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Ecology Letters Sep 2011Ecology Letters (2011) 14: 841-851 ABSTRACT: Ecological specialisation concerns all species and underlies many major ecological and evolutionary patterns. Yet its status... (Review)
Review
Ecology Letters (2011) 14: 841-851 ABSTRACT: Ecological specialisation concerns all species and underlies many major ecological and evolutionary patterns. Yet its status as a unifying concept is not always appreciated because of its similarity to concepts of the niche, the many levels of biological phenomena to which it applies, and the complexity of the mechanisms influencing it. The evolution of specialisation requires the coupling of constraints on adaptive evolution with covariation of genotype and environmental performance. This covariation itself depends upon organismal properties such as dispersal behaviour and life history and complexity in the environment stemming from factors such as species interactions and spatio-temporal heterogeneity in resources. Here, we develop a view on specialisation that integrates across the range of biological phenomena with the goal of developing a more predictive conceptual framework that specifically accounts for the importance of biotic complexity and coevolutionary events.
Topics: Adaptation, Physiological; Biological Evolution; Ecosystem; Genetic Fitness; Models, Biological
PubMed: 21699641
DOI: 10.1111/j.1461-0248.2011.01645.x -
Frontiers in Cellular and Infection... 2021Ticks are blood-sucking parasites with different strategies of feeding depending on the tick family. The major families are Ixodidae or Argasidae, being slow or fast...
Ticks are blood-sucking parasites with different strategies of feeding depending on the tick family. The major families are Ixodidae or Argasidae, being slow or fast feeders, respectively. In the recent years, the advances in molecular sequencing techniques have enabled to gain knowledge about the proteome of the tick's salivary glands. But an holistic view of the biological processes underlying the expression of the sialome has been neglected. In this study we propose the use of standard biological processes as a tool to draw the physiology of the tick's salivary glands. We used published data on the sialome of s.l. (Ixodidae) and (Argasidae). A partial set of proteins obtained by these studies were used to define the biological process(es) in which proteins are involved. We used a directed network construction in which the nodes are proteins (source) and biological processes (target), separately for the low-level processes ("children") and the top-level ones ("parents"). We applied the method to feeding at different time slices, and to different organs of . The network connects the proteins and the processes with a strength directly proportional to the transcript per millions of each protein. We used PageRank as a measure of the importance of each biological process. As suggested in previous studies, the sialome of unfed express about 30% less biological processes than feeding ticks. Another decrease (25%) is noticed at the middle of the feeding and before detachment. However, top-level processes are deeply affected only at the onset of feeding, demonstrating a redundancy in the feeding. When ixodid-argasid are compared, large differences were observed: they do not share 91% of proteins, but share 90% of the biological processes. However, caution must be observed when examining these results. The hypothesis of different proteins linked to similar biological process(es) in both ticks is an extreme not confirmed in this study. Considering the limitations of this study, carried out with a selected set of proteins, we propose the networks of proteins of sialome linked to their biological processes as a tool aimed to explain the biological processes behind families of proteins.
Topics: Animals; Biological Phenomena; Ixodidae; Ornithodoros; Proteins; Rhipicephalus sanguineus
PubMed: 35059322
DOI: 10.3389/fcimb.2021.767845 -
Bioresource Technology Feb 2022Vermicomposting is a biological process for efficient cattle manure treatment, but the vermicomposting time determines the quality of the vermicompost. The objective of...
Vermicomposting is a biological process for efficient cattle manure treatment, but the vermicomposting time determines the quality of the vermicompost. The objective of this study was to evaluate the effect of cattle manure vermicomposting time on earthworm biomass and the changes in physical, chemical, and biological in properties of the vermicompost. The cattle manure was inoculated with Eisenia andrei earthworms and conducted vermicomposting for 0, 15, 30, 45, 60, and 120 days. The analysis of 44 chemical, physical, and biological properties allowed the vermicomposting process to be divided into initial (<45 days) and final (45-120 days) phases. The initial phase was characterized by high microbial activity and the final by high physical-chemical transformation of the vermicompost and an increase in earthworm density. The organic matter aromaticity increased until the 45th day, subsequently decreasing. Although 30 d of vermicompost are sufficient to obtain a high-quality organic fertilizer, 120 d are necessary for producing matrices.
Topics: Animals; Biomass; Cattle; Female; Manure; Oligochaeta; Soil
PubMed: 34921917
DOI: 10.1016/j.biortech.2021.126572 -
Biological Reviews of the Cambridge... Oct 2022Learning is a familiar process to most people, but it currently lacks a fully developed theoretical position within evolutionary biology. Learning (memory and...
