Niche Structure Research Articles

Acute Myeloid Leukemia and the Bone Marrow Niche—Take a Closer Look

The bone marrow is the home of hematopoiesis and is therefore a hotspot for the development of hematopoietic diseases. Complex interactions between the bone marrow microenvironment and hematopoietic stem cells must find a balance between proliferation, differentiation and homeostasis of the stem cell compartment. Changes in this tightly regulated network can provoke malignant transformation, leading to hematopoietic diseases. Here we focus on acute myeloid leukemia (AML), since this is the most frequent acute leukemia in adulthood with very poor overall survival rates and where relapse after chemotherapy continues to be a major challenge, driving demand for new therapeutic strategies. Current research is focusing on the identification of specific interactions between leukemic blasts and their niche components, which may be exploited as novel treatment targets along with induction chemotherapy. Significant progress has been gained over the last few years in the field of high-resolution imaging. Confocal ex vivo and intravital microscopy have revealed a detailed map of bone marrow structures and components; as well as identifying numerous alterations in the stem cell niche that correspond to disease progression. However, the underlying mechanisms are still not completely understood and due to the complexity, their elucidation remains a challenging. This review discusses the constitution of the AML niche in the bone marrow, the improvement in visualization of the complex three-dimensional niche structures and points out new therapeutic strategies to increase the overall survival of AML patients.

Design and Development of a Tri-Coil Bellows Transducer for RW-Drive Implantable Middle-Ear Hearing Aid Using FEA

We describe the design and development of a tri-coil bellows transducer (TCBT) for use in an implantable middle-ear hearing aid for round window (RW) drive. The TCBT provides easy implantation and a better frequency response than previous RW middle-ear transducers. It consisted of three cylindrical coils, a bonded magnet, and a tiny bellows with multiple corrugations. The simulation started with the calculation of the vibrational force required for the RW-drive transducer. Based on the anatomical structure of the RW niche and its volume, the designed TCBT was 1.75 mm in diameter and 2.3 mm long. To maximize the electromagnetic force of a TCBT installed within the limited volume of the RW niche, its structure was designed using an electromagnetic analysis based on finite-element analysis to determine the each length of the three cylindrical coils and the bonded magnet inside the TCBT. Additionally, the resonance frequency characteristics of the TCBT were determined using mechanical vibration analysis. A prototype TCBT was fabricated according to the simulation results, and an experiment to evaluate its vibrational characteristics was performed with the TCBT in an unloaded condition. Finally, the performance of the TCBT for use in RW-drive implantable middle-ear hearing aids was confirmed in experiments with cadaveric temporal bones.

Emergent niche structuring leads to increased differences from neutrality in species abundance distributions.

Species abundance distributions must reflect the dynamic processes involved in community assembly, but whether and when specific processes lead to distinguishable signals is not well understood. Biodiversity and species abundances may be shaped by a variety of influences, but particular attention has been paid to competition, which can involve neutral dynamics, where competitor abundances are governed only by demographic stochasticity and immigration, and dynamics driven by trait differences that enable stable coexistence through the formation of niches. Key recent studies of the species abundance patterns of communities with niches employ simple models with pre-imposed niche structure. These studies suggest that species abundance distributions are insensitive to the relative contributions of niche and neutral processes, especially when diversity is much higher than the number of niches. Here we analyze results from a stochastic population model with competition driven by trait differences. With this model, niche structure emerges as clumps of species that persist along the trait axis, and leads to more substantial differences from neutral species abundance distributions than have been previously shown. We show that heterogeneity in "between-niche" interaction strength (i.e., in the strength of competition between species in different niches) plays the dominant role in shaping the species abundances along the trait axis, acting as a biotic filter favoring species at the centers of niches. Furthermore, we show that heterogeneity in "within-niche" interactions (i.e., in the competition between species in the same niche) counteracts the influence of heterogeneity in "between-niche" interactions on the SAD to some degree. Our results suggest that competitive interactions that produce niches can also influence the shapes of SADs.

