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Results for “Spatial niche”

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PubMed1993

Geographical clinal variation at seven esterase-coding loci in Indian populations of Zaprionus indianus.

Twelve Indian natural populations of Zaprionus indianus, collected along 22 degrees latitudinal range, were analysed electrophoretically for allozymic variation of esterase gene-enzyme system. Interestingly, all the seven Est loci were found to be highly polymorphic in all the populations of Z. indianus. The genetic structure of Z. indianus populations was characterized by extensive inter-populational genotypic as well as allelic frequency heterogeneity and higher genic differentiation at all the esterase-coding loci. All the polymorphic loci in geographical populations of Z. indianus revealed latitudinal clines, and changes in allelic frequencies were found to correlate with latitude. The occurrence of higher genetic variability in Z. indianus populations was in agreement with its habitat-generalist or broad niche-width characteristics, i.e., the species populations utilized diverse food resources and displayed adaptation to variable climatic conditions. Thus, the observed genic divergence patterns in colonizing populations of Z. indianus could be maintained by balancing natural selection varying spatially along the north-south axis of the Indian sub-continent.

Animals↗

PubMed2004

Geographic and ecologic distributions of the Anopheles gambiae complex predicted using a genetic algorithm.

The distribution of the Anopheles gambiae complex of malaria vectors in Africa is uncertain due to under-sampling of vast regions. We use ecologic niche modeling to predict the potential distribution of three members of the complex (A. gambiae, A. arabiensis, and A. quadriannulatus) and demonstrate the statistical significance of the models. Predictions correspond well to previous estimates, but provide detail regarding spatial discontinuities in the distribution of A. gambiae s.s. that are consistent with population genetic studies. Our predictions also identify large areas of Africa where the presence of A. arabiensis is predicted, but few specimens have been obtained, suggesting under-sampling of the species. Finally, we project models developed from African distribution data for the late 1900s into the past and to South America to determine retrospectively whether the deadly 1929 introduction of A. gambiae sensu lato into Brazil was more likely that of A. gambiae sensu stricto or A. arabiensis.

Africa↗

PubMed2026

HIF1A+CSF3R+ neutrophils-dominated hypoxic niche induced metabolic reprogramming for neoadjuvant therapy resistance in NSCLC.

BACKGROUND: Non-small cell lung cancer (NSCLC) is one of the frequently occurring cancers characterized by molecular heterogeneity and multiple immune cell infiltration patterns, which are associated with treatment sensitivity and resistance. However, the specific microenvironmental cells and their mechanisms that lead to treatment resistance in patients need to be explored in greater depth. METHODS: On the basis of patients receiving neoadjuvant therapy in our center, a multicenter, multicohort NSCLC spatial transcriptome, single-cell transcriptome, T-cell receptor repertoire sequencing, bulk RNA transcriptome, phosphorylated proteome, genome mutation, and clinical data were included for a comprehensive assessment of the therapeutic and prognostic impact of HIF1A+ CSF3R+ neutrophils in NSCLC. In vitro experiments validated the functional phenotype of HIF1A+ CSF3R+ neutrophils and co-localization interactions with other cellular subpopulations. Gradient boosting machine (GBM) constructed region of interest (ROI) models for evaluation. Computer-aided drug design (CADD) was used to predict targeted small molecule drugs, and in vivo mouse models were constructed to assess the effectiveness of the combination treatment regimen. RESULTS: Centered on HIF1A+ CSF3R+ neutrophils, recruited exhausted T cells and stromal cells form a hypoxic niche within the tumor region, which was enriched in non-response patients. ROI composed of these specific cellular subpopulations, associated with senescence and glycolysis, accurately predicting NSCLC progression, prognosis, and microenvironment composition. CADD analysis identified that platycodin-D2 specifically targeted CSF3R, reducing HIF1A expression and inhibiting neutrophil activity. Combining navitoclax, platycodin-D2 with anti-programmed cell death protein 1 (PD-1) significantly suppressed tumor proliferation and improved the immunosuppressive microenvironment. CONCLUSION: Our study emphasized the role of HIF1A+ CSF3R+ neutrophils in immunotherapeutic resistance of NSCLC, constructed a microenvironmental immune dysregulation network in a hypoxic ecological niche with HIF1A+ CSF3R+ neutrophils as the center. Platycodin-D2 specifically targeted HIF1A+ CSF3R+ neutrophils, enhancing the efficacy of anti-PD-1 therapy in NSCLC.

