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Niche construction

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https://www.readbyqxmd.com/read/29126393/genomic-characterisation-of-clinical-and-environmental-pseudomonas-putida-group-strains-and-determination-of-their-role-in-the-transfer-of-antimicrobial-resistance-genes-to-pseudomonas-aeruginosa
#1
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
https://www.readbyqxmd.com/read/29106267/a-novel-ecological-account-of-prefrontal-cortex-functional-development
#2
Denise M Werchan, Dima Amso
In this paper, we argue that prefrontal cortex ontogenetic functional development is best understood through an ecological lens. We first begin by reviewing evidence supporting the existing consensus that PFC structural and functional development is protracted based on maturational constraints. We then examine recent findings from neuroimaging studies in infants, early life stress research, and connectomics that support the novel hypothesis that PFC functional development is driven by reciprocal processes of neural adaptation and niche construction...
November 2017: Psychological Review
https://www.readbyqxmd.com/read/29090082/the-trochoblasts-in-the-pilidium-larva-break-an-ancient-spiralian-constraint-to-enable-continuous-larval-growth-and-maximally-indirect-development
#3
George von Dassow, Svetlana A Maslakova
BACKGROUND: Nemertean embryos undergo equal spiral cleavage, and prior fate-mapping studies showed that some also exhibit key aspects of spiralian lineage-based fate specification, including specification of the primary trochoblasts, which differentiate early as the core of the prototroch of the spiralian trochophore larva. Yet it remains unclear how the nemertean pilidium larva, a long-lived planktotroph that grows substantially as it builds a juvenile body from isolated rudiments, develops within the constraints of spiral cleavage...
2017: EvoDevo
https://www.readbyqxmd.com/read/29079730/engineering-of-an-angiogenic-niche-by-perfusion-culture-of-adipose-derived-stromal-vascular-fraction-cells
#4
Giulia Cerino, Emanuele Gaudiello, Manuele Giuseppe Muraro, Friedrich Eckstein, Ivan Martin, Arnaud Scherberich, Anna Marsano
In vitro recapitulation of an organotypic stromal environment, enabling efficient angiogenesis, is crucial to investigate and possibly improve vascularization in regenerative medicine. Our study aims at engineering the complexity of a vascular milieu including multiple cell-types, a stromal extracellular matrix (ECM), and molecular signals. For this purpose, the human adipose stromal vascular fraction (SVF), composed of a heterogeneous mix of pericytes, endothelial/stromal progenitor cells, was cultured under direct perfusion flow on three-dimensional (3D) collagen scaffolds...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29076547/the-sphagnome-project-enabling-ecological-and-evolutionary-insights-through-a-genus-level-sequencing-project
#5
David J Weston, Merritt R Turetsky, Matthew G Johnson, Gustaf Granath, Zoë Lindo, Lisa R Belyea, Steven K Rice, David T Hanson, Katharina A M Engelhardt, Jeremy Schmutz, Ellen Dorrepaal, Eugénie S Euskirchen, Hans K Stenøien, Péter Szövényi, Michelle Jackson, Bryan T Piatkowski, Wellington Muchero, Richard J Norby, Joel E Kostka, Jennifer B Glass, Håkan Rydin, Juul Limpens, Eeva-Stiina Tuittila, Kristian K Ullrich, Alyssa Carrell, Brian W Benscoter, Jin-Gui Chen, Tobi A Oke, Mats B Nilsson, Priya Ranjan, Daniel Jacobson, Erik A Lilleskov, R S Clymo, A Jonathan Shaw
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking...
October 27, 2017: New Phytologist
https://www.readbyqxmd.com/read/29076257/homeostasis-maintenance-of-encapsulated-cells
#6
Volha Liaudanskaya, Claudio Migliaresi, Antonella Motta
Cell niche homeostasis plays a critical role in many bodily functions including tissue functionality, stem cell maintenance and differentiation, wound healing, cancer development and propagation, and many others. Many tissue engineering approaches overlook the importance of engineered constructs homeostasis, in particular for transplantation purposes. Here we present a study of the effect of encapsulation duration on engineered tissue maturation and provide a protocol for the evaluation of critical conditions for transplantation purposes...