Using neurogenic explants to assess the role of the stem cell niche structure fractones in adult neurogenesis and pathology

Neurogenesis occurs throughout adulthood in restricted zones of the adult brain. Growth factors influence neural stem cell proliferation and differentiation. However, the mechanisms orchestrating growth factors to regulate neurogenesis are not well known. In the adult brain, neural stem cells and their immediate progeny reside in a nurturing stem cell niche environment. These niches are located in the ventricular/sub ventricular zone (VZ/SVZ) of the lateral ventricles. In the SVZ, stem cells are directly contacted by extracellular matrix (ECM) structures that we have named fractones. Using in vivo experiments, we have previously shown that fractones contain heparan sulfate proteoglycans (HSPG) that bind, concentrate and dispatch growth factors to the target stem cells to ultimately regulate stem cell fate. Here, an ex vivo model was devised to expand our ability to study fractones, stem cells, and growth factor interactions in culture in a near‐physiological context. This model consists of brain tissue pieces of the neurogenic zone, termed neurogenic explant. Neurogenic explants survive for months in a simple culture medium. They contain neural stem cells, their immediate progeny, ependymocytes, fractones, all forming the VZ/SVZ, plus the adjacent superficial part of the caudate nucleus. Using mini‐incubator and fluorescence microscopy, we demonstrate that we can visualize fractones, cell proliferation and growth factor binding on the living neurogenic explants. The ease in altering the ECM of explants and assessing the effects on neurogenic stem cells will allow us to understand the role of fractones in neurogenesis. By using explants originating from animal models, we will also be able to understand the relationship between disrupted adult neurogenesis and neural pathology. We anticipate that we can determine from the neurogenic explant model which HSPGs are responsible for the binding of individual growth factors. This will provide insight into the possibility of manipulating HSPG expression in explants to ultimately alter the cell‐fractone interactions responsible for the progression of disease.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Lineage-Biased Hematopoietic Stem Cells Are Regulated by Distinct Niches

The spatial localization of hematopoietic stem cells (HSCs) in the bone marrow (BM) remains controversial, with some studies suggesting that they are maintained in homogeneously distributed niches while others have suggested the contributions of distinct niche structures. Subsets of quiescent HSCs have been reported to associate with megakaryocytes (MK) or arterioles in the BM. However, these HSC subsets have not been prospectively defined. Here, we show that platelet and myeloid-biased HSCs, marked by von Willebrand factor (vWF) expression, are highly enriched in MK niches. Depletion of MK selectively expands vWF+ HSCs, whereas the depletion of NG2+ arteriolar niche cells selectively depletes vWF- lymphoid-biased HSCs. In addition, MK depletion compromises vWF+ HSC function by reducing their long-term self-renewal capacity and eliminating their lineage bias after transplantation. These studies demonstrate the existence of two spatially and functionally separate BM niches for HSC subsets with distinct developmental potential.

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche.

Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.

On the Statistical Mechanics of Alien Species Distribution

Many species of plants are found in regions to which they are alien. Their global distributions are characterised by a family of exponential functions of the kind that arise in elementary statistical mechanics (an example in ecology is MacArthur’s broken stick). We show here that all these functions are quantitatively reproduced by a model containing a single parameter—some global resource partitioned at random on the two axes of species number and site number. A dynamical model generating this equilibrium is a two-fold stochastic process and suggests a curious and interesting biological interpretation in terms of niche structures fluctuating with time and productivity, with sites and species highly idiosyncratic. Idiosyncrasy implies that attempts to identify a priori those species likely to become naturalised are unlikely to be successful. Although this paper is primarily concerned with a particular problem in population biology, the two-fold stochastic process may be of more general interest.

SUPPRESSOR OF GAMMA RESPONSE1 Links DNA Damage Response to Organ Regeneration.

In Arabidopsis, DNA damage-induced programmed cell death is limited to the meristematic stem cell niche and its early descendants. The significance of this cell-type-specific programmed cell death is unclear. Here, we demonstrate in roots that it is the programmed destruction of the mitotically compromised stem cell niche that triggers its regeneration, enabling growth recovery. In contrast to wild-type plants, sog1 plants, which are defective in damage-induced programmed cell death, maintain the cell identities and stereotypical structure of the stem cell niche after irradiation, but these cells fail to undergo cell division, terminating root growth. We propose DNA damage-induced programmed cell death is employed by plants as a developmental response, contrasting with its role as an anticarcinogenic response in animals. This role in plants may have evolved to restore the growth of embryos after the accumulation of DNA damage in seeds.

The ‘Hutchinsonian niche’ as an assemblage of demographic niches: implications for species geographic ranges

Hutchinson defined the ecological niche as a hypervolume shaped by the environmental conditions under which a species can ‘exist indefinitely’. Although several authors further discussed the need to adopt a demographic perspective of the ecological niche theory, very few have investigated the environmental requirements of different components of species’ life cycles (i.e. vital rates) in order to examine their internal niche structures. It therefore remains unclear how species’ demography, niches and distributions are interrelated. Using comprehensive demographic data for two well‐studied, short‐lived plants (Plantago coronopus, Clarkia xantiana), we show that the arrangement of species’ demographic niches reveals key features of their environmental niches and geographic distributions. In Plantago coronopus, opposing geographic trends in some individual vital rates, through different responses to environmental gradients (demographic compensation), stabilize population growth across the range. In Clarkia xantiana, a lack of demographic compensation underlies a gradient in population growth, which could translate in a directional geographic range shift. Overall, our results highlight that occurrence and performance niches cannot be assumed to be the same, and that studying their relationship is essential for a better understanding of species’ ecological niches. Finally, we argue for the value of considering the assemblage of species’ demographic niches when studying ecological systems, and predicting the dynamics of species geographical ranges.