Humans↗

PubMed2026

Genomic insights into local adaptation of indigenous chickens.

Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1 022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.

Animals↗

PubMed2006

Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments.

Cyanobacteria are important primary producers in many marine ecosystems and their abundances and growth rates depend on their ability to assimilate various nitrogen sources. To examine the diversity of nitrate-utilizing marine cyanobacteria, we developed PCR primers specific for cyanobacterial assimilatory nitrate reductase (narB) genes. We obtained amplification products from diverse strains of cultivated cyanobacteria and from several marine environments. Phylogenetic trees constructed with the narB gene are congruent with those based on ribosomal RNA genes and RNA polymerase genes. Analysis of sequence library data from coastal and oligotrophic marine environments shows distinct groups of Synechococcus sp. in each environment; some of which are represented by sequences from cultivated organisms and others that are unrelated to known sequences and likely represent novel phylogenetic groups. We observed spatial differences in the distribution of sequences between two sites in Monterey Bay and differences in the vertical distribution of sequence types at the Hawai'i Ocean Time-series Station ALOHA, suggesting that nitrogen assimilation in Synechococcus living in different ecological niches can be followed with the nitrate reductase gene.

Classification↗

PubMed2001

Gill parasites of Cephalopholis argus (Teleostei: Serranidae) from Moorea (French Polynesia): site selection and coexistence.

The distribution and coexistence of gill ectoparasites of 121 specimens of Cephalopholis argus Bloch et Schneider, caught between October 1994 and October 1995, were investigated. Adults of the monogenean Benedenia sp. and copepod Hatschekia sp., the larval caligid copepod Caligus sp. (copepodite and chalimus stages), and praniza larvae of the isopod Gnathia sp. were found. All species were aggregated within the host population. Infracommunities were poor, with only 40.5% of fish infected by two parasite species. Only two individual fish harboured all the parasite species observed at the component community level. Prevalences were less than 50% and mean intensities were low (less than 6 parasites/host). No dominant parasite species were observed in the host population. The spatial distribution of each parasite species was studied on different partitions of the gill arches. Adult parasite stages that are mobile showed much overlap in their distribution, whereas temporarily attached larvae of Caligidae were more site specific. Copepodite and chalimus larvae showed niche restriction that is probably due to gregarious behaviour. Positive associations between caligid larvae reflected intraspecific interaction for site and/or resources. Each of the Caligus sp. larval stages prefers specific sites, as do the adults, which occur exclusively in the buccal cavity of the host. Infracommunities were too poor and too few to induce processes of interspecific competition.

Animals↗

PubMed2004

DNA analysis on fox faeces and competition induced niche shifts.

Interference competition can force inferior competitors to change their distribution patterns. It is, however, possible that the dominant competitor poses a higher threat during certain times of the year, for example during reproduction. In such cases, the inferior competitor is expected to change its distribution accordingly. We used a molecular species identification method on faeces to investigate how the spatial overlap between arctic and red foxes changes between seasons. The results show that arctic and red foxes are sympatric during winter, but allopatric in summer as arctic foxes retreat to higher altitudes further from the tree-line during the breeding season.

Analysis of Variance↗

PubMed2003

Geographical isolation in hot spring cyanobacteria.