Learning is a familiar process to most people, but it currently lacks a fully developed theoretical position within evolutionary biology. Learning (memory and forgetting) involves adjustments in behaviour in response to cumulative sequences of prior experiences or exposures to environmental cues. We therefore suggest that all forms of learning (and some similar biological phenomena in development, aging, acquired immunity and acclimation) can usefully be viewed as special cases of phenotypic plasticity, and formally modelled by expanding the concept of reaction norms to include additional environmental dimensions quantifying sequences of cumulative experience (learning) and the time delays between events (forgetting). Memory therefore represents just one of a number of different internal neurological, physiological, hormonal and anatomical 'states' that mediate the carry-over effects of cumulative environmental experiences on phenotypes across different time periods. The mathematical and graphical conceptualisation of learning as plasticity within a reaction norm framework can easily accommodate a range of different ecological scenarios, closely linking statistical estimates with biological processes. Learning and non-learning plasticity interact whenever cumulative prior experience causes a modification in the reaction norm (a) elevation [mean phenotype], (b) slope [responsiveness], (c) environmental estimate error [informational memory] and/or (d) phenotypic precision [skill acquisition]. Innovation and learning new contingencies in novel (laboratory) environments can also be accommodated within this approach. A common reaction norm approach should thus encourage productive cross-fertilisation of ideas between traditional studies of learning and phenotypic plasticity. As an example, we model the evolution of plasticity with and without learning under different levels of environmental estimation error to show how learning works as a specific adaptation promoting phenotypic plasticity in temporally autocorrelated environments. Our reaction norm framework for learning and analogous biological processes provides a conceptual and mathematical structure aimed at usefully stimulating future theoretical and empirical investigations into the evolution of plasticity across a wider range of ecological contexts, while providing new interdisciplinary connections regarding learning mechanisms.
Topics: Acclimatization; Adaptation, Physiological; Biological Evolution; Humans; Phenotype
PubMed: 35790067
DOI: 10.1111/brv.12879 -
Annual Review of Physical Chemistry 2009Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at... (Review)
Review
Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations, and experiments pertaining to large-scale hydrophobicity in physical and biomolecular systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we cannot review all the significant and interesting work in this active field.
Topics: Biological Phenomena; Chemical Phenomena; Hydrophobic and Hydrophilic Interactions; Ligands; Proteins; Wettability
PubMed: 18928403
DOI: 10.1146/annurev.physchem.58.032806.104445 -
Current Opinion in Cell Biology Oct 2022Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here, we review some of this recent evidence, focusing on both the molecular... (Review)
Review
Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here, we review some of this recent evidence, focusing on both the molecular mechanisms that potentially underlie such dynamical behavior, and the potential advantages that signaling oscillations might have in cell function. The biological processes considered include cellular differentiation and tissue maintenance, intermittent responses in pluripotent stem cells, and collective cell migration during wound healing. With the aid of mathematical modeling, we review recent examples in which delayed negative feedback has been seen to act as a unifying principle that underpins this wide variety of phenomena.
Topics: Biological Phenomena; Cell Movement; Feedback; Models, Biological; Signal Transduction
PubMed: 36130445
DOI: 10.1016/j.ceb.2022.102130 -
The ISME Journal Dec 2016There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community... (Review)
Review
There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.
Topics: Bacteria; Bacterial Physiological Phenomena; Biodiversity; Ecosystem; Microbiota; Models, Biological
PubMed: 27137125
DOI: 10.1038/ismej.2016.75 -
Proceedings of the National Academy of... Apr 2020
Topics: Arabidopsis; Biological Phenomena; Chloroplasts; Endocytosis; Phosphatidylinositols
PubMed: 32317382
DOI: 10.1073/pnas.2004189117 -
EMBO Reports Jun 2021Timely removal of dying or pathogenic cells by phagocytes is essential to maintaining host homeostasis. Phagocytes execute the clearance process with high fidelity while... (Review)
Review
Timely removal of dying or pathogenic cells by phagocytes is essential to maintaining host homeostasis. Phagocytes execute the clearance process with high fidelity while sparing healthy neighboring cells, and this process is at least partially regulated by the balance of "eat-me" and "don't-eat-me" signals expressed on the surface of host cells. Upon contact, eat-me signals activate "pro-phagocytic" receptors expressed on the phagocyte membrane and signal to promote phagocytosis. Conversely, don't-eat-me signals engage "anti-phagocytic" receptors to suppress phagocytosis. We review the current knowledge of don't-eat-me signaling in normal physiology and disease contexts where aberrant don't-eat-me signaling contributes to pathology.
Topics: Apoptosis; Biological Phenomena; Phagocytes; Phagocytosis; Signal Transduction
PubMed: 34041845
DOI: 10.15252/embr.202152564 -
PloS One 2009The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic...
BACKGROUND
The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning patterns of interactions between biological processes by analyzing protein-protein interactions, transcriptional co-expression and genetic interactions. At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN).
RESULTS
We construct, catalogue, and analyze different types of PLNs derived from different data sources and different species. When applied to the Gene Ontology, many of the resulting links connect processes that are distant from each other in the hierarchy, even though the connection makes eminent sense biologically. Some others, however, carry an element of surprise and may reflect mechanisms that are unique to the organism under investigation. In this aspect our method complements the link structure between processes inherent in the Gene Ontology, which by its very nature is species-independent. As a practical application of the linkage of processes we demonstrate that it can be effectively used in protein function prediction, having the power to increase both the coverage and the accuracy of predictions, when carefully integrated into prediction methods.
CONCLUSIONS
Our approach constitutes a promising new direction towards understanding the higher levels of organization of the cell as a system which should help current efforts to re-engineer ontologies and improve our ability to predict which proteins are involved in specific biological processes.
Topics: Algorithms; Biological Phenomena; Computational Biology; Databases, Protein; Gene Regulatory Networks; Protein Interaction Mapping; Proteins; Saccharomyces cerevisiae
PubMed: 19390589
DOI: 10.1371/journal.pone.0005313