Article
Multidisciplinary Sciences
Ignasi Bartomeus, Serguei Saavedra, Rudolf P. Rohr, Oscar Godoy
Summary: This study shows the importance of considering species interactions within and across trophic levels when estimating species persistence. By integrating mathematical approaches and experiments, the researchers demonstrated that idiosyncratic changes occur in the persistence probabilities of both plants and pollinators when manipulating the multitrophic structure, highlighting the need for a more comprehensive understanding of species interactions in ecological communities.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Lynette H. L. Loke, Ryan A. Chisholm
Summary: A central goal in ecology is to understand the factors that maintain species diversity in local communities. Classic ecological theory suggests that niches determine the maximum number of coexisting species in a community, while a new alternative theory proposes that niches determine the minimum number of coexisting species. We conducted an experimental test in tropical intertidal communities and found supporting evidence for the new theory, indicating that observed species richness is usually well above the minimum dictated by niches due to ongoing immigration.
Article
Microbiology
Panji Cahya Mawarda, Cyrus A. Mallon, Xavier Le Roux, Jan Dirk van Elsas, Joana Falcao Salles
Summary: Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. Spore-forming bacteria with better resource use capacity are more likely to survive and affect bacterial community niches, especially in less diverse communities.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Ecology
Mark A. McPeek, Sarah J. McPeek, Judith L. Bronstein
Summary: Numerous analyses have shown that antagonistic interactions can promote the coexistence of two species competing for a single resource, while the impact of mutualistic partners on coexistence is less understood. A mechanistic model was derived to illustrate that plant coexistence requires specific relationships, with pollinators being able to shape competitive hierarchy among plant species. Data on pollen limitation and nectar production across competing plant species will be crucial for evaluating the role pollinators play in promoting plant coexistence.
Article
Ecology
Xue Zhang, Mark van Kleunen, Chunling Chang, Yanjie Liu
Summary: A study investigated the effects of environmental mean conditions and variability on plant invasion, specifically looking at the role of soil microbes. The study found that nutrient fluctuation promoted nonnative plant dominance under different nutrient availability conditions depending on whether the soil was sterilized or not. The analysis of soil microbial communities indicated that nutrient fluctuation influenced the abundance of pathogenic fungi, which in turn affected plant invasion. This study highlights the importance of considering soil microbial communities when studying plant invasions.
Article
Ecology
Susan. M. M. Magnoli, Kane. R. R. Keller, Jennifer. A. A. Lau
Summary: In nature, plants interact with multiple mutualistic partners, and these interactions can be influenced by competition for resources, alteration of plant traits, and environmental conditions. This study focused on the effects of global warming on interactions between plants and their mutualistic partners. The results showed that warming affected the benefits plants received from rhizobium resource mutualists but not ant mutualists, and it also altered plant investment in all mutualists. Additionally, mutualist partners were found to interact and affect the availability of plant-produced rewards. These findings highlight the potential impact of global changes on mutualistic relationships and the complex interactions among multiple mutualists associated with a shared host.
Article
Ecology
Patrick D. Milligan, Timothy A. Martin, Grace P. John, Corinna Riginos, Jacob R. Goheen, Scott M. Carpenter, Todd M. Palmer
Summary: The study in East Africa showed that the invasion of Pheidole megacephala ants led to a significant decrease in photosynthesis of Acacia drepanolobium trees, with an interaction between invasive ants and large herbivores causing further declines in leaf- and canopy-level photosynthesis. The results suggest the potential of invasive species to alter ecosystem-level carbon fixation and other biogeochemical cycles.
Article
Ecology
Naven Narayanan, Allison K. Shaw
Summary: Mutualisms, or mutually beneficial interspecific interactions, play a crucial role in shaping population dynamics of species in ecological communities. This study investigates the impact of mutualistic dependence on the speed of range expansion and spatial distribution of species. The research findings highlight the importance of considering mutualisms and dependence in a spatial context for understanding species' distributions and range limits.
Article
Multidisciplinary Sciences
Boram Kim, Makoto I. Kanai, Yangkyun Oh, Minsoo Kyung, Eun-Kyoung Kim, In-Hwan Jang, Ji-Hoon Lee, Sang-Gyu Kim, Greg S. B. Suh, Won-Jae Lee
Summary: A balanced intake of macronutrients is important for the well-being of organisms. Inadequate protein consumption can lead to various ailments. The microbiome-gut-brain axis in Drosophila can detect a deficit of essential amino acids and stimulate a compensatory appetite for them.
Review
Ecology
Lindsey K. Albertson, Michael J. MacDonald, Benjamin B. Tumolo, Michelle A. Briggs, Zachary Maguire, Sierra Quinn, Jose A. Sanchez-Ruiz, Jaris Veneros, Laura A. Burkle
Summary: The study found that positive interactions in freshwater habitats can significantly increase the number of beneficiaries, especially mollusks and amphibians. Invasive facilitators have stronger positive effects on beneficiaries compared to non-invasive facilitators.
