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PubMed2002

Two-dimensional small-scale variability of pore water phosphate in freshwater lakes: results from a novel dialysis sampler.

Vertical concentration profiles of soluble reactive phosphorus (SRP) in the upper sedimentary zone of freshwater lakes are an important means for studying internal phosphorus (P) loading and to gain insight into early diagenetic processes. The interpretation of such pore water profiles generally neglects the occurrence of horizontal variability at a specific sampling site. To further examine this variability, we have designed a novel two-dimensional sampler (2D peeper) consisting of 2280 chambers at a spatial resolution of 9 mm providing a sampling area of 43 x 44 cm. This new device was deployed in three eutrophic lakes in north-eastern Germany. The resulting 2D images of the SRP concentrations, diffusive fluxes, and turnover rates revealed systematic vertical and horizontal structures with local niches of increased phosphorus release. Thus, the extrapolation of P flux calculations based on one-dimensional pore water profiles may lead to a considerable error. The observed small-scale horizontal heterogeneity, probably mainly caused by organisms, was larger in the biologically more active Lake Müllrose and Süsser See than in the deeper Arendsee where meio- and macrozoobenthos were missing. In all cases, the variability was highest at the sediment-water interface and diminished with sediment depth.

Environmental Monitoring↗

PubMed2026

Spatially Contextualized Integrative Genomics Highlights Neuronal and Glial Regulatory Programs in Low Back Pain.

PURPOSE: Low back pain (LBP) is a heterogeneous pain condition with a measurable genetic contribution, but the genes, brain cell types, and spatial tissue contexts through which inherited risk is expressed remain unclear. We aimed to define cell-type-specific and spatially contextualized genetic mechanisms underlying LBP. METHODS: FinnGen R12 LBP GWAS summary statistics (42,521 cases and 353,224 controls) were integrated with brain single-nuclei eQTL data across eight major brain cell classes. We evaluated genome-wide polygenic signal using LDSC, prioritized genes using MAGMA and PoPS, and performed brain cell-type-specific eQTL-anchored Mendelian randomization, primarily based on single-instrument Wald ratio estimates, followed by Bayesian colocalization. Spatial genetic mapping was conducted using gsMap in an E16.5 murine embryonic atlas and two adult human lumbar spinal cord Visium sections. Selected candidates were assessed by RT-qPCR in neuronal-like and astroglial-like inflammatory cell models. RESULTS: LDSC supported interpretable polygenic signal for LBP. MAGMA and PoPS showed partial gene-level convergence, with TCF4 and TMEFF2 supported by both approaches. Across 1641 tested gene-cell type exposures, significant eQTL-anchored MR associations were concentrated in excitatory neurons, oligodendrocytes, inhibitory neurons, and astrocytes. Integrated eQTL-anchored MR, colocalization, and gene-prioritization evidence highlighted CLEC18A, QPRT, and GMPPB as higher-priority non-MHC candidates with moderate, but not strong, colocalization support. gsMap localized LBP-associated enrichment to neuroaxis-related embryonic regions, including brain, spinal cord, sympathetic nerve, and dorsal root ganglion, and to neuronal-like niches in adult lumbar spinal cord. RT-qPCR showed model-dependent expression changes, with QPRT and LGI4 preferentially responsive in neuronal-like SH-SY5Y cells and GMPPB and DPYSL5 responsive in astroglial-like U251 cells. CONCLUSION: These findings support neuronal and glial regulatory programs as plausible contributors to LBP genetic susceptibility and highlight CLEC18A, QPRT, and GMPPB as higher-priority non-MHC candidates with moderate colocalization support. The results provide a spatially contextualized framework for candidate prioritization in LBP, while emphasizing the need for larger cell-type-specific eQTL resources and functional validation before therapeutic or mechanistic conclusions can be drawn.

Mendelian randomization↗

PubMed2001

Accelerated nervous system development contributes to behavioral efficiency in the laboratory mouse: a behavioral review and theoretical proposal.