Niche centrality and human influence predict rangewide variation in population abundance of a widespread mammal: The collared peccary (Pecari tajacu)

AbstractAim(1) To evaluate whether geographic variation in population abundance of a widespread mammal (Pecari tajacu) is related to its location with respect to the centroid of its ecological niche or to the centroid of its geographic range. (2) To assess whether the abundance–niche centrality relationship defines the maximum expected abundance at any location, rather than the realized abundance. (3) To test whether including human impacts improves the abundance–niche centrality relationship, and therefore the prediction of geographic variation in population abundance.LocationThe Americas.MethodsWe modelled the ecological niche of the species using occurrence and environmental data and created spatial models of distance to the niche centroid (DNC) and to the geographic centroid (DGC). We tested the relationships between population abundance andDNCand between abundance andDGC. We evaluated whether the rate of change in the abundance–DNCrelationship was steeper near the upper boundary of quantile regressions. We tested whether the human influence index (HII) contributed to improve niche‐based predictions of population abundance. Finally, we generated broad‐scale predictions of collared peccary population abundances.ResultsWe found a negative relationship between abundance andDNCand a non‐significant relationship between abundance andDGC. The abundance–DNCrelationship was wedge‐shaped, steeper in the upper quantile boundary than in the median.HIIalso had a negative effect on abundance. The model includingDNCandHIIwas best supported for predicting the median abundance, whileDNCalone was the best to predict the upper boundary of population abundances.Main conclusionsPopulation abundances are associated with the structure of the ecological niche, especially the maximum abundance expected in an area. Thus, theDNCapproach can be useful in obtaining a spatial approximation of potential abundance patterns at biogeographic extents. To achieve a better prediction of realized abundances, it is critical to consider the human influence.

Environmental stability increases relative individual specialisation across populations of an aquatic top predator

The concept of the niche has long been a central pillar in ecological theory, with a traditional focus on quantifying niches at the species or population level. However, the importance of individual‐level niche variation is increasingly being recognised, with a strong focus on individual specialisation. While examples illustrating the contribution of the individual niche to whole population niche structure are accumulating rapidly, surprisingly little is known about the conditions that shape the differences between these two potentially divergent components. Though theory predicts that stability should influence the extent of such intra‐specific specialisation, we know of no previous study that has investigated its role in individual specialisation, and the differentiation between individual‐ and population niches. Here, we studied the diet of individuals from multiple populations of an aquatic top‐predator, Salmo trutta, inhabiting contrasting stable, groundwater fed and unstable, surface water fed pre‐alpine streams. Based on stomach content analysis, we found that individuals living in stable environments displayed a higher degree of specialisation than those in unstable environments, with the between‐individual component of niche width being approximately twice as high in the former. We subsequently validated these results by evidence gained from stable isotope analysis of muscle tissue. As such, we reveal that environmental stability can significantly influence individual niches within populations, leading to increased specialisation.

The pathological structure of the perivascular niche in different microvascular patterns of glioblastoma.

The perivascular niche is critical for intercellular communication between resident cell types in glioblastoma (GBM), and it plays a vital role in maintaining the glioma stem cell (GSC) microenvironment. It is shown in abundant research that different microvascular patterns exist in GBM; and it can be implied that different microvascular patterns are associated with different pathological structures in the perivascular niche. However, the pathological structure of the perivascular niche is still not clear. Here, we investigated the distribution and biological characteristics of different microvascular pattern niches (MVPNs) in GBM by detecting the expression of CD34, CD133, Nestin, α-SMA, GFAP and CD14 in the perivascular niche using multiple -fluorescence. The four basic microvascular patterns are microvascular sprouting (MS), vascular cluster (VC), vascular garland (VG), and glomeruloid vascular proliferation (GVP). By analyzing the proportion of the area of each marker in four types of formations, the results indicated that the expression of CD34, CD133 and Nestin in MS and VC was significantly lower than that in VG and GVP (P<0.05). Furthermore, the results showed that α-SMA expression different in the MS, VC, VG and GVP (P<0.05). However, the expression of GFAP and CD14 in each type of formation exhibited no significant difference (P>0.05). According to the area distributions of different markers, we mapped four precise simulation diagrams to provide an effective foundation for the accurate simulation of glioblastoma in vitro.