Article
Ecology
Yichao Zeng, John J. Wiens
Summary: Ecology aims to reveal generalities in species interactions and explain differences in species richness among groups. Through a systematic review, it was found that different types of interactions can predictably impact species diversification and richness patterns.
Article
Ecology
Yasmin Quintana, Friedrich Wolfgang Keppeler, Kirk O. Winemiller
Summary: Popular armored catfishes from South America have become invasive and can deplete basal resources, potentially impacting native fauna. A study in the Usumacinta River Basin, Guatemala, analyzed stable isotopes in fish tissues and basal resources to assess the trophic ecology of native fishes in the presence of Pterygoplichthys. The study found that the invasive catfish and environmental factors impact the trophic ecology of native fish.
Article
Multidisciplinary Sciences
Rong Zhang, Hanah Goetz, Juan Melendez-Alvarez, Jiao Li, Tian Ding, Xiao Wang, Xiao-Jun Tian
Summary: Resource competition between gene circuit modules can lead to unexpected circuit functions. By building cascading bistable switches to achieve two successive cell fate transitions, a 'winner-takes-all' behavior was observed which was overcome by a division of labor strategy.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Pu Jia, Jiayi Wang, Haolin Liang, Zhuo-hui Wu, Fenglin Li, Weihua Li
Summary: The legumes Desmodium heterocarpon and Senna tora have been found to effectively prevent and control the invasive weed Mikania micrantha due to their higher competitiveness, shade tolerance, and drought tolerance. The control effect of D. heterocarpon is better than that of S. tora. Therefore, the replacement control of Mikania micrantha by D. heterocarpon is expected to be a sustainable ecological management strategy for controlling this invasive species in dryland orchard habitats. These findings provide a theoretical basis for future alternative control species selection and offer new ideas to solve the issue of repeated regeneration in the existing M. micrantha control process.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Benjamin C. Calfee, Liz D. Glasgo, Erik R. Zinser
Summary: The marine cyanobacterium Prochlorococcus dominates the nutrient-limited open ocean and is the most abundant photosynthetic organism on Earth. In this study, it was found that Prochlorococcus outcompetes its rival cyanobacterium Synechococcus for scarce nutrients in nitrogen-limited waters, with the help of a heterotrophic bacterium Alteromonas macleodii. This interaction between Prochlorococcus and Alteromonas promotes the numerical success of Prochlorococcus in nutrient-limited regions of the ocean.
Article
Plant Sciences
Silmar Primieri, Susan M. Magnoli, Thomas Koffel, Sidney L. Sturmer, James D. Bever
Summary: The study found that perennial legumes may have synergistic effects with AMF and rhizobia, while annual plants do not. AMF and rhizobia can increase phosphorus and nitrogen tissue concentrations in plants to varying degrees. Microbial responses to co-infection are closely related to synergisms in plant growth.
Article
Biology
Ravi Ranjan, Christopher A. Klausmeier
Summary: Competition is a key factor in structuring ecological communities, and the width and shape of resource distribution play an important role in determining species diversity and traits. Narrow resource distributions result in strong competition and exclusion of most species, while wider resource distributions enable stable coexistence and support diversity. Competition also drives maximal resource utilization among competing species.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Katriona E. Lyons, Carol-Anne O. ' Shea, Ghjuvan Grimaud, C. Anthony Ryan, Eugene Dempsey, Alan L. Kelly, R. Paul Ross, Catherine Stanton
Summary: This study analysed the composition of the milk microbiome in 80 lactating women and found that there is a significant decrease in diversity over the course of lactation from birth to 6 months. The study also found that the stage of lactation has a significant effect on the microbiome, while mode of delivery does not.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Harsh Mathur, Kevin Linehan, James Flynn, Noel Byrne, Pat Dillon, Muireann Conneely, Ghjuvan Grimaud, Colin Hill, Catherine Stanton, R. Paul Ross
Summary: Bovine mastitis is a significant concern in the dairy industry, and there is a need for alternative therapies due to antibiotic resistance. Live bio-therapeutics, such as Lactococcus lactis DPC3147, have shown efficacy in treating mastitis. This study investigated the response to heat-killed cells (a postbiotic) and found that it can also stimulate a localized immune response in cows with chronic mastitis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Jing Yang, Qiang Zhang, Jun Zhang, Yan Ouyang, Zepeng Sun, Xinlong Liu, Feng Qaio, Li-Qun Xu, Yunfei Niu, Jian Li
Summary: Chronic obstructive pulmonary disease (COPD) is a respiratory disease caused by the interaction between genes and environmental conditions. The composition of airway bacteria changes significantly during acute exacerbations in COPD patients, accompanied by alterations in host inflammatory responses.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Thomas Koffel, Kaito Umemura, Elena Litchman, Christopher A. Klausmeier
Summary: Species-abundance distributions describe the commonness and rarity of species in a community, but their shape and underlying mechanisms are still controversial, lacking a general, non-neutral theory. A trait-based framework can offer new insights into SADs and generate more-testable hypotheses on controls over commonness and rarity in communities.