The emergence of the laboratory mouse as a favored species for genetic research has posed a number of problems for scientists interested in the reflection of genetic influences in mouse behavior. It is commonly thought that rat behavior, which has been studied more extensively than mouse behavior, could be easily generalized to mice. In this article, a number of categories of behavior displayed by the mouse (motor, spatial, defensive, social) are reviewed and contrasted with the same categories of behavior displayed by the rat. The comparison suggests that mouse behavior is simpler and more dependent upon elementary actions than the behavior of the rat. We suggest that the behavioral simplification in the mouse adapts it for a different ecological niche than that occupied by the rat. We propose that this simplification may be mediated by accelerated brain maturation during development. We further propose that this developmental acceleration in the mouse renders it less dependent upon complex social behavior and plastic nervous system changes associated with learning than the rat. This difference poses problems for the development of relevant methods of behavioral analysis and interpretation. Since the mouse's biological adaptations will be reflected in laboratory behavior, suggestions are made for behavioral approaches to the study and interpretation of mouse behavior.

Animals↗

PubMed2006

In search of quorum effects in metacommunity structure: species co-occurrence analyses.

Alternative models of community assembly emphasize regional, stochastic, dispersal-based processes or local, deterministic, niche-based processes. Community ecology's historical focus on local processes implicitly assumes that local processes surpass regional processes over time or across space to derive nonrandom metacommunity structure (i.e., a quorum effect). Quorum effects are expected late in succession among nearby sites, whereas quorum effects are not expected early in succession among distant sites. I conducted a meta-analysis of zooplankton data sets encompassing time scales of one to thousands of years and spatial scales of <1 m to thousands of kilometers. Species co-occurrence analyses statistically evaluated presence/absence patterns relative to random patterns obtained with Monte Carlo null models. A series of weighted analyses was conducted and alternative randomization algorithms and null models were evaluated. Most zooplankton metacommunities were randomly structured in unweighted analyses, and the distribution of significant structure did not follow quorum effect predictions. Weighted analyses (e.g., by habitat area) revealed significant, nonrandom structure in most zooplankton metacommunities, but the distribution of significant structure still did not adhere well to quorum effect predictions. Finally, additional weighting for study scale (number of sites) nullified most significant area-weighted structure, and again, the distribution of significant structure did not follow quorum effect predictions. Overall, a quorum effect was not supported, perhaps related to zooplankton life histories and energetics and/or the quorum effect itself. Results at the presence/absence level of resolution indicated that local processes did not generally override regional processes over time or across space to drive community structure. A full integration of dispersal- and niche-based concepts in metacommunity dynamics will be most fruitful for unraveling community assembly. Species co-occurrence analyses were scale dependent (habitat area and study size). Future analyses should use weights for important factors (e.g., habitat area), and meta-analyses should include study scale as an additional factor contributing to apparent patterns.

Animals↗

PubMed2001

Biofilm formation by Candida dubliniensis.

Candida dubliniensis is an opportunistic yeast closely related to Candida albicans that has been recently implicated in oropharyngeal candidiasis in human immunodeficiency virus-infected patients. Most manifestations of candidiasis are associated with biofilm formation, with cells in biofilms displaying properties dramatically different from free-living cells grown under normal laboratory conditions. Here, we report on the development of in vitro models of C. dubliniensis biofilms on the surfaces of biomaterials (polystyrene and acrylic) and on the characteristics associated with biofilm formation by this newly described species. Time course analysis using a formazan salt reduction assay to monitor metabolic activities of cells within the biofilm, together with microscopy studies, revealed that biofilm formation by C. dubliniensis occurred after initial focal adherence, followed by growth, proliferation, and maturation over 24 to 48 h. Serum and saliva preconditioning films enhanced the initial attachment of C. dubliniensis and subsequent biofilm formation. Scanning electron microscopy and confocal scanning laser microscopy were used to further characterize C. dubliniensis biofilms. Mature C. dubliniensis biofilms consisted of a dense network of yeasts cells and hyphal elements embedded within exopolymeric material. C. dubliniensis biofilms displayed spatial heterogeneity and an architecture showing microcolonies with ramifying water channels. Antifungal susceptibility testing demonstrated the increased resistance of sessile C. dubliniensis cells, including the type strain and eight different clinical isolates, against fluconazole and amphotericin B compared to their planktonic counterparts. C. dubliniensis biofilm formation may allow this species to maintain its ecological niche as a commensal and during infection with important clinical repercussions.