Artificial Hematopoietic Stem Cell Niches-Dimensionality Matters

Hematopoietic stem cell niches are perhaps the best described niche system in mammals. The niches themselves, as well as their cellular and structural constituents and factors that play a role in maintaining the niche structure and function, are being refined on a more or less daily basis. Despite this, it seems as if the more we know the harder it gets to mimic the in vivo-situation using in vitro-systems. This is due to the fact that hematopoiesis is a multi step maturation process leading to HSC heterogeneity. Subpopulations of HSCs and niche supporting cells can be defined depending on characteristics such as their potency of leading to successful reconstitution of sub lethally irradiated mice in serial transplantation experiments or, with less scientific impact, clonogenic assays. Since the bone marrow obviously provides all necessary information to maintain the stem cell pool constant and to adapt the number of blood cells according to physiologic needs, it has been the goal to engineer artificial niches that display at least one or several of the major characteristics of the in vivo-situation to make use of these systems for not only fundamental research purposes but, moreover, also for clinical applications. This review will give an overview of approaches to engineering artificial hematopoietic niches with a focus on the complexity/dimensionality of the systems used.

ALLERGY AND PSEUDO-ALLERGY: ECOLOGIC ASPECTS OF GEOGRAPHIC PATHOLOGY

Those problems of modern people, which are related to their lifestyle in terms of the formation of geographic pathology, are deep and multi-faceted. Organism adaptive reconstruction caused by environmental changes is taking practical significance both for evaluation of functional state of organs and systems as well as for working out scientifically grounded principles of primary prophylaxis of geographical pathology, caused by the influence of natural conditions and anthropogenic factors. In the structure of geographic pathology huge niche belongs to allergic diseases, which are qualified not only as genetically, but also as ecologically determined «civilization diseases». Differentiated approach to studying the prevalence of allergic diseases in the North is considered in terms of the main pathogenic mechanisms: true allergy and pseudo allergy. As an example the results of epidemiologic examination for Evenkia population are presented. Epidemiology of allergic diseases distinctively shows that mankind should not only enlarge the spectrum of new anthropogenic factors and create new so called «blessings of civilization», which negatively influence an organism, contributing to the diseases, but should know the laws of living in consonance with nature, following those laws and not disturb them with mindless and massive persistency. Specific of the allergy mechanisms triggering in extreme ecologic conditions of the North is calling for solutions.

Identification for Differential Localization of Putative Corneal Epithelial Stem Cells in Mouse and Human

Human Corneal epithelial stem cells (CESCs) have been identified to reside in limbus for more than 2 decades. However, the precise location of CESCs in other mammalian remains elusive. This study was to identify differential localization of putative CESCs in mice. Through a series of murine corneal cross-sections from different directions, we identified that anatomically and morphologically the murine limbus is composed of the thinnest epithelium and the thinnest stroma without any palisades of Vogt-like niche structure. The cells expressing five of stem/progenitor cell markers are localized in basal layer of entire murine corneal epithelium. BrdU label-retaining cells, a key characteristic of epithelial stem cells, are detected in both limbal and central cornea of mouse eye. Functionally, corneal epithelium can be regenerated in cultures from central and limbal explants of murine cornea. Such a distribution of mouse CESCs is different from human cornea, where limbal stem cell concept has been well established and accepted. We are aware that some new evidence supports limbal stem cell concept in mouse recently. However, it is important to know that central cornea may provide an alternative source of stem cells when one utilizes mice as animal model for corneal research.

Niche Structures in Television. Video Poetry - Visually Reading the Reality

Niche Structures in Television. Video Poetry - Visually Reading the Reality

Systems biology analysis of the WOX5 gene and its functions in the root stem cell niche

