Niche Structure Research Articles

Three‐dimensional structure of the mammalian limbal stem cell niche

PurposeAlthough the existence of the limbal stem cell (LSC) niche is accepted, precise knowledge of its 3D architecture remains incomplete.MethodsThe LSC niche was explored on freshly excised corneoscleral rims from human donors (n = 47), pigs (n = 15) and mice (n = 27) with full‐field optical coherence microscopy (FFOCM).ResultsLimbal crypt features were detected in 90% of human corneoscleral rims, extending between the palisades of Vogt as radial (74%) and/or rounded (23%) forms, often branching off to or becoming interconnected by sub‐scleral radially or circumferentially oriented crypts (56%). [kg1] Mean crypt volume represented 16% of sampled limbal volume on the vertical axis and 8% on the horizontal axis. In pigs, palisades were finer and crypts wider with relatively uniform distribution around the eye, and radial orientation, connecting to numerous narrow criss‐crossing invaginations beneath the sclera. In mice, only a circumferential limbal trough was detected. Mean crypt volume represented 13% of limbal volume in humans, 9% in pigs and 7% in mice. FFOCM combined with fluorescence showed presence of p63‐α+ cells and cytokeratin‐3 + cells in the limbal crypts. LSC density increased with percentage limbal volume occupied by crypts. Colony Forming Efficiency increased with limbal crypt volume. [kg1] See how to rephrase all this.ConclusionsCrypt architecture in the three species appears associated with eye exposure to light. Clone production correlated strongly with the limbal crypt volume in humans indicating that limbal crypts constitute a niche for adult limbal stem cells. FFOCM imaging could assist in assessment of the richness of the limbal crypts and targeted biopsy for cell culture.

Three-dimensional structure of the mammalian limbal stem cell niche

Although the existence of the limbal stem cell (LSC) niche is accepted, precise knowledge of its three-dimensional (3D) architecture remains incomplete. The LSC niche was explored on freshly excised and organ-cultured corneoscleral rims from human donors (n = 47), pigs (n = 15) and mice (n = 27) with full-field optical coherence microscopy (FFOCM). Limbal crypt features were detected in 90% of organ-cultured human corneoscleral rims, extending between the palisades of Vogt as radially oriented rectangular (74% of eyes) and/or rounded (23% of eyes) forms, often branching off to, or becoming interconnected by, sub-scleral radially or circumferentially oriented crypts (in 56% of eyes). Mean crypt volume represented 16% of sampled limbal volume on the vertical axis and 8% on the horizontal axis. In pigs, palisades were finer and crypts wider with relatively uniform distribution around the eye, and radial orientation, connecting to numerous narrow criss-crossing invaginations beneath the scleral surface. In mice, only a circumferential limbal trough was detected. Mean crypt volume represented 13% of sampled limbal volume in humans and 9% in pigs. FFOCM combined with fluorescence, and confocal fluorescence microscopy, showed presence of p63-α+ cells and cytokeratin-3+ cells in the limbal crypts. To assess colony forming efficiency (CFE), limbal epithelial cells were cultured at low density with mitomycin-arrested 3T3 feeders. CFE increased with limbal crypt volume and was not significantly decreased in organ-cultured cornea, despite degradation of the epithelial roof, suggesting that stem cells remain protected at the base of crypts during organ culture. CFE in human samples was significantly greater than in pig, and CFE in mouse was zero. Crypt architecture in the three species appears associated with eye exposure to light. LSC density increased with percentage limbal volume occupied by crypts.

Microhabitat use and activity budget of four Himalayan river-birds, India

A wide variety of river-birds are found in the Eastern Himalayan region of Northeast India, but the literature on microhabitat use and resource use patterns of these river-birds is very sparse. The fundamental processes that determine niche structures and influence niche segregation in coexisting species is a basic concern of community ecology. For example, when territories of different species overlap, those species utilize different local resources or the same resources differently due to either niche complementarity or resource partitioning. Understanding the role of microhabitat has been an unending quest of avian autecology and community ecology. Such studies, particularly when understood in terms of resource partitioning, have been successful largely because of the fundamental importance of microhabitat to bird ecology. In the present study, we looked at the microhabitat preferences of four species of birds namely plumbeous water-redstart (Rhyacornis fuliginosa), white-capped water-redstart (Chaimarrornis leucocephalus), brown dipper (Cinclus pallasii) and slaty-backed forktail (Enicurus schistaceus) in Kamlang Wildlife Sanctuary (KWS).