AIDS-Related Opportunistic Infections↗

PubMed2006

Network-based predictions of retail store commercial categories and optimal locations.

I study the spatial organization of retail commercial activities. These are organized in a network comprising "antilinks," i.e., links of negative weight. From pure location data, network analysis leads to a community structure that closely follows the commercial classification of the U.S. Department of Labor. The interaction network allows one to build a "quality" index of optimal location niches for stores, which has been empirically tested.

Journal Article↗

PubMed1996

Cognitive function in mammals: the evolutionary perspective.

The work of behavioural pharmacologists has concentrated on small animals, such as rodents and pigeons. The validity of extrapolation of their findings to humans depends upon the existence of parallels in both physiology and psychology between these animals and humans. This paper considers the question whether there are in fact substantial cognitive parallels between, first, different non-human groups of vertebrates and, second, non-humans and humans. Behavioural data from 'simple' tasks, such as habituation and conditioning, do not point to species differences among vertebrates. Using examples that concentrate on the performance of rodents and birds, it is argued that, similarly, data from more complex tasks (learning-set formation, transitive inference, and spatial memory serve as examples) reveal few if any cognitive differences amongst non-human vertebrates. This conclusion supports the notion that association formation may be the critical problem-solving process available to non-human animals; associative mechanisms are assumed to have evolved to detect causal links between events, and would therefore be relevant in all ecological niches. In agreement with this view, recent advances in comparative neurology show striking parallels in functional organisation of mammalian and avian telencephalon. Finally, it is argued that although the peculiarly human capacity for language marks a large cognitive contrast between humans and non-humans, there is good evidence-in particular, from work on implicit learning--that the learning mechanisms available to non--humans are present and do play an important role in human cognition.

Animals↗

PubMed2003

Competing populations in flows with chaotic mixing.

We investigate the effects of spatial heterogeneity on the coexistence of competing species in the case when the heterogeneity is dynamically generated by environmental flows with chaotic mixing properties. We show that one effect of chaotic advection on the passively advected species (such as phytoplankton, or self-replicating macro-molecules) is the possibility of coexistence of more species than that limited by the number of niches they occupy. We derive a novel set of dynamical equations for competing populations.

Competitive Behavior↗

PubMed1992

Computer-aided three-dimensional reconstruction and measurement of microfissures.

The spatial anatomy of microfissures in the round and oval window areas was investigated in 24 randomly selected normal human temporal bones by our computer-aided three-dimensional reconstruction and measurement method. Microfissures that communicated with the middle ear surface in the round window area were seen in 21 cases (87%) and were located on the posteromediosuperior aspect of the round window niche; whereas microfissures in the oval window area, seen in seven cases (29%), were located at various sites, but mostly in the area below the oval window. Of the 21 microfissures seen in the round window niche, only four were found to be visible through the aperture of the round window niche when viewed from the lateral direction. The mean lengths of the microfissures seen on the middle ear surface in the round and oval window areas were 0.95 +/- 0.66 mm and 0.74 +/- 0.44 mm, respectively. The microfissures in the round window area were significantly longer in individuals 20 years of age and older, than in those less than 20 years (Wilcoxon test, t = 21.5, p less than 0.01); this tendency for microfissures to be longer in older subjects was also found for microfissures in the oval window area. The possible clinical and pathologic significance of these results is discussed.

Adolescent↗

PubMed2026

Genomic and ecological systems-thinking framework for pathogenic Leptospira in Puerto Rico.