It has been proposed that free-living microorganisms exhibit ubiquitous dispersal, do not form geographically isolated populations and rarely (if ever) speciate via allopatry. We studied island-like hot spring cyanobacterial communities in which geographical isolation should be prominent and detectable if it influences the evolution of bacteria. The genetic diversity of cyanobacteria indigenous to North American, Japanese, New Zealand and Italian springs was surveyed by (i) amplification and cloning of 16S rRNA and 16S-23S internal transcribed spacer regions; (ii) lineage-specific oligonucleotide probing (used to verify the predominance of cloned sequences); and (iii) lineage-specific polymerase chain reaction (PCR) (used to search for possible rare genotypes). Phylogenetic and distribution patterns were found to be consistent with the occurrence of geographical isolation at both global and local spatial scales, although different cyanobacterial lineages were found to vary in their distribution. A lack of correspondence between biological patterning and the chemical character of springs sampled suggested that the geographical distribution of thermophilic cyanobacteria cannot be explained by the 20 potential niche-determining chemical parameters that we assayed. Thus, geographical isolation (i.e. genetic drift) must in part be responsible for driving the observed evolutionary divergences. Geographical isolation may be an important underestimated aspect of microbial evolution.

Biological Evolution↗

PubMed2004

Biofilms promote altruism.

The origin of altruism is a fundamental problem in evolution, and the maintenance of biodiversity is a fundamental problem in ecology. These two problems combine with the fundamental microbiological question of whether it is always advantageous for a unicellular organism to grow as fast as possible. The common basis for these three themes is a trade-off between growth rate and growth yield, which in turn is based on irreversible thermodynamics. The trade-off creates an evolutionary alternative between two strategies: high growth yield at low growth rate versus high growth rate at low growth yield. High growth yield at low growth rate is a case of an altruistic strategy because it increases the fitness of the group by using resources economically at the cost of decreased fitness, or growth rate, of the individual. The group-beneficial behaviour is advantageous in the long term, whereas the high growth rate strategy is advantageous in the short term. Coexistence of species requires differences between their niches, and niche space is typically divided into four 'axes' (time, space, resources, predators). This neglects survival strategies based on cooperation, which extend the possibilities of coexistence, arguing for the inclusion of cooperation as the fifth 'axis'. Here, individual-based model simulations show that spatial structure, as in, for example, biofilms, is necessary for the origin and maintenance of this 'primitive' altruistic strategy and that the common belief that growth rate but not yield decides the outcome of competition is based on chemostat models and experiments. This evolutionary perspective on life in biofilms can explain long-known biofilm characteristics, such as the structural organization into microcolonies, the often-observed lack of mixing among microcolonies, and the shedding of single cells, as promoting the origin and maintenance of the altruistic strategy. Whereas biofilms enrich altruists, enrichment cultures, microbiology's paradigm for isolating bacteria into pure culture, select for highest growth rate.

Altruism↗

PubMed1992

Fundamental motor patterns of the mammalian fetus.

Techniques that permit direct observation of fetuses in vivo recently have expanded our understanding of prenatal behavioral development in mammals. Although fetal motor activity seems to lack the dynamic, goal-directed character of postnatal behavior, the dimensions that define behavioral organization after birth are applicable to the movements expressed by fetuses. Fetal activity exhibits temporal, sequential, and spatial organization that emerges between the inception of movement and term. Fetal rodents, for example, exhibit coordinated motor patterns antecedent to postnatal righting, locomotion, suckling, maternal-infant communication and grooming behavior, while other action patterns appear to be functional adaptations to the intrauterine niche. Fetuses also are behaviorally responsive to sensory stimulation and changes in environmental conditions in utero. Expression of these behavioral properties emphasizes continuity between prenatal and postnatal life while implying an adaptive role for behavior before birth.

Animals↗

PubMed2025

Spatial genomics: Mapping the landscape of fibrosis.