The role of the bi-compartmental stem cell niche in delaying cancer

In recent years, by using modern imaging techniques, scientists have found evidence of collaboration between different types of stem cells (SCs), and proposed a bi-compartmental organization of the SC niche. Here we create a class of stochastic models to simulate the dynamics of such a heterogeneous SC niche. We consider two SC groups: the border compartment, S1, is in direct contact with transit-amplifying (TA) cells, and the central compartment, S2, is hierarchically upstream from S1. The S1 SCs differentiate or divide asymmetrically when the tissue needs TA cells. Both groups proliferate when the tissue requires SCs (thus maintaining homeostasis). There is an influx of S2 cells into the border compartment, either by migration, or by proliferation. We examine this model in the context of double-hit mutant generation, which is a rate-limiting step in the development of many cancers. We discover that this type of a cooperative pattern in the stem niche with two compartments leads to a significantly smaller rate of double-hit mutant production compared with a homogeneous, one-compartmental SC niche. Furthermore, the minimum probability of double-hit mutant generation corresponds to purely symmetric division of SCs, consistent with the literature. Finally, the optimal architecture (which minimizes the rate of double-hit mutant production) requires a large proliferation rate of S1 cells along with a small, but non-zero, proliferation rate of S2 cells. This result is remarkably similar to the niche structure described recently by several authors, where one of the two SC compartments was found more actively engaged in tissue homeostasis and turnover, while the other was characterized by higher levels of quiescence (but contributed strongly to injury recovery). Both numerical and analytical results are presented.

Hemocompatible Thin-Film Materials Recreating the Structure of the Cell Niches with High Potential for Endothelialization

Hemocompatible Thin-Film Materials Recreating the Structure of the Cell Niches with High Potential for Endothelialization

Evaluation of the osteoinductive potential of a bio-inspired scaffold mimicking the osteogenic niche for bone augmentation

Augmentation of regenerative osteogenesis represents a premier clinical need, as hundreds of thousands of patients are left with insufficient healing of bony defects related to a host of insults ranging from congenital abnormalities to traumatic injury to surgically-induced deficits. A synthetic material that closely mimics the composition and structure of the human osteogenic niche represents great potential to successfully address this high demand. In this study, a magnesium-doped hydroxyapatite/type I collagen scaffold was fabricated through a biologically-inspired mineralization process and designed to mimic human trabecular bone. The composition of the scaffold was fully characterized by XRD, FTIR, ICP and TGA, and compared to human bone. Also, the scaffold microstructure was evaluated by SEM, while its nano-structure and nano-mechanical properties were evaluated by AFM. Human bone marrow-derived mesenchymal stem cells were used to test the in vitro capability of the scaffold to promote osteogenic differentiation. The cell/scaffold constructs were cultured up to 7 days and the adhesion, organization and proliferation of the cells were evaluated. The ability of the scaffold to induce osteogenic differentiation of the cells was assessed over 3 weeks and the correlate gene expression for classic genes of osteogenesis was assessed. Finally, when tested in an ectopic model in rabbit, the scaffold produced a large volume of trabecular bone in only two weeks, that subsequently underwent maturation over time as expected, with increased mature cortical bone formation, supporting its ability to promote bone regeneration in clinically-relevant scenarios. Altogether, these results confirm a high level of structural mimicry by the scaffold to the composition and structure of human osteogenic niche that translated to faster and more efficient osteoinduction in vivo – features that suggest such a biomaterial may have great utility in future clinical applications where bone regeneration is required.