Article
Biochemical Research Methods
Brian A. Lerch, Derek A. Smith, Thomas Koffel, Sarah C. Bagby, Karen C. Abbott
Summary: This study investigates the ecological and evolutionary dynamics of public goods production and finds that highly privatized and low-investment goods are more likely to be stably produced in environments with limited resources.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zepeng Sun, Xinlong Liu, Wei Liu, Jiahui Li, Jing Yang, Feng Qiao, Jianjun Ma, Jingjie Sha, Jian Li, Li-Qun Xu
Summary: In this study, an automated adaptive method called AutoNanopore is developed for fast and accurate event detection in current traces. The method has a high coverage ratio and performs well in detecting events with significantly varying baselines.
Review
Microbiology
Pin Chen, Zepeng Sun, Jiawei Wang, Xinlong Liu, Yun Bai, Jiang Chen, Anna Liu, Feng Qiao, Yang Chen, Chenyan Yuan, Jingjie Sha, Jinghui Zhang, Li-Qun Xu, Jian Li
Summary: Sequencing technology is widely used in molecular biology research and is crucial for the development and applications of molecular biology. It has undergone three generations of development since 1977, and is applied in various fields such as disease diagnosis, drug target discovery, and species protection. Nanopore sequencing technology has emerged as an advanced portable sequencing technology with the advantages of small size, portability, and direct reading using physical methods.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Li-Qun Xu, Jing Yang, Weicheng Liang, Jiang Chen, Zepeng Sun, Qiang Zhang, Xinlong Liu, Feng Qiao, Jian Li
Summary: Initially thought to be sterile, the lungs of healthy humans have been found to contain various commensal microorganisms, especially bacteria, with the development of sequencing technologies. Studies have also linked lung microbes to infectious lung diseases. However, there is a lack of databases focusing on the metagenomics of lungs to provide microbial compositions and metadata information. Such a database would be valuable for researching and treating lung diseases.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Ecology
Francois Munoz, Christopher A. Klausmeier, Pierre Gauzere, Gaurav Kandlikar, Elena Litchman, Nicolas Mouquet, Annette Ostling, Wilfried Thuiller, Adam C. Algar, Arnaud Auber, Marc W. Cadotte, Leo Delalandre, Pierre Denelle, Brian J. Enquist, Claire Fortunel, Matthias Grenie, Nicolas Loiseau, Lucie Mahaut, Anthony Maire, David Mouillot, Catalina Pimiento, Cyrille Violle, Nathan J. B. Kraft
Summary: Recent work has demonstrated that evaluating the distinctiveness of functional traits, which is the average trait distance of a species to other species in a community, can provide valuable insights into the dynamics of biodiversity and ecosystem functioning. However, the underlying ecological mechanisms that drive the emergence and persistence of functionally distinct species are not well understood. In this study, we address this issue by considering a heterogeneous fitness landscape, where functional dimensions encompass peaks that represent trait combinations resulting in positive population growth rates in a community. We identify four ecological cases that contribute to the emergence and persistence of functionally distinct species and provide examples and guidelines to distinguish between them. Additionally, we explore how stochastic dispersal limitation can lead to functional distinctiveness. Our framework offers a novel perspective on the relationship between fitness landscape heterogeneity and the functional composition of ecological assemblages.
Article
Biology
Laura A. Twardochleb, Phoebe L. Zarnetske, Christopher A. Klausmeier
Summary: Climate warming is causing changes in the life cycles of ectotherms, such as advancing phenology and decreasing generation times. However, existing theory and models do not consider the effects of warming on organisms with complex life cycles in seasonal environments. A size-structured consumer-resource model was developed to explore the impacts of climate warming in a seasonal environment on a freshwater insect population, showing that warming can lead to increases in consumer population sizes through various mechanisms, thus delaying population extinctions.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Catherine O'Reilly, Ghjuvan M. Grimaud, Mairead Coakley, Paula M. O'Connor, Harsh Mathur, Veronica L. Peterson, Ciara M. O'Donovan, Peadar G. Lawlor, Paul D. Cotter, Catherine Stanton, Mary C. Rea, Colin Hill, R. Paul Ross
Summary: Nisin, a broad spectrum bacteriocin, can survive intact through the pig gastrointestinal tract and affect the composition and functioning of the microbiota. It leads to reversible changes in the abundance of Gram positive and Gram negative bacteria, as well as the synthesis pathways of short chain fatty acids. These findings demonstrate the potential of bacteriocins like nisin to shape mammalian microbiomes and impact the functionality of the community.
SCIENTIFIC REPORTS
(2023)
Article
Infectious Diseases
Dhrati V. Patangia, Ghjuvan Grimaud, Kevin Linehan, R. Paul Ross, Catherine Stanton
Summary: This study investigated the impact of different drying off methods on the microbiota and resistome profile in colostrum and milk samples from cows. The results showed that the use of antibiotics during drying off increased microbial diversity and antibiotic resistance genes in milk. In contrast, the non-antibiotic group had a lower abundance of mastitis-causing pathogens and was associated with specific genera. These findings support the use of non-antibiotic alternatives for drying off in cows.
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)