INTRODUCTION: Leptospirosis is a complex zoonotic disease requiring high-resolution surveillance. A systems-thinking framework was used to connect genomic and ecological data and map the geographic and host-based structuring of co-circulating pathogenic Leptospira lineages in Puerto Rico. METHODS: Forty-four core genomes of L. interrogans, L. borgpetersenii, and L. kirschneri from human, domestic, and wildlife hosts were analyzed. Spatiotemporal and landscape metadata were integrated using root-to-tip regression, isolation-by-distance profiling and calibrated single-nucleotide polymorphism (SNP) thresholds (≤1, ≤5, and ≤10 SNPs) to define transmission clusters. RESULTS: Leptospira species exhibited distinct ecological pathways partitioned by geography, explaining 56% of genomic variance for L. interrogans and 91% for L. borgpetersenii (PERMANOVA). L. interrogans displayed high landscape connectivity across multiple hosts, forming localized networks (≤1 to ≤10 SNPs) that capture active spillovers (human-to-rat linkages at ≤1 SNP) and resolved into rodent host-specific lineages (R2 = 0.34). Conversely, L. borgpetersenii showed spatial and temporal genomic homogeneity and a lack of host-associated structure within an unpartitioned transmission pool dominated by Mus musculus. As a result, fixed genomic thresholds yielded disparate outcomes: L. interrogans resolved into 4 to 5 discrete, expanding clusters, whereas L. borgpetersenii grouped into a single uniform population at the ≤10-SNP threshold. CONCLUSION: Co-circulating pathogenic leptospires occupy distinct ecological niches shaped by varying host restriction and environmental persistence. Fixed genomic thresholds lack universal applicability; effective genomic epidemiological surveillance must employ species-specific threshold calibration to accurately map transmission pathways.

Puerto Rico↗

PubMed2006

Hydra, a niche for cell and developmental plasticity.

The silencing of genes whose expression is restricted to specific cell types and/or specific regeneration stages opens avenues to decipher the molecular control of the cellular plasticity underlying head regeneration in hydra. In this review, we highlight recent studies that identified genes involved in the immediate cytoprotective function played by gland cells after amputation; the early dedifferentiation of digestive cells into blastema-like cells during head regeneration, and the early late proliferation of neuronal progenitors required for head patterning. Hence, developmental plasticity in hydra relies on spatially restricted and timely orchestrated cellular modifications, where the functions played by stem cells remain to be characterized.

Animals↗

PubMed2006

Jack of all trades, master of some? On the role of phenotypic plasticity in plant invasions.

Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because these sciences are typically interested in different temporal and spatial scales, we describe what is required to assess phenotypic plasticity at different levels. We explore the inevitable tradeoffs of experiments conducted at the genotype vs. species level, outline components of experimental design required to identify plasticity at different levels, and review some examples from the recent literature. Moreover, we suggest that a successful invader may benefit from plasticity as either (1) a Jack-of-all-trades, better able to maintain fitness in unfavourable environments; (2) a Master-of-some, better able to increase fitness in favourable environments; or (3) a Jack-and-master that combines some level of both abilities. This new framework can be applied when testing both ecological or evolutionary oriented hypotheses, and therefore promises to bridge the gap between the two perspectives.

Adaptation, Physiological↗

PubMed2026

Metabolic depot for nucleated erythrocyte degradation: molecular and structural elucidation of the teleost melanomacrophage center.

The function of melanomacrophage centers (MMCs) has long been controversial. While their foundational function is widely accepted as "metabolic dumps" for waste processing, a widely circulated hypothesis posits that they are primitive germinal centers (GCs) executing adaptive immunity. To elucidate this controversy, this study systematically evaluated the splenic MMCs in a higher teleost ( Micropterus salmoides) by combining transmission electron microscopy (TEM) and high-resolution spatial transcriptomics. Structurally, TEM revealed that the MMC comprises a core with characteristic sparse cellular density, filled with cellular debris and encapsulated by a fibrous layer. Molecularly, under physiological conditions, MMC regions exhibited low transcriptional activity. We did not detect clear enrichment of B cell and T cell lineage genes, and the key GC marker aicda was not observed. Conversely, its predominant molecular signature was characterized by macrophage-driven iron metabolism (e.g., ferritin) and erythrocyte degradation (e.g., hba1). Furthermore, the physicochemical properties of MMCs pigments (e.g., argyrophilia) suggest that traditional histological staining methods warrant cautious interpretation regarding potential non-specific signals. In conclusion, our findings characterize the MMC as a highly specialized metabolic processing and sequestration niche. This study provides new perspectives on the evolution of immune-metabolic homeostasis in poikilothermic vertebrates, advances comparative immunology, and offers a critical scientific reference for the accurate interpretation of MMCs as a biological indicator in pathology and ecotoxicology.