Local-scale disturbances can benefit an endangered, fire-adapted plant species in Western Mediterranean heathlands in the absence of fire

Fire-prone Mediterranean heathlands are biodiversity hotspots and home to a multitude of fire-dependent species. Fire-suppression policies worldwide have increased the risk of extinction of such species or have delegated relative prominence to other disturbances. This study explores how such a substitution of disturbances can alter the realized niche and population structure of a post-fire specialist. Using multi-model inference, we evaluate the relative magnitude and directionality (positive or negative) in the effect of large-scale (entire range) and local-scale (southern Spain) anthropogenic disturbances on the occurrence and abundance of Drosophyllum lusitanicum. This rare carnivorous plant is endemic to heathlands in the Southwestern Iberian Peninsula and northwestern Morocco managed under strict fire suppression policies. An increase in regional-scale anthropogenic disturbances did not affect regional-scale occurrence but significantly decreased abundance of Drosophyllum. On the other hand, local-scale anthropogenic disturbances positively affected both population occurrence and abundance. We demonstrate that non-fire anthropogenic disturbances can drive the population structure and distribution of an endemic post-fire specialist in Mediterranean heathlands, but their impacts change with their spatial scale. Although large-scale disturbances may threaten populations, small-scale disturbances may be more significant for species occurrence, and positively affect the distribution and abundances of pyrophytic species. In heathlands where fire suppression is a common practice, applying such disturbance regimes can be crucial for the preservation of fire-adapted species.

Niche structure of marine sponges from temperate hard-bottom habitats within Gray's Reef National Marine Sanctuary

Many species of marine sponges on tropical reefs host abundant and diverse symbiont communities capable of varied metabolic pathways. While such communities may confer a nutritional benefit to some hosts (termed High Microbial Abundance (HMA) sponges), other sympatric species host only sparse symbiont communities (termed Low Microbial Abundance (LMA) sponges) and obtain a majority of their C and N from local sources. Sponge communities are widespread across large latitudinal gradients, however, and recent evidence suggests that these symbioses may also extend beyond the tropics. We investigated the role that symbionts play in the ecology of sponges from the temperate, hard-bottom reefs of Gray's Reef National Marine Sanctuary by calculating the niche size (as standard ellipse area (SEAc)) and assessing the relative placement of five HMA and four LMA sponge species within bivariate (δ13C and δ15N) isotopic space. Although photosymbiont abundance was low across most of these species, sponges were widespread across isotopic niche space, implying that microbial metabolism confers an ecological benefit to temperate sponges by expanding host metabolic capability. To examine how these associations vary across a latitudinal gradient, we also compared the relative placement of temperate and tropical conspecifics within isotopic space. Surprisingly, shifts in sponge δ13C and δ15N values between these regions suggest a reduced reliance on symbiont-derived nutrients in temperate sponges compared with their tropical conspecifics. Despite this, symbiotic sponges in temperate systems likely have a competitive advantage, allowing them to grow and compete for space within these habitats.

Invasion success of a global avian invader is explained by within‐taxon niche structure and association with humans in the native range

AbstractAimTo mitigate the threat invasive species pose to ecosystem functioning, reliable risk assessment is paramount. Spatially explicit predictions of invasion risk obtained through bioclimatic envelope models calibrated with native species distribution data can play a critical role in invasive species management. Forecasts of invasion risk to novel environments, however, remain controversial. Here, we assess how species’ association with human‐modified habitats in the native range and within‐taxon niche structure shape the distribution of invasive populations at biogeographical scales and influence the reliability of predictions of invasion risk.LocationAfrica, Asia and Europe.MethodsWe use ~1200 native and invasive ring‐necked parakeet (Psittacula krameri) occurrences and associated data on establishment success in combination with mtDNA‐based phylogeographic structure to assess niche dynamics during biological invasion and to generate predictions of invasion risk. Niche dynamics were quantified in a gridded environmental space while bioclimatic models were created using the biomod2 ensemble modelling framework.ResultsRing‐necked parakeets show considerable niche expansion into climates colder than their native range. Only when incorporating a measure of human modification of habitats within the native range do bioclimatic envelope models yield credible predictions of invasion risk for parakeets across Europe. Invasion risk derived from models that account for differing niche requirements of phylogeographic lineages and those that do not achieve similar statistical accuracy, but there are pronounced differences in areas predicted to be susceptible for invasion.Main conclusionsInformation on within‐taxon niche structure and especially association with humans in the native range can substantially improve predictive models of invasion risk. To provide policymakers with robust predictions of invasion risk, including these factors into bioclimatic envelope models is recommended.

