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Niche construction

Noa Katz, Roni Shavit, Jonathan N Pruitt, Inon Scharf
Most habitats in nature are heterogeneous, incorporating favorable and unfavorable microhabitats for different animals, based on their ecological niche. Unsuitable microhabitats have negative consequences for individual growth and survival. Animals, therefore, should fine-tune their location within the habitat by dispersing away from such microhabitats. We studied the suitability of different constant microhabitat conditions for wormlion larvae, a trap-building predator, tested in groups under laboratory conditions...
December 2017: Current Zoology
Felix Riede, Niels N Johannsen, Anders Högberg, April Nowell, Marlize Lombard
In this contribution, we address a major puzzle in the evolution of human material culture: If maturing individuals just learn their parental generation's material culture, then what is the origin of key innovations as documented in the archeological record? We approach this question by coupling a life-history model of the costs and benefits of experimentation with a niche-construction perspective. Niche-construction theory suggests that the behavior of organisms and their modification of the world around them have important evolutionary ramifications by altering developmental settings and selection pressures...
January 2018: Evolutionary Anthropology
Hiroshi Ikeda, Kayoko Fukumori, Etsuko Shoda-Kagaya, Masamichi Takahashi, Masamichi T Ito, Yoshimi Sakai, Kazuma Matsumoto
Underground community assemblies have not been studied well compared with aboveground communities, despite their importance for our understanding of whole ecosystems. To investigate underground community assembly over evolutionary timescales, we examined terrestrial earthworm communities (Oligochaeta: Haplotaxida) in conserved mountainous primary forests in Japan as a model system. We collected 553 earthworms mostly from two dominant families, the Megascolecidae and the Lumbricidae, from 12 sites. We constructed a molecular taxonomic unit tree based on the analysis of three genes to examine the effects of a biogeographic factor (dispersal ability) and an evolutionary factor (habitat adaptation) on the earthworm community assembly process...
February 2018: Ecology and Evolution
Mara A Freilich, Evie Wieters, Bernardo R Broitman, Pablo A Marquet, Sergio A Navarrete
Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically-based, species interaction network from the same region...
January 16, 2018: Ecology
S V Balasundaram, J Hess, M B Durling, S C Moody, L Thorbek, C Progida, K LaButti, A Aerts, K Barry, I V Grigoriev, L Boddy, N Högberg, H Kauserud, D C Eastwood, I Skrede
Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives, enabling an extremely rapid decay in buildings under suitable conditions...
January 5, 2018: ISME Journal
Lorenzo Giordani, Alice Parisi, Fabien Le Grand
Adult skeletal muscle is endowed with regenerative potential through partially recapitulating the embryonic developmental program. Upon acute injury or in pathological conditions, quiescent muscle-resident stem cells, called satellite cells, become activated and give rise to myogenic progenitors that massively proliferate, differentiate, and fuse to form new myofibers and restore tissue functionality. In addition, a proportion of activated cells returns back to quiescence and replenish the pool of satellite cells in order to maintain the ability of skeletal muscle tissue to repair...
2018: Current Topics in Developmental Biology
Josefa Predestinación García-Ruíz, Andrés Díaz Lantada
In this study, we present a novel approach towards the straightforward, rapid, and low-cost development of biomimetic composite scaffolds for tissue engineering strategies. The system is based on the additive manufacture of a computer-designed lattice structure or framework, into which carbon fibers are subsequently knitted or incorporated. The 3D-printed lattice structure acts as support and the knitted carbon fibers perform as driving elements for promoting cell colonization of the three-dimensional construct...
December 24, 2017: Materials
Carsta Simon, Dag O Hessen
The behavioral phenotype of an organism results from selective processes acting on variation in behavioral traits during ontogeny (during life span) and phylogeny (across generations). Different adaptive processes can be categorized as environment-phenotype feedback loops. In this cross-disciplinary approach, we discuss the interaction of ontogenetic selective processes, traditionally studied by behavior analysts, and phylogenetic selection processes, traditionally studied by biologists. We elaborate upon the Extended Evolutionary Synthesis by addressing the connection between selection as a domain-general process and phenomena such as classical and operant conditioning, imprinting, adjunctive behavior, and gene-culture coevolution...
December 23, 2017: Behavioural Processes
J S Torday, William B Miller
Recent advances in our understanding of evolutionary development permit a reframed appraisal of Terminal Addition as a continuous historical process of cellular-environmental complementarity. Within this frame of reference, evolutionary terminal additions can be identified as environmental induction of episodic adjustments to cell-cell signaling patterns that yield the cellular-molecular pathways that lead to differing developmental forms. Phenotypes derive, thereby, through cellular mutualistic/competitive niche constructions in reciprocating responsiveness to environmental biophysical stresses and epigenetic impacts...
December 19, 2017: Progress in Biophysics and Molecular Biology
Zhangjiang He, Xin Zhao, Zhuoyue Lu, Huifang Wang, Pengfei Liu, Fanqin Zeng, Yongjun Zhang
Sensing, responding, and adapting to the surrounding environment are crucial for all living organisms to survive, proliferate, and differentiate in their biological niches. Beauveria bassiana is an economically important insect-pathogenic fungus which is widely used as a biocontrol agent to control a variety of insect pests. The fungal pathogen unavoidably encounters a variety of adverse environmental stresses and defense response from the host insects during application of the fungal agents. However, few are known about the transcription response of the fungus to respond or adapt varied adverse stresses...