Animals↗

PubMed2026

A spatiotemporal resolution to genetic redundancy: MIR164 diversification coordinates development and metabolism in Brassica.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

MicroRNAs↗

PubMed2001

Spatio-temporal gait characteristics of level and vertical locomotion in a ground-dwelling and a climbing gecko.

The effects of incline (vertical versus horizontal) on spatio-temporal gait characteristics (stride and step length, frequency, duty factor, degree of sprawling) were measured over a range of speeds in a ground-dwelling (Eublepharis macularius) and a climbing (Gekko gecko) species of gecko. Surprisingly, the climbing species also performs very well when moving on the horizontal substratum. In the present experiments, climbing speeds ranged from 0.6 to 1.2 m s(-1), whereas speeds for level locomotion were between 0.6 and 1.8 m s(-1). In contrast, the vertical climbing capacities of the ground-dweller are limited (speeds below 0.1 m s(-1 )versus level speeds between 0.2 and 1.1 m s(-1)). In general, we demonstrate that very little adjustment in gait characteristics is made by either species when they are forced to move on their non-habitual substratum. Moreover, gait characteristics differ little between the species despite the clear differences in ecological niche. Higher level or climbing speeds are realized mainly (or exclusively in the case of level locomotion in G. gecko) by increasing stride frequency. Stride lengths and duty factors vary with speed in the ground-dweller, but not in the climbing species. Step length and the degree of sprawling are speed-independent (except for hind-limb sprawling in G. gecko on the level). It is argued that this common strategy suits climbing (fixed spatial variables, no floating phases) rather than level locomotion.

Adaptation, Physiological↗

PubMed2002

Chemical warfare between microbes promotes biodiversity.

Evolutionary processes generating biodiversity and ecological mechanisms maintaining biodiversity seem to be diverse themselves. Conventional explanations of biodiversity such as niche differentiation, density-dependent predation pressure, or habitat heterogeneity seem satisfactory to explain diversity in communities of macrobial organisms such as higher plants and animals. For a long time the often high diversity among microscopic organisms in seemingly uniform environments, the famous "paradox of the plankton," has been difficult to understand. The biodiversity in bacterial communities has been shown to be sometimes orders of magnitudes higher than the diversity of known macrobial systems. Based on a spatially explicit game theoretical model with multiply cyclic dominance structures, we suggest that antibiotic interactions within microbial communities may be very effective in maintaining diversity.

Anti-Bacterial Agents↗

PubMed2006

How does cellular senescence prevent cancer?

It is widely believed that cellular senescence is a tumor suppressor mechanism; however, it has not been understood why it is advantageous for organisms to retain mutant cells is a postmitotic state rather than simply eliminating them by apoptosis. It has recently been proposed that the primary role of cellular senescence is in mitotic compartments of fixed size in which spatial considerations dictate that a deleted cell is replaced by a neighboring cell. In these situations, rather than eliminating the neoplastic clone, deletion of mutant cells can paradoxically lead to their increased turnover. If mutant cells become senescent, then the compartment is instead progressively filled by senescent cells until the mutant clone is eliminated. Since most of the genetic alterations responsible for malignancy arise in stem cells, this mechanism may have particular relevance to the stem cell niche. In this article the implications of this hypothesis are examined in detail and related to experimental results. It is further proposed here that blockage of stem cell niches by senescent stem cells may account for some of the functional alterations observed in stem cell compartments at old age. Clearly, the existence of senescent stem cells is central to the proposed hypothesis, and although there is preliminary evidence for this assertion it has yet to be proven in vivo. An experimental strategy involving double labeling of stem cells with a nucleotide label is described that can address this question.

Animals↗

PubMed2006

African cichlid fish: a model system in adaptive radiation research.

The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and 'non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.

Adaptation, Physiological↗