Organ fibrosis causes major morbidity and mortality worldwide. Treatments for fibrosis are limited, with organ transplantation being the only cure. Here, we review how various state-of-the-art spatial genomics approaches are being deployed to interrogate fibrosis across multiple organs, providing exciting insights into fibrotic disease pathogenesis. These include the detailed topographical annotation of pathogenic cell populations and states, detection of transcriptomic perturbations in morphologically normal tissue, characterization of fibrotic and homeostatic niches and their cellular constituents, and in situ interrogation of ligand-receptor interactions within these microenvironments. Together, these powerful readouts enable detailed analysis of fibrosis evolution across time and space.

Humans↗

PubMed1994

Genetic polymorphisms in subterranean mammals (Spalax ehrenbergi superspecies) in the near east revisited: patterns and theory.

Allozyme diversity in the superspecies Spalax ehrenbergi has been revisited by studying 36 gene loci in 241 subterranean mole rats from 22 populations and nine chromosomal species, four from Turkey (2n = 52E (east), 52W (west), 56 and 58), four from Israel (2n = 52, 54, 58 and 60), and one from Egypt (2n = 60). The following results were indicated. (1) Genetic patterns: 11 of the 36 loci analysed (30.5 per cent) were monomorphic across the range, fifteen (41.7 per cent) were weakly polymorphic and the remaining 10 loci (27.8 per cent) were strongly polymorphic. (2) Heterozygosity: the average H was 0.051, range 0.00-0.098. In Israel, H increased with aridity and climatic unpredictability towards the northern Negev Desert, and was remarkably high in small steppic semi-isolates and desert isolates. (3) Species discrimination: some of the S. ehrenbergi species can be discriminated qualitatively. (4) Genetic distances (D): between species these values averaged 0.077, range 0.001-0.269, with the highest D between the ancestor Turkish and descendant Israeli and Egyptian species. The phylogenetic tree supports the Turkish origin of the Israeli Spalax ehrenbergi species, and the recent speciation of the Egyptian Spalax. (5) Genetic diversity is mostly (58 per cent) within populations. (6) Allozyme correlates: allozyme diversity was significantly correlated with the external physical (both climatic and edaphic) and biotic (parasite infection and plant cover) environment. (7) Spatial autocorrelation of allozyme frequencies suggests that migration is not influential. (8) Gametic phase disequilibria were significant in four out of five species tested, and were associated with climatic and edaphic factors. These results support the environmental selection hypothesis of genetic diversity including the niche-width variation hypothesis in space and time. Natural selection appears to play a major role in genetic differentiation of proteins in adaptive radiation and speciation.

Animals↗

PubMed2006

Bacterial metapopulations in nanofabricated landscapes.

We have constructed a linear array of coupled, microscale patches of habitat. When bacteria are inoculated into this habitat landscape, a metapopulation emerges. Local bacterial populations in each patch coexist and weakly couple with neighbor populations in nearby patches. These spatially distributed bacterial populations interact through local extinction and colonization processes. We have further built heterogeneous habitat landscapes to study the adaptive dynamics of the bacterial metapopulations. By patterning habitat differences across the landscape, our device physically implements an adaptive landscape. In landscapes with higher niche diversity, we observe rapid adaptation to large-scale, low-quality (high-stress) areas. Our results illustrate the potential lying at the interface between nanoscale biophysics and landscape evolutionary ecology.

Adaptation, Biological↗

PubMed2005

The Drosophila lymph gland as a developmental model of hematopoiesis.

Drosophila hematopoiesis occurs in a specialized organ called the lymph gland. In this systematic analysis of lymph gland structure and gene expression, we define the developmental steps in the maturation of blood cells (hemocytes) from their precursors. In particular, distinct zones of hemocyte maturation, signaling and proliferation in the lymph gland during hematopoietic progression are described. Different stages of hemocyte development have been classified according to marker expression and placed within developmental niches: a medullary zone for quiescent prohemocytes, a cortical zone for maturing hemocytes and a zone called the posterior signaling center for specialized signaling hemocytes. This establishes a framework for the identification of Drosophila blood cells, at various stages of maturation, and provides a genetic basis for spatial and temporal events that govern hemocyte development. The cellular events identified in this analysis further establish Drosophila as a model system for hematopoiesis.