October 26, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29061900/the-niche-construction-of-cultural-complexity-interactions-between-innovations-population-size-and-the-environment
#7
Laurel Fogarty, Nicole Creanza
Niche construction is a process through which organisms alter their environments and, in doing so, influence or change the selective pressures to which they are subject. 'Cultural niche construction' refers specifically to the effect of cultural traits on the selective environments of other biological or cultural traits and may be especially important in human evolution. In addition, the relationship between population size and cultural accumulation has been the subject of extensive debate, in part because anthropological studies have demonstrated a significant association between population size and toolkit complexity in only a subset of studied cultures...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29056332/mouse-genetic-analysis-of-bone-marrow-stem-cell-niches-technological-pitfalls-challenges-and-translational-considerations
#8
REVIEW
Kevin G Chen, Kory R Johnson, Pamela G Robey
The development of mouse genetic tools has made a significant contribution to the understanding of skeletal and hematopoietic stem cell niches in bone marrow (BM). However, many experimental designs (e.g., selections of marker genes, target vector constructions, and choices of reporter murine strains) have unavoidable technological limitations and bias, which lead to experimental discrepancies, data reproducibility issues, and frequent data misinterpretation. Consequently, there are a number of conflicting views relating to fundamental biological questions, including origins and locations of skeletal and hematopoietic stem cells in the BM...
November 14, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/29049298/using-worldwide-edaphic-data-to-model-plant-species-niches-an-assessment-at-a-continental-extent
#9
Santiago José Elías Velazco, Franklin Galvão, Fabricio Villalobos, Paulo De Marco Júnior
Ecological niche modeling (ENM) is a broadly used tool in different fields of plant ecology. Despite the importance of edaphic conditions in determining the niche of terrestrial plant species, edaphic data have rarely been included in ENMs of plant species perhaps because such data are not available for many regions. Recently, edaphic data has been made available at a global scale allowing its potential inclusion and evaluation on ENM performance for plant species. Here, we take advantage of such data and address the following main questions: What is the influence of distinct predictor variables (e...
2017: PloS One
https://www.readbyqxmd.com/read/29043038/habitat-niche-breadth-predicts-invasiveness-in-solitary-ascidians
#10
Itai Granot, Noa Shenkar, Jonathan Belmaker
A major focus of invasion biology is understanding the traits associated with introduction success. Most studies assess these traits in the invaded region, while only few compare nonindigenous species to the pool of potential invaders in their native region. We focused on the niche breadth hypothesis, commonly evoked but seldom tested, which states that generalist species are more likely to become introduced as they are capable of thriving under a wide set of conditions. Based on the massive introduction of tropical species into the Mediterranean via the Suez Canal (Lessepsian migration), we defined ascidians in the Red Sea as the pool of potential invaders...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29029631/neurotrophic-support-by-traumatized-muscle-derived-multipotent-progenitor-cells-role-of-endothelial-cells-and-vascular-endothelial-growth-factor-a
#11
Heidi R H Zupanc, Peter G Alexander, Rocky S Tuan
BACKGROUND: Adult mesenchymal stem cells (MSCs) have been shown to increase nerve regeneration in animal models of nerve injury. Traumatized muscle-derived multipotent progenitor cells (MPCs) share important characteristics with MSCs and are isolated from severely damaged muscle tissue following surgical debridement. Previous investigations have shown that MPCs may be induced to increase production of several neurotrophic factors, suggesting the possible utility of autologous MPCs in peripheral nerve regeneration following injury...
October 13, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29027331/when-does-it-pay-to-invest-in-a-patch-the-evolution-of-intentional-niche-construction
#12
Kathryn A Mohlenhoff, Brian F Codding
Humans modify their environments in ways that significantly transform the earth's ecosystems. Recent research suggests that such niche-constructing behaviors are not passive human responses to environmental variation, but instead should be seen as active and intentional management of the environment. Although such research is useful in highlighting the interactive dynamics between humans and their natural world, the niche-construction framework, as currently applied, fails to explain why people would decide to modify their environments in the first place...
September 2017: Evolutionary Anthropology
https://www.readbyqxmd.com/read/29021252/a-chemical-and-biological-toolbox-for-type-vd-secretion-characterization-of-the-phospholipase-a1-autotransporter-fpla-from-fusobacterium-nucleatum
#13
Michael A Casasanta, Christopher C Yoo, Hans B Smith, Alison J Duncan, Kyla Cochrane, Ann C Varano, Emma Allen-Vercoe, Daniel J Slade
Fusobacterium nucleatum is an oral pathogen that is linked to multiple human infections and colorectal cancer. Strikingly, F. nucleatum achieves virulence in the absence of large, multi-protein secretion systems (Type I, II, III, IV, and VI) which are widely used by Gram-negative bacteria for pathogenesis. By contrast, F. nucleatum strains contain genomic expansions of Type V secreted effectors (autotransporters) that are critical for host cell adherence, invasion, and biofilm formation. Here we present the first characterization of a F...