Co‐existence in a species‐rich grassland: competition, facilitation and niche structure over a soil depth gradient

AbstractQuestionNiche differentiation may promote species co‐existence because it precludes competitive exclusion. However, in stressful environments, facilitation may predominate, and large niche overlaps may result from niche widening and positive spatial associations. We analysed the niche structure of a species‐rich system over a soil depth gradient (a niche axis positively correlated with water availability) and tested for various patterns expected from competition or facilitation.LocationSemi‐arid grassland, Oaxaca, Mexico.MethodsWe recorded species abundance and soil depth in 1200 0.1 × 0.1 m quadrats from four sites. Community structure was described through correspondence analysis and correlated with soil depth. We measured niche breadth (Levine's index), position (mean depth) and overlap (Hurlbert's index). We used a null model to estimate the expected overlap if interactions play no role in determining community structure. We tested whether overlap changed along the depth gradient. We also analysed if niches become narrow with higher competition.ResultsData supported three predictions derived from competition: most species’ niches were relatively narrow and differed in their position along the gradient, a pattern reflected in a changing community structure; realized niches became narrower where competition was stronger; and niche overlap was smaller than expected by chance. Facilitation had no support: large niche overlaps expected from stress amelioration were as frequent as predicted by chance. Overlap increased in the most stressful (shallow) soils, as expected if facilitation predominates there, but also in the deepest ones where evidence for competition was strong, suggesting an artifact at the extremes of the gradient.ConclusionsIn this grassland, competition seems to restrict species distribution, abating richness in the deepest soils and relegating poor competitors (succulent and poikilohydric species) to the shallow soils. There, drought tolerance rather than facilitation determined community composition and richness. Our results support the idea that hydrological niches play an important role in maintaining plant diversity because (1) differentiation in hydrological requirements (small niche overlaps over the water‐use axis) reduces competition, and (2) spatial heterogeneity and stress create competition‐free patches. Our results also support the hypothesis that facilitation is rare when stress is caused by resource (in this case, water) scarcity.

Evaluating the performance of neutrality tests of a local community using a niche‐structured simulation model

Understanding the processes that underlie species diversity and abundance in a community is a fundamental issue in community ecology. While the species abundance distributions (SADs) of various natural communities may be well explained by Hubbell's neutral model, it has been repeatedly pointed out that Hubbell's SAD‐fitting approach lacks the ability to detect the effects of non‐neutral factors such as niche differentiation; however, our understanding of its quantitative effect is limited. Herein, we conducted extensive simulations to quantitatively evaluate the performance of the SAD‐fitting method and other recently developed tests. For simulations, we developed a niche model that incorporates the random stochastic demography of individuals and the nonrandom replacements of those individuals, i.e. niche differentiation. It therefore allows us to explore situations with various degrees of niche differentiation. We found that niche differentiation has strong effects on SADs and the number of species in the community under this model. We then examined the performance of these neutrality tests, including Hubbell's SAD‐fitting method, using extensive simulations. It was demonstrated that all these tests have relatively poor performance except for the cases with very strong niche structure, which is in accordance with previous studies. This is likely because two important parameters in Hubbell's model are usually unknown and are commonly estimated from the data to be tested. To demonstrate this point, we showed that the precise estimation of the two parameters substantially improved the performance of these neutrality tests, indicating that poor performance can be owed to overfitting Hubbell's neutral model with unrealistic parameters. Our results therefore emphasize the importance of accurate parameter estimation, which should be obtained from data independent of the local community to be tested.

Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras.