The WUSCHEL-RELATED HOMEOBOX 5 (WOX5) gene encodes the transcription factor, which is one of the key regulators maintaining the structure and functioning of the stem cell niche in plant root tips. WOX5 is expressed in the quiescent center of the root apical meristem, preventing the differentiation of the columella initials and, together with SCR, SHR, PLT1, and PLT2, participating in controlling the differentiation of other initials of the root meristem. However, the details of the WOX5 functioning are unclear. The WOX5 protein belongs to the WUSCHEL-related homeobox (WOX) family, the founder of which is the transcription factor WUSCHEL (WUS), maintaining the stem cell niche in the shoot apical meristem. WOX5 and WUS diverged from a common ancestor at the base of angiosperms, which resulted in a specialization of the shoot and root stem cell niches. However, the WOX5 structural and functional divergence during angiosperm evolution has been poorly addressed. In this review we present a systems biology analysis of the WOX5 gene to reveal specific features of its evolution and functioning. For this, we performed a phylogenetic analysis on 62 publicly available WOX5 amino acid sequences, integrated published data about WOX5 expression domain in Arabidopsis and other species and its role in development, and summarize the results of experiments on primary and secondary targets for this transcription factor. The data on the possible mechanisms of direct and indirect regulation of WOX5 expression were discussed. In particular, we analyzed the WOX5 promoter regions from 30 species. Possible direct regulators of WOX5 gene expression were proposed based on the presence of putative binding sites for the candidate transcription factors in the conserved WOX5 promoter regions.

Selective laser melting-enabled electrospinning: Introducing complexity within electrospun membranes.

Additive manufacturing technologies enable the creation of very precise and well-defined structures that can mimic hierarchical features of natural tissues. In this article, we describe the development of a manufacturing technology platform to produce innovative biodegradable membranes that are enhanced with controlled microenvironments produced via a combination of selective laser melting techniques and conventional electrospinning. This work underpins the manufacture of a new generation of biomaterial devices that have significant potential for use as both basic research tools and components of therapeutic implants. The membranes were successfully manufactured and a total of three microenvironment designs (niches) were chosen for thorough characterisation. Scanning electron microscopy analysis demonstrated differences in fibre diameters within different areas of the niche structures as well as differences in fibre density. We also showed the potential of using the microfabricated membranes for supporting mesenchymal stromal cell culture and proliferation. We demonstrated that mesenchymal stromal cells grow and populate the membranes penetrating within the niche-like structures. These findings demonstrate the creation of a very versatile tool that can be used in a variety of tissue regeneration applications including bone healing.

The Geography of Ecological Niche Evolution in Mammals

Convergent adaptive evolution of species' ecological niches-i.e., the appearance of similar niches in independent lineages-is the result of natural selection acting on niche-related species traits ("traits" hereafter) and contrasts with neutral evolution [1-4]. Although trait convergences are recognized as being of importance at the species scale, we still know little about the impact of species convergence on the overall trait and niche structure of entire biotas at large spatial scales [5]. Here, we map the convergent evolution of four traits (diet, body mass, activity cycle, and foraging strata) for mammal species and assemblages (defined at 200× 200km resolution) at a global scale. Using data on the geographic distributions, traits, and phylogenetic relationships of species and by comparing observed patterns of trait β-diversity to evolutionary neutral expectations, we show that trait convergence is not restricted to particular lineages but scales up to entire assemblages (i.e., whole species communities). We find region-wide biota convergence in traits between regions with similar climates, particularly between Australia and other continents. Pairs of assemblages that show trait divergence often involves Arctic regions where rapid evolutionary changes occurred in response to extreme climatic constraints. By integrating both macroecological and macroevolutionary approaches into a single framework, our study quantifies the crucial role of evolutionary processes such as natural selection in the spatial distribution and structure of large-scale species assemblages.

Competition and feeding ecology in two sympatric Xenopus species (Anura: Pipidae).

The widespread African clawed frog (Xenopus laevis) occurs in sympatry with the IUCN Endangered Cape platanna (Xenopus gilli) throughout its entire range in the south-western Cape, South Africa. In order to investigate aspects of the interspecific competition between populations of X. laevis and X. gilli, an assessment of their niche differentiation was conducted through a comprehensive study on food composition and trophic niche structure at two study sites: the Cape of Good Hope (CoGH) and Kleinmond. A total of 399 stomach contents of X. laevis (n = 183) and X. gilli (n = 216) were obtained together with samples of available prey to determine food preferences using the Electivity index (E*), the Simpson’s index of diversity (1 − D), the Shannon index (H′), and the Pianka index (Ojk). Xenopus gilli diet was more diverse than X. laevis, particularly in Kleimond where the Shannon index was nearly double. Both species were found to consume large amounts of tadpoles belonging to different amphibian species, including congeners, with an overall higher incidence of anurophagy than previously recorded. However, X. laevis also feeds on adult X. gilli, thus representing a direct threat for the latter. While trophic niche overlap was 0.5 for the CoGH, it was almost 1 in Kleinmond, suggesting both species utilise highly congruent trophic niches. Further, subdividing the dataset into three size classes revealed overlap to be higher in small frogs in both study sites. Our study underlines the importance of actively controlling X. laevis at sites with X. gilli in order to limit competition and predation, which is vital for conservation of the south-western Cape endemic.