S. mutans strains (i.e., genotypes) have greater odds of developing ECC, studies investigating intraspecies interactions in dental caries are lacking. This study investigates the impact of intraspecies interactions on cariogenic and fitness traits of clinical S. mutans isolates using in vitro and in vivo approaches. Association analysis evaluated if presence of multiple S. mutans genotypes within the first year of colonization was associated with caries. Initially, clinical S. mutans isolates from 10 children were evaluated. S. mutans strains (G09 and G18, most prevalent) isolated from one child were used for subsequent analysis. Biofilm analysis was performed for single and mixed cultures to assess cariogenic traits, including biofilm biomass, intra-polysaccharide, pH, and glucan. Confocal laser scanning microscopy (CLSM) and time-lapse imaging were used to evaluate spatial and temporal biofilm dynamics, respectively. A Drosophila model was used to assess colonization in vivo. Results showed the mean biofilm pH was significantly lower in co-cultured biofilms versus monoculture. Doubling of S. mutans biofilms was observed by CLSM and in vivo colonization in Drosophila for co-cultured S. mutans. Individual strains occupied specific domains in co-culture and G09 contributed most to increased co-culture biofilm thickness and colonization in Drosophila. Biofilm formation and acid production displayed distinct signatures in time-lapsed experiments. This study illuminates that intraspecies interactions of S. mutans significantly impacts biofilm acidity, architecture, and colonization.IMPORTANCEThis study sheds light on the complex dynamics of a key contributor to early childhood dental caries (ECC) by exploring intraspecies interactions of different S. mutans strains and their impact on cariogenic traits. Utilizing clinical isolates from children with ECC, the research highlights significant differences in biofilm architecture and acid production in mixed versus single genotype cultures. The findings reveal that co-cultured S. mutans strains exhibit increased cell density and acidity, with individual strains occupying distinct domains. These insights, enhanced by use of time-lapsed confocal laser scanning microscopy and a Drosophila model, offer a deeper understanding of ECC pathogenesis and potential avenues for targeted interventions.

Bioecology of African Catfish and Poisonous Marine Fish (Actinopterygii: Teleostei)

Clarias gariepinus (Burchell, 1822) (Siluriformes: Clariidae) the African catfish is a large, eel-like fish, usually dark gray or black on the back and white on the ventral part, a smoother flat bony head compared to other catfish, and a wide, terminal mouth with four pairs of barbels. It has an accessory respiratory organ that allows it to breathe atmospheric air and survive in environments with low oxygen levels. They remain in the muddy substrates of lakes and occasionally swallow air through their mouths. It can leave the water at night and walk on dry land using its strong fins and spines, in search of food or migrating to other bodies of water to reproduce. During aggressive intraspecies interactions, this species was observed to generate single-phase discharges through electrical organs in its head that lasted from 5 to 260 ms. The manuscript aimed to investigate the bioecology of African catfish and venomous marine fish (Actinopterygii: Teleostei). To develop the study, the methodology used an integrative literature review, which is a synthesis process with the objective of expanding the understanding of knowledge and achieving the expected results. In this way, the researcher can prepare an integrative review with different purposes, which can be aimed at defining concepts, reviewing theories, or methodological analysis of studies included on a given topic. In its construction process, it is necessary to go through six distinct stages, which are: identification of the theme and selection of the hypothesis or research question; establishment of inclusion and exclusion criteria for studies/sample or literature search; definition of information to be extracted from selected studies/categorization of studies; evaluation of included studies; interpretation of results; and presentation of knowledge review/synthesis. To carry out the study, a search for scientific articles was carried out through the Virtual Health Library, in the SCIELO, LILACS, and Pubmed databases.

Allorecognition behaviors in Myxomycetes respond to intraspecies factors.

Myxomycetes are multinucleate unicellular organisms. They form a Plasmodium that moves by protoplasmic flow and prey on microorganisms. When encountering intraspecifics, the plasmodium has the capacity for 'fusion', actively approaching and fusing its cells, or 'avoidance', altering its direction to avoid the other individual. This is an allorecognition ability. However, it remains unclear whether the range of allorecognition extends to other species, and its ecological significance is also obscure. Here, we conducted a quantitative evaluation of contact responses from closely related species of plasmodium to clarify the range of allorecognition behaviors in Myxomycetes. Behavioral assays demonstrated that allorecognition behaviors are specifically observed within individuals of the same species, indicating that these behaviors are a phenomenon unique to intraspecies interactions. Myxomycetes allorecognition is an extremely narrow and inward-focused behavior, suggesting a highly specialized mechanism.