Hosting symbionts provides many eukaryotes with access to the products of microbial metabolism that are crucial for host performance. On tropical coral reefs, many (High Microbial Abundance [HMA]) but not all (Low Microbial Abundance [LMA]) marine sponges host abundant symbiont communities. Although recent research has revealed substantial variation in these sponge-microbe associations (termed holobionts), little is known about the ecological implications of this diversity. We investigated the expansion of diverse sponge species across isotopic niche space by calculating niche size (as standard ellipse area [SEAc]) and assessing the relative placement of common sponge species in bivariate (δ13C and δ15N) plots. Sponges for this study were collected from the relatively isolated reefs within the Miskito Cays of Honduras. These reefs support diverse communities of HMA and LMA species that together span a gradient of photosymbiont abundance, as revealed by chlorophyll a analysis. HMA sponges occupied unique niche space compared to LMA species, but the placement of some HMA sponges was driven by photosymbiont abundance. In addition, photosymbiont abundance explained a significant portion of the variation in isotope values, suggesting that access to autotrophic metabolism provided by photosymbionts is an important predictor in the location of species within isotopic space. Host identity accounted for over 70% of the variation in isotope values within the Miskito Cays and there was substantial variation in the placement of individual species within isotopic niche space, suggesting that holobiont metabolic diversity may allow taxonomically diverse sponge species to utilize unique sources of nutrients within a reef system. This study provides initial evidence that microbial symbionts allow sponges to expand into novel physiochemical niche space. This expansion may reduce competitive interactions within coral reefs and promote diversification of these communities.

Species interactions during diversification and community assembly in Malagasy Miniopterus bats

The habitat first rule (HFR) proposes that radiating species initially diversify into habitat specialists and later into dietary specialists within a given habitat, whereas the general vertebrate model (GVM) adds divergence of sexually selected traits as a possible third axis of specialization subsequent to habitat and dietary divergence. In this study, using 12 Miniopterus spp. from Madagascar we test predictions of the HFR and GVM from ecological and evolutionary perspectives on Grinnellian and Eltonian niche structures. We used environmental niche models (ENMs) to quantify the Grinnellian niche, both for current and last inter-glacial climates. We used null models to examine Eltonian niche patterns of sympatric species in terms of their phylogenetic relatedness and phenotypic and sensory characters associated with the trophic niche—body size, skull morphology and echolocation. As predicted by the HFR, we found evidence for labile Grinnellian niches: there was no similarity in ENMs between sister species; overlap in ENMs was significantly low in >65 % of all possible species pairs; there was no relationship between ENM niche overlap and phylogenetic distances between species; and there was no phylogenetic signal in suitable bioclimatic zones among species. Conversely, we found equivocal support for the HFR regarding Eltonian niche patterns. Closely related species tended to be distributed among ensembles rather than within ensembles, although there was no evidence for overdispersion in phylogenetic patterns in ensembles. In <50 % of the observed combinations of sympatric Miniopterus spp., we found significant signal for overdispersion of phenotypic and sensory characters. We hypothesize that selective processes associated with the adaptive radiation of Miniopterus spp. on Madagascar may have favoured bats to diversify first into broad scale habitat specialists, but argue that understanding the relative influence of bionomic processes at a local spatial scale will require more reciprocal comparisons of Eltonian niches.

Dietary Competition in an Extant Mammalian Guild: Application of a Quantitative Method to Evaluate Reconstructed Niche Overlap in Paleocommunities

The evaluation of competition, contingent on the identification of niche similarity, is a challenge in the fossil record. Specifically, a method for quantifying the degree of niche overlap is needed, as niches in paleocommunities can be reconstructed only using ecomorphological characters. In this study, I suggest the use of nonparametric multivariate pairwise comparisons for testing the presence or absence of niche overlap, wherein niches are defined as Hutchinsonian multidimensional hypervolumes. I applied this method to an extant mammalian guild, comprising primates and their dietary competitors, to determine the significance of dimensionality in niche construction and to examine the ability of molar morphology to capture dietary niche overlap. I conducted principal component analyses of eight molar measurements across all members of this guild, and dietary niches were defined by principal component scores. Niche overlap was assessed through the comparison of distances among individuals both within and between niches. To demonstrate the application of the proposed method, I compared dietary niches of 1) seven predefined dietary groups and 2) genera within and across dietary groups using multivariate pairwise comparisons. Results indicated that the typically unexplored higher principal components, or “niche axes,” may be integral to niche separation. As predicted, almost all niches of genera from different dietary groups did not overlap; however, niche overlap among genera within the same dietary category was less than expected. This highlights our need to investigate further the structure of niches within extant guilds to better inform our examination of competition in paleocommunities.