October 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29017922/building-kit-for-metal-cation-binding-sites-in-proteins
#14
Alexander I Denesyuk, Sergei E Permyakov, Mark S Johnson, Eugene A Permyakov, Konstantin Denessiouk
Starting with conformations of calcium-binding sites in parvalbumin and integrin (representative structures of EF-hand and calcium blade zones, respectively) we introduce four new different local Ca(2+)-recognition units in proteins: a one-residue unit type I (ORI); a three-residue unit type I (TRI); a one-residue unit type II (ORII) and a three-residue unit type II (TRII). Based on the amount and nature of variable atoms, the type I and II units theoretically can have four and twelve variants, respectively...
December 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28992215/thermal-performance-curves-reveal-variation-in-the-seasonal-niche-of-a-short-lived-annual
#15
Joe Hereford
An organism's environment can vary over spatial and temporal scales. Seasonal variation is an important but overlooked source of environmental variation that often shapes the ranges of organisms. The seasonal niche is a description of the spatiotemporal range of an organism resulting from spatial variation in seasonal conditions. In this study, I describe the seasonal niche of a short-lived annual plant, and variation within the species in seasonal niche breadth. I construct a seasonal species distribution model (SDM) for the species, and using thermal performance curves (TPCs), construct mechanistic SDMs (MSDMs) for individual genotypes...
November 1, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28991922/clonal-dominance-and-transplantation-dynamics-in-hematopoietic-stem-cell-compartments
#16
Peter Ashcroft, Markus G Manz, Sebastian Bonhoeffer
Hematopoietic stem cells in mammals are known to reside mostly in the bone marrow, but also transitively passage in small numbers in the blood. Experimental findings have suggested that they exist in a dynamic equilibrium, continuously migrating between these two compartments. Here we construct an individual-based mathematical model of this process, which is parametrised using existing empirical findings from mice. This approach allows us to quantify the amount of migration between the bone marrow niches and the peripheral blood...
October 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28984359/strategies-to-retain-properties-of-bone-marrow-derived-mesenchymal-stem-cells-ex-vivo
#17
REVIEW
Yaxian Zhou, Tsung-Lin Tsai, Wan-Ju Li
Mesenchymal stem cells (MSCs) have been extensively used for cell therapies and tissue engineering. The current MSC strategy requires a large quantity of cells for such applications, which can be achieved through cell expansion in culture. In the body, stem cell fate is largely determined by their microenvironment, known as the niche. The complex and dynamic stem cell niche provides physical, mechanical, and chemical cues to collaboratively regulate cell activities. It remains a great challenge to maintain the properties of MSCs in culture...
October 6, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28969852/comparative-trophic-structures-of-macrobenthic-food-web-in-two-macrotidal-wetlands-with-and-without-a-dike-on-the-temperate-coast-of-korea-as-revealed-by-stable-isotopes
#18
Hyun Je Park, Hee Yoon Kang, Tae Hee Park, Chang-Keun Kang
This study characterized trophic structures of the macrobenthic food webs in two contrasting estuarine wetlands, with and without a dike, on the southern coast of Korea, based on the δ(13)C and δ(15)N values of dominant macrobenthic consumers. The pelagic algal biomasses were similar in the upper Phragmites australis-covered and lower bare intertidal habitats partitioned by the dike, but the microphytobenthos (MPB) biomasses were extremely low in the Phragmites bed. The consumer δ(13)C values were more negative and their isotopic niche width was much narrower in the upper than in the lower habitat at the diked site...
October 2017: Marine Environmental Research
https://www.readbyqxmd.com/read/28965671/environmental-niche-separation-between-native-and-non-native-benthic-invertebrate-species-case-study-of-the-northern-baltic-sea
#19
Holger Jänes, Kristjan Herkül, Jonne Kotta
Knowledge and understanding of geographic distributions of species is crucial for many aspects in ecology, conservation, policy making and management. In order to reach such an understanding, it is important to know abiotic variables that impact and drive distributions of native and non-native species. We used an existing long-term macrobenthos database for species presence-absence information and biomass estimates at different environmental gradients in the northern Baltic Sea. Region specific abiotic variables (e...
October 2017: Marine Environmental Research
https://www.readbyqxmd.com/read/28948216/glaciation-as-a-migratory-switch
#20
Robert M Zink, Aubrey S Gardner
Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents...
September 2017: Science Advances
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