Animals↗

PubMed2026

A conserved grain-associated immunosuppressive niche in Sudanese patients with mycetoma.

Mycetoma is a neglected tropical disease caused by various bacterial and fungal pathogens that has a significant health impact across a broad geographically defined "mycetoma belt" spanning South America, Africa and Asia. Histologically, mycetoma is characterised by invasive and destructive granuloma development in the skin, deep tissues and bone, leading to tissue destruction, deformities and high morbidity. The presence of macroscopic, highly compacted pathogen microcolonies, or "grains," is a key diagnostic feature, and the formation of grains supports pathogen persistence and disease chronicity. However, there is a paucity of information on immune responses in mycetoma patients and on the relative importance of phylogeny and/or grains in establishing the local immune landscape. Here, we used spatial proteomics to examine the distribution of 43 immune-related proteins in surgical biopsies from 11 patients with mycetoma of bacterial (actinomycetoma; Actinomadura pelletierii and Streptomyces somaliensis; n = 6) and fungal (eumycetoma; Madurella mycetomatis; n = 5) origin. Using mixed-effects modelling, an exploratory analysis across species and pathogen classes revealed few significant differences in immune marker expression. In contrast, and independently of pathogen class, the cellular infiltrate closest to grain boundaries had higher per-cell expression of CD66b+ neutrophils, ARG1, and VISTA. The preferential accumulation of CD66b+ARG1+VISTA+ cells at grain boundaries was confirmed by quantitative immunofluorescence analysis. Hence, the local tissue microenvironment surrounding the mycetoma grain represents a specialised immunosuppressive niche, with parallels to the tumour microenvironment. Trial Registration The study was prospectively registered on ClinicalTrials.gov NCT04401969.

Adult↗

PubMed1987

Contrasting patterns of geographic variation in the cosmopolitan sibling species Drosophila melanogaster and Drosophila simulans.

An electrophoretic study was carried out to compare the geographic pattern of genetic variation in Drosophila simulans with that of its sibling species, Drosophila melanogaster. An identical set of 32 gene-protein loci was studied in four geographically distant populations of D. simulans and two populations of D. melanogaster, all originating from Europe and Africa. The comparison yielded the following results: tropical populations of D. simulans were, in terms of the number of unique alleles, average heterozygosity per locus, and percentage of loci polymorphic, more variable than conspecific-temperate populations; some loci in both species showed interpopulation differences in allele frequencies that suggest latitudinal clines; and temperate-tropical genetic differentiation between populations was much less in D. simulans than in D. melanogaster. Similar differences between these two species have previously been shown for chromosomal, quantitative, physiological, and middle-repetitive DNA variation. Estimates of Nm (number of migrants per generation) from the spatial distribution of rare alleles suggest that both species have similar levels of interpopulation gene flow. These observations lead us to propose two competing hypotheses: the low level of geographic differentiation in D. simulans is due to its evolutionarily recent worldwide colonization and, alternatively, D. simulans has a narrower niche than D. melanogaster. Geographic variation data on different genetic elements (e.g., mitochondrial DNA, two-dimensional proteins, etc.) are required before these hypotheses can be adequately tested.

Animals↗

PubMed2004

Ecology of prokaryotic viruses.

The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.

Bacteria↗

PubMed2006

A simulation model to assess herd-level intervention strategies against E. coli O157.

A simulation model of a herd of grazing cattle, which has been developed to provide insight into the infection dynamics of E. coli O157 is described. The spatially explicit model enables the modelling of the infection transmission processes to be realistically addressed under field management conditions. The model is used to explore the efficacy of various potential control strategies in reducing the levels of within-herd infection. These measures include restricting the size of herds, niche engineering, improving housing hygiene and vaccination. While a vaccination strategy remains a hypothetical option, it has the potential to be particularly effective. It is likely that the most successful strategy will involve the implementation of a combination of measures.

Animals↗