A comparative assessment of hand preference in captive red howler monkeys, Alouatta seniculus and yellow-breasted capuchin monkeys, Sapajus xanthosternos.

There are two major theories that attempt to explain hand preference in non-human primates–the ‘task complexity’ theory and the ‘postural origins’ theory. In the present study, we proposed a third hypothesis to explain the evolutionary origin of hand preference in non-human primates, stating that it could have evolved owing to structural and functional adaptations to feeding, which we refer to as the ‘niche structure’ hypothesis. We attempted to explore this hypothesis by comparing hand preference across species that differ in the feeding ecology and niche structure: red howler monkeys, Alouatta seniculus and yellow-breasted capuchin monkeys, Sapajus xanthosternos. The red howler monkeys used the mouth to obtain food more frequently than the yellow-breasted capuchin monkeys. The red howler monkeys almost never reached for food presented on the opposite side of a wire mesh or inside a portable container, whereas the yellow-breasted capuchin monkeys reached for food presented in all four spatial arrangements (scattered, on the opposite side of a wire mesh, inside a suspended container, and inside a portable container). In contrast to the red howler monkeys that almost never acquired bipedal and clinging posture, the yellow-breasted capuchin monkeys acquired all five body postures (sitting, bipedal, tripedal, clinging, and hanging). Although there was no difference between the proportion of the red howler monkeys and the yellow-breasted capuchin monkeys that preferentially used one hand, the yellow-breasted capuchin monkeys exhibited an overall weaker hand preference than the red howler monkeys. Differences in hand preference diminished with the increasing complexity of the reaching-for-food tasks, i.e., the relatively more complex tasks were perceived as equally complex by both the red howler monkeys and the yellow-breasted capuchin monkeys. These findings suggest that species-specific differences in feeding ecology and niche structure can influence the perception of the complexity of the task and, consequently, hand preference.

A stochastic biodiversity model with overlapping niche structure

The niche is a fundamental ecological concept that underpins many explanations of patterns of biodiversity. The complexity of niche processes in ecological systems, however, means that it is difficult to capture them accurately in theoretical models of community assembly. In this study, we build upon simple neutral biodiversity models by adding the important ingredient of overlapping niche structure. Our model is spatially implicit and contains a fixed number of equal-sized habitats. Each species in the metacommunity arises through a speciation event; at which time, it is randomly assigned a fundamental niche or set of environments/habitats in which it can persist. Within each habitat, species compete with other species that have different but overlapping fundamental niches. Species abundances then change through ecological drift; each, however, is constrained by its maximum niche breadth and by the presence of other species in its habitats. Using our model, we derive analytical expressions for steady-state species abundance distributions, steady-state distributions of niche breadth across individuals and across species, and dynamic distributions of niche breadth across species. With this framework, we identify the conditions that produce the log-series species abundance distribution familiar from neutral models. We then identify how overlapping niche structure can lead to other species abundance distributions and, in particular, ask whether these new distributions differ significantly from species abundance distributions predicted by non-overlapping niche models. Finally, we extend our analysis to consider additional distributions associated with realized niche breadths. Overall, our results show that models with overlapping niches can exhibit behavior similar to neutral models, with the caveat that species with narrow fundamental niche breadths will be very rare. If narrow-niche species are common, it must be because they are in a non-overlapping niche or have countervailing advantages over broad-niche species. This result highlights the role that niches can play in establishing demographic neutrality.

In vivo confocal microscopy assessment of the corneoscleral limbal stem cell niche before and after biopsy for cultivated limbal epithelial transplantation to restore corneal epithelium.