Softening in Two-Component Lipid Mixtures by Spontaneous Curvature Variance.

The bending modulus of a lipid bilayer quantifies its mechanical resistance to curvature. It is typically understood in terms of thickness; e.g., thicker bilayers are usually stiffer. Here, we describe an additional and powerful molecular determinant of stiffness─the variance in the distribution of curvature sensitivity of lipids and lipid conformations. Zwitterionic choline and ethanolamine headgroups of glycerophospholipids dynamically explore inter- and intraspecies interactions, leading to transient clustering. We demonstrate that these clusters couple strongly to negative curvature, exciting undulatory membrane modes and reducing the apparent bending modulus. Three force fields (Martini 2, Martini 3, and all-atom CHARMM C36) each show the effect to a different extent, with the coarse-grained Martini models showing the most clustering and thus the most softening. The theory is a guide to understanding the stiffness of biological membranes with their complex composition, as well as how choices of force field parameterization are translated into mechanical stiffness.

Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes.

The presence of β-lactamase positive microorganisms imparts a pharmacological effect on a variety of organisms that can impact drug efficacy by influencing the function or composition of bacteria. Although studies to assess dynamic intra- and interspecies communication with bacterial communities exist, the efficacy of drug treatment and quantitative assessment of multiorganism response is not well understood due to the lack of technological advances that can be used to study coculture interactions in a dynamic format. In this study, we investigate how β-lactamase positive microorganisms can neutralize the effect of β-lactam antibiotics in a dynamic format at the inter- and intraspecies level using microbial bead technology. Three interactive models for the biological compartmentalization of organisms were demonstrated to evaluate the effect of β-lactam antibiotics on coculture systems. Our model at the intraspecies level attempts to mimic the biofilm matrix more closely as a community-level feature of microorganisms, which acknowledges the impact of nondrug-resistant species in shaping the dynamic response. In particular, the results of intraspecies studies are highly supportive of the biofilm mode of bacterial growth, which can provide structural support and protect the bacteria from an assault on host or environmental factors. Our findings also indicate that β-lactamase positive bacteria can neutralize the cytotoxic effect of β-lactam antibiotics at the interspecies level when cocultured with cancer cells. Results were validated using β-lactamase positive bacteria isolated from environmental niches, which can trigger phenotypical alteration of β-lactams when cocultured with other organisms. Our compartmentalization strategy acts as an independent ecosystem and provides a new avenue for multiscale studies to assess intra- and interspecies interactions.

Could Climate Crisis Lead to Novel Pandemics?

Climate, an integral part of life, varies by region. Climate change and deterioration could lead to significant problems. The Industrial Revolution introduced anthropogenic factors in climate change for the first time in the 19th century. Due to the increase in energy requirements, large volumes of greenhouse gases were released into the atmosphere due to the utilization of fossil fuels such as coal, natural gas and oil. The Industrial Revolution led to rapid climate change and environmental problems. The consequences of these problems are felt in our age. The most affected area is human health by the climate crisis. Its effect on health could be direct or indirect. Infectious diseases that spread globally, crossing both international and intercontinental borders, are described as pandemics. Today, infectious diseases continue to be the most common cause of death in developed countries.Population growth, unplanned urbanization, consumption of unhealthy industrial food items, high exposure toradiation, air pollution and climate change play a role in the development of pandemics. It was reported that climate change altered intra-species interaction and increased the risk of infection. Nations should adopt various measures to mitigate the effects of climate change to preserve public health and minimize human loss or health risks. The present study aimed to determine whether we should expect novel pandemics due to the climate crisis induced by climate change. Thus, studies on the issue were reviewed and the findings are discussed in the present study.

Living the good life? A systematic review of behavioural signs of affective state in the domestic horse (Equus caballus) and factors relating to quality of life. Part I: Fulfilment of species-specific needs.