December 16, 2017: Journal of Invertebrate Pathology
Marius Vital, André Karch, Dietmar H Pieper
Given the key role of butyrate for host health, understanding the ecology of intestinal butyrate-producing communities is a top priority for gut microbiota research. To this end, we performed a pooled analysis on 2,387 metagenomic/transcriptomic samples from 15 publicly available data sets that originated from three continents and encompassed eight diseases as well as specific interventions. For analyses, a gene catalogue was constructed from gene-targeted assemblies of all genes from butyrate synthesis pathways of all samples and from an updated reference database derived from genome screenings...
November 2017: MSystems
G Janani, Samit K Nandi, Biman B Mandal
The creation of in vitro functional hepatic tissue simulating micro-environmental niche of native liver is a keen area of research due to its demand in bioartificial liver (BAL) and cell-based tissue engineering. Here, we investigated the potential of novel blend (BA) silk scaffold fabricated by blending mulberry (Bombyx mori, BM) silk fibroin with cell adhesion motif (RGD) rich non-mulberry (Antheraea assamensis, AA) silk fibroin, in generating a functional liver construct. Three-dimensional (3D) porous silk scaffolds (BM, AA and BA) were physico-chemically characterized and functionally evaluated using human hepatocarcinoma cells (HepG2) and primary neonatal rat hepatocytes...
February 2018: Acta Biomaterialia
Hajo Greif
Two aspects of cognitive coupling, as brought forward in the Extended Mind Hypothesis, are discussed in this paper: (1) how shall the functional coupling between the organism and some entity in his environment be spelled out in detail? (2) What are the paradigmatic external entities to enter into that coupling? These two related questions are best answered in the light of an aetiological variety of functionalist argument that adds historical depth to the "active externalism" promoted by Clark and Chalmers and helps to counter some of the core criticisms levelled against this view...
2017: Synthese
Dilip Thomas, Timothy O'Brien, Abhay Pandit
The primary aim in tissue engineering is to repair, replace, and regenerate dysfunctional tissues to restore homeostasis. Cell delivery for repair and regeneration is gaining impetus with our understanding of constructing tissue-like environments. However, the perpetual challenge is to identify innovative materials or re-engineer natural materials to model cell-specific tissue-like 3D modules, which can seamlessly integrate and restore functions of the target organ. To devise an optimal functional microenvironment, it is essential to define how simple is complex enough to trigger tissue regeneration or restore cellular function...
January 2018: Advanced Materials
Richard Gawne, Kenneth Z McKenna, H Frederik Nijhout
The question of whether the modern evolutionary synthesis requires an extension has recently become a topic of discussion, and a source of controversy. We suggest that this debate is, for the most part, not about the modern synthesis at all. Rather, it is about the extent to which genetic mechanisms can be regarded as the primary determinants of phenotypic characters. The modern synthesis has been associated with the idea that phenotypes are the result of gene products, while supporters of the extended synthesis have suggested that environmental factors, along with processes such as epigenetic inheritance, and niche construction play an important role in character formation...
January 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
Jingjing Sun, Ziqing Deng, Danny Ka Chun Fung, Aixin Yan
Bacterial multidrug efflux pumps belong to a class of membrane transporter proteins that dedicate to the extrusion of a diverse range of substances out of cells including all classes of currently available antibiotics. They constitute an important mechanism of bacterial antibiotic and multidrug resistance. Since many ecological niches of bacteria and the infection foci in animal host display low oxygen tension under which condition bacterial pathogens undergo fundamental changes on their metabolic modes, it is necessary to study the expression profiles of drug efflux pumps under these physiologically and clinically relevant conditions...
2018: Methods in Molecular Biology
William B Miller
An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction...
November 22, 2017: Progress in Biophysics and Molecular Biology
Qinghao Zhang, Jörg C Gerlach, Eva Schmelzer, Ian Nettleship
Foamed hydroxyapatite offers a three-dimensional scaffold for the development of bone constructs, mimicking perfectly the in vivo bone structure. In vivo, calcium release at the surface is assumed to provide a locally increased gradient supporting the maintenance of the hematopoietic stem cells niche. We fabricated hydroxyapatite scaffolds with high surface calcium concentration by infiltration, and used human umbilical vein endothelial cells (HUVECs) as a model to study the effects on hematopoietic lineage direction...
2017: Journal of Vascular Research
Eric D Becraft, Jeremy A Dodsworth, Senthil K Murugapiran, Scott C Thomas, J Ingemar Ohlsson, Ramunas Stepanauskas, Brian P Hedlund, Wesley D Swingley
Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U...
2017: Frontiers in Microbiology
Silke Peter, Philipp Oberhettinger, Leonard Schuele, Ariane Dinkelacker, Wichard Vogel, Daniela Dörfel, Daniela Bezdan, Stephan Ossowski, Matthias Marschal, Jan Liese, Matthias Willmann
BACKGROUND: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Some have suggested that P. putida functions as an exchange platform for antibiotic resistance genes (ARG), and thus represents a serious concern in the spread of ARGs to more pathogenic organisms within a hospital. Though poorly understood, the frequency of ARG exchange between P...
November 10, 2017: BMC Genomics
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