Autologous cultivated limbal epithelial transplantation (CLET) is a successful therapy to restore corneal epithelium when limbal epithelial stem cells are damaged unilaterally, which can result in corneal blindness. We used in vivo confocal microscopy (IVCM) to identify the best location in the corneoscleral limbal niche and to harvest autologous epithelial stem cells for CLET. We also ascertained the completeness of limbal structure removal after biopsy and followed the healing process for any evidence of limbal structure reappearance. The 4 meridians of the corneoescleral limbus of 5 healthy donor eyes were scanned clinically and by IVCM before biopsy and 1 week, 1, 3, and 6 months after. IVCM detected palisades of Vogt, the limbal niche hallmark, more efficiently (100%) than clinically (60%), and were consistently better defined at the 12 o'clock meridian, and so this was the site selected for biopsy. The depth of palisades was 80.4±19.8 μm, and of the limbal biopsies was 136.8±19.1 μm, thus assuring that the limbal niche was completely harvested in all cases. Re-epithelialization of the donor site was complete at 1 week. The limbal wound was refilled with fibrovascular tissue, and no limbal-like structures reappeared. The study shows that clinical absence of palisades of Vogt is not necessarily an exclusionary criterion for autologous CLET. IVCM was useful to select the best place for limbal biopsy and identified features not visible clinically. IVCM also confirmed complete removal of limbal tissue by the biopsy. Limbal niche structures did not reappear by 6 months after surgery.

Models of regulation of stem cell niche structure in shoot apical meristem

The experimental data obtained to date has provided grounds for certain concepts of stem cell niche regulation in shoot apical meristem (SAM). Mathematical modeling is used to check their consistency and coherence with the experimental data. In this paper, we summarize mathematical models of stem cell niche structure regulation proposed by different authors, analyze the experimental base and working hypotheses formalized in these models, and identify methodological differences in the approaches to the construction of these models.

Optimization of Femtosecond Laser Polymerized Structural Niches to Control Mesenchymal Stromal Cell Fate in Culture

We applied two-photon polymerization to fabricate 3D synthetic niches arranged in complex patterns to study the effect of mechano-topological parameters on morphology, renewal and differentiation of rat mesenchymal stromal cells. Niches were formed in a photoresist with low auto-fluorescence, which enabled the clear visualization of the fluorescence emission of the markers used for biological diagnostics within the internal niche structure. The niches were structurally stable in culture up to three weeks. At three weeks of expansion in the niches, cell density increased by almost 10-fold and was 67% greater than in monolayer culture. Evidence of lineage commitment was observed in monolayer culture surrounding the structural niches, and within cell aggregates, but not inside the niches. Thus, structural niches were able not only to direct stem cell homing and colony formation, but also to guide aggregate formation, providing increased surface-to-volume ratios and space for stem cells to adhere and renew, respectively.

A unimodal species response model relating traits to environment with application to phytoplankton communities.

In this paper we attempt to explain observed niche differences among species (i.e. differences in their distribution along environmental gradients) by differences in trait values (e.g. volume) in phytoplankton communities. For this, we propose the trait-modulated Gaussian logistic model in which the niche parameters (optimum, tolerance and maximum) are made linearly dependent on species traits. The model is fitted to data in the Bayesian framework using OpenBUGS (Bayesian inference Using Gibbs Sampling) to identify according to which environmental variables there is niche differentiation among species and traits. We illustrate the method with phytoplankton community data of 203 lakes located within four climate zones and associated measurements on 11 environmental variables and six morphological species traits of 60 species. Temperature and chlorophyll-a (with opposite signs) described well the niche structure of all species. Results showed that about 25% of the variance in the niche centres with respect to chlorophyll-a were accounted for by traits, whereas niche width and maximum could not be predicted by traits. Volume, mucilage, flagella and siliceous exoskeleton are found to be the most important traits to explain the niche centres. Species were clustered in two groups with different niches structures, group 1 high temperature-low chlorophyll-a species and group 2 low temperature-high chlorophyll-a species. Compared to group 2, species in group 1 had larger volume but lower surface area, had more often flagella but neither mucilage nor siliceous exoskeleton. These results might help in understanding the effect of environmental changes on phytoplankton community. The proposed method, therefore, can also apply to other aquatic or terrestrial communities for which individual traits and environmental conditioning factors are available.