The welfare of horses involved in sport and leisure activities has come under increasing scrutiny, both from within the equine sector and from the public. A systematic review of scientific evidence was conducted to derive observable, evidence-based behavioural measures of positive or negative affective state and factors relating to quality of life in the domestic horse (Equus caballus). Two separate searches (including the terms 'emotion/affect', or 'stress') were conducted, with 179 articles being retained. In Part I of this two-part review (companion paper published simultaneously), articles relating to the extent to which the species-specific needs of the horse are fulfilled in the home environment (n = 21), in relation to social grouping (n=20), and during weaning (n = 14) were reviewed. Experimental tests of affective state in relation to housing and management (n = 8), and studies relating to stereotypical behaviour (n = 7) were also included. Opportunities for behavioural expression were dependent upon the provision of social and physical resources. Withdrawn or agitated behaviours in situ, avoidance behaviour during handling and agonistic intra-species interactions were indicative of negative affective state. Affiliative intra-specific social interactions, and forage ingestion were considered positive signs. For horses to live a good life, their need for space, companionship, and forage must be prioritised from birth and throughout their lives.

The relationship of personality traits with breed, sex, and racing performance in sport horses

The aim of the study was to evaluate the personality components of Arabian and Thoroughbred horses (TB) using the Horse Personality Questionnaire (HPQ) and examine their relationship with breed, sex, and racing performance. Within the scope of the research, race data of 96 horses from Thoroughbred (n = 56) and Arabian horse (n = 40) breeds that participated in flat races were taken from the official websites of Turkish Jockey Club. HPQ was constructed using 26 behaviorally defined adjectives. Thereafter, latent class analysis was carried out to determine distinct classes (subgroups) by using the questionnaire that described the personalities of horses. Three distinct personality classes of both TB and Arabian horses were compared. While there was a significant difference in sex distribution among the personality classes of TB (P = 0.023), this difference was not observed in the classes of Arabian horses (P = 0.580). There was no significant difference in terms of age and some racing characteristics in the per- sonality classes of both Arabian and TB horses (P > 0.05). In conclusion, it was seen that some personality classes of the horses could not be determined in the type of management system where there was no paddock and horses cannot display some of their intra-species social behaviors. For understanding horse personality, it is crucial to observe their intra-species interactions Simultaneously, by evaluating the data on horse personality from a scientific perspective and appraising the sportive performance of horses with a holistic approach, ethical equitation would be possible.

Construction and Analysis of Multi-Species Ecological Network, a Case Study of the Southeast Qinghai–Tibetan Plateau

In recent years, rapid global changes have accelerated the loss of habitats and fragmentation of landscapes, emerging as primary drivers of the alarming decline in global biodiversity. Through the construction of ecological networks (ENs) that simulate the interactions between animal and plant species with their environment, it is possible to mitigate landscape fragmentation and the loss of biodiversity. In this study, we focused on the ecologically diverse southeastern region of the Qinghai–Tibetan Plateau (QTP) as our research area and developed a comprehensive Multi-Species Ecological Network (MEN) consisting of ten species. Through employing complex network analysis methods, we thoroughly examined the intra-species and inter-species interactions within the MEN, integrating the findings with the natural characteristics of the study area to yield valuable insights. The results of our study revealed considerable spatial variations in the MEN. Specifically, the western and eastern regions experienced significant ecological resistance, leading to fragmented ecological sources and a limited connectivity of ecological corridors. Furthermore, the application of complex network analysis revealed inadequate connectivity and stability in specific localized areas within the MEN. This emphasizes the pressing requirement for effective ecological preservation plans. Through this study, our aim is to advance research on multi-species ecological spatial networks and to offer novel perspectives and methodologies for biodiversity conservation and habitat maintenance in the Qinghai–Tibetan Plateau.

DensePPI: A Novel Image-Based Deep Learning Method for Prediction of Protein-Protein Interactions.

Protein-protein interactions (PPI) are crucial for understanding the behaviour of living organisms and identifying disease associations. This paper proposes DensePPI, a novel deep convolution strategy applied to the 2D image map generated from the interacting protein pairs for PPI prediction. A colour encoding scheme has been introduced to embed the bigram interaction possibilities of Amino Acids into RGB colour space to enhance the learning and prediction task. The DensePPI model is trained on 5.5 million sub-images of size 128×128 generated from nearly 36,000 interacting and 36,000 non-interacting benchmark protein pairs. The performance is evaluated on independent datasets from five different organisms; Caenorhabditis elegans, Escherichia coli, Helicobacter Pylori, Homo sapiens and Mus Musculus. The proposed model achieves an average prediction accuracy score of 99.95% on these datasets, considering inter-species and intra-species interactions. The performance of DensePPI is compared with the state-of-the-art methods and outperforms those approaches in different evaluation metrics. Improved performance of DensePPI indicates the efficiency of the image-based encoding strategy of sequence information with the deep learning architecture in PPI prediction. The enhanced performance on diverse test sets shows that the DensePPI is significant for intra-species interaction prediction and cross-species interactions. The dataset, supplementary file, and the developed models are available at https://github.com/Aanzil/DensePPI for academic use only.

Fermionization of a few-body Bose system immersed into a Bose-Einstein condensate

We study the recently introduced self-pinning transition [Phys. Rev. Lett. 128, 053401 (2022)] in a quasi-one-dimensional two-component quantum gas in the case where the component immersed into the Bose-Einstein condensate has a finite intraspecies interaction strength. As a result of the matter-wave backaction, the fermionization in the limit of infinite intraspecies repulsion occurs via a first-order phase transition to the self-pinned state, which is in contrast to the asymptotic behavior in static trapping potentials. The system also exhibits an additional superfluid state for the immersed component if the interspecies interaction is able to overcome the intraspecies repulsion. We approximate the superfluid state in an analytical model and derive an expression for the phase transition line that coincides with well-known phase separation criteria in binary Bose systems. The full phase diagram of the system is mapped out numerically for the case of two and three atoms in the immersed component.

Exploring the role of beyond mean-field interaction in the structure and dynamics of one-dimensional quantum droplets

We present simulation results of the ground state structure and dynamics of quantum droplets (QDs) in one-dimensional spin–orbit coupled binary Bose–Einstein condensates. We have considered two cases for this analysis, such as (i) the mean-field term has a vanishingly small contribution utilizing the equal and opposite inter- and intraspecies interactions and (ii) unequal inter- and intraspecies interactions. The QD exhibits remarkably different natures in each case. In the former case, it exhibits a bright sech-like droplet nature, while in the latter case, we find the flattened sech-like shape of the droplet. Further, we analyze the effect of velocity perturbation on the dynamics in both cases. For the first case, we find a systematic change from the solitonic droplet nature to the breathing droplet, which finally has a moving droplet feature upon increasing the velocity. However, the second case shows similar dynamics except having more dynamically stable features than the first. Finally, we present various dynamics that ensued in the QD due to the quenching of the interaction parameters, coupling parameters or allowing the droplet to undergo collisions.

Modeling bacteria pairwise interactions in human microbiota by Sparse Identification of Nonlinear Dynamics (SINDy).

The gut microbiota is a community of high complexity; its composition changes due to ecological interactions, these are studied to understand the relationship with the human health. External stimuli like the administration of probiotics, prebiotics, or drugs are known to modify these interactions. The high complexity of microbiota composition can be studied by considering pairwise interactions. Pairwise interactions in bacterial communities consider each species' directionality and impact on one another, e.g., commensalism (unidirectional positive interaction) or competition (bidirectional negative interaction). These interactions can either be interspecies or intraspecies. The Lotka-Volterra (LV) model has been implemented to characterize these bacteria interactions, considering the ecological relationship among the different species presented. One of the main challenges is determining the specific interaction parameters in LV structure from experimental data. This study implemented a novel approach based on the sparse identification of nonlinear dynamic method (SINDy). One of the assumptions in SINDy method implies the knowledge of the data derivative structure. To fulfill this requirement, a differential neural network algorithm was implemented. We assessed the performance of this approach considering both a simulated and experimental interspecies scenario. A two-species bacterial LV model was simulated in the initial validation stage, and the resulting kinetic growth data was recorded. This data was utilized for training a differential neural network algorithm, which was used to derive a time-derivative structure for the dataset. After this step, SINDy method was implemented to calculate the interaction parameters. Three conditions were evaluated in intraspecies competition, obtaining an average identification parametric error of less than 2%. For experimental data, parametric analysis results are sensitive to detect the influence of a drug presence over the intraspecies interaction with a reduction of 50% in its typical values.Clinical Relevance- In this study, we devised a strategy to determine how two species of the human gastrointestinal microbiota interact and the impact of drug administration on these interactions.

The putative role of the epipeptide EpeX in Bacillus subtilis intra-species competition.

Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.