Genome-scale investigation of olfactory system spatial heterogeneity.
Ontology highlight
ABSTRACT:
SUBMITTER: Noto T
PROVIDER: S-EPMC5443560 | biostudies-literature | 2017
REPOSITORIES: biostudies-literature
Publications
Genome-scale investigation of olfactory system spatial heterogeneity.
Noto Torben T Barnagian Derrick D Castro Jason B JB
PloS one 20170524 5
The early olfactory system is organized in parallel, with numerous, specialized subsystems established by the modular and topographic projections of sensory inputs. While these anatomical sub-systems are in many cases demarcated by well-known marker genes, we stand to learn considerably more about their possible functional specializations from comprehensive, genome-scale descriptions of their molecular anatomy. Here, we leverage the resources of the Allen Brain Atlas (ABA)-a spatially registered ...[more]
Similar Datasets
Project description:BACKGROUND: Methylotrophic microorganisms are playing a key role in biogeochemical processes - especially the global carbon cycle - and have gained interest for biotechnological purposes. Significant progress was made in the recent years in the biochemistry, genetics, genomics, and physiology of methylotrophic bacteria, showing that methylotrophy is much more widespread and versatile than initially assumed. Despite such progress, system-level description of the methylotrophic metabolism is currently lacking, and much remains to understand regarding the network-scale organization and properties of methylotrophy, and how the methylotrophic capacity emerges from this organization, especially in facultative organisms. RESULTS: In this work, we report on the integrated, system-level investigation of the metabolic network of the facultative methylotroph Methylobacterium extorquens AM1, a valuable model of methylotrophic bacteria. The genome-scale metabolic network of the bacterium was reconstructed and contains 1139 reactions and 977 metabolites. The sub-network operating upon methylotrophic growth was identified from both in silico and experimental investigations, and 13C-fluxomics was applied to measure the distribution of metabolic fluxes under such conditions. The core metabolism has a highly unusual topology, in which the unique enzymes that catalyse the key steps of C1 assimilation are tightly connected by several, large metabolic cycles (serine cycle, ethylmalonyl-CoA pathway, TCA cycle, anaplerotic processes). The entire set of reactions must operate as a unique process to achieve C1 assimilation, but was shown to be structurally fragile based on network analysis. This observation suggests that in nature a strong pressure of selection must exist to maintain the methylotrophic capability. Nevertheless, substantial substrate cycling could be measured within C2/C3/C4 inter-conversions, indicating that the metabolic network is highly versatile around a flexible backbone of central reactions that allows rapid switching to multi-carbon sources. CONCLUSIONS: This work emphasizes that the metabolism of M. extorquens AM1 is adapted to its lifestyle not only in terms of enzymatic equipment, but also in terms of network-level structure and regulation. It suggests that the metabolism of the bacterium has evolved both structurally and functionally to an efficient but transitory utilization of methanol. Besides, this work provides a basis for metabolic engineering to convert methanol into value-added products.
| S-EPMC3227643 | biostudies-literature
Project description:The mammalian olfactory system is able to discriminate among tens of thousands of odorant molecules. In mice, each odorant is sensed by a small subset of the approximately 1000 odorant receptor (OR) types, with one OR gene expressed by each olfactory sensory neuron (OSN). However, the sum of the large repertoire of OR-OSN types and difficulties with heterologous expression have made it almost impossible to analyze odorant-responsiveness across all OR-OSN types. We have developed a microfluidic approach that allowed us to screen over 20,000 single cells at once in microwells. By using calcium imaging, we were able to detect and analyze odorant responses of about 2900 OSNs simultaneously. Importantly, this technique allows for both the detection of rare responding OSNs as well as the identification of OSN populations broadly responsive to odorants of unrelated structures. This technique is generally applicable for screening large numbers of single cells and should help to characterize rare cell behaviors in fields such as toxicology, pharmacology, and cancer research.
| S-EPMC3135426 | biostudies-literature
Project description:Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults [1]. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility [2, 3]. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium [4, 5], collectively moving metachronal waves [6-10], and more generally the hydrodynamics of active matter [11, 12]. However, the connection between local cilia architecture and the topology of the flows they generate remains largely unexplored. Here, we image the mouse airway from the sub-cellular (nm) to the organ scales (mm), characterising quantitatively its ciliary arrangement and the generated flows. Locally we measure heterogeneity in both cilia organisation and flow structure, but across the trachea fluid transport is coherent. To examine this result, a hydrodynamic model was developed for a systematic exploration of different tissue architectures. Surprisingly, we find that disorder enhances particle clearance, whether it originates from fluctuations, heterogeneity in multiciliated cell arrangement or ciliary misalignment. This resembles elements of 'stochastic resonance' [13-15], in the sense that noise can improve the function of the system. Taken together, our results shed light on how the microstructure of an active carpet [16, 17] determines its emergent dynamics. Furthermore, this work is also directly applicable to human airway pathologies [1], which are the third leading cause of deaths worldwide [18].
| S-EPMC9355487 | biostudies-literature
Project description:Several general principles of global 3D genome organization have recently been established, including non-random positioning of chromosomes and genes in the cell nucleus, distinct chromatin compartments, and topologically associating domains (TADs). However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are still poorly characterized. Here, we systematically probe heterogeneity in genome organization. High-throughput optical mapping of several hundred intra-chromosomal interactions in individual human fibroblasts demonstrates low association frequencies, which are determined by genomic distance, higher-order chromatin architecture, and chromatin environment. The structure of TADs is variable between individual cells, and inter-TAD associations are common. Furthermore, single-cell analysis reveals independent behavior of individual alleles in single nuclei. Our observations reveal extensive variability and heterogeneity in genome organization at the level of individual alleles and demonstrate the coexistence of a broad spectrum of genome configurations in a cell population.
| S-EPMC6408223 | biostudies-literature
Project description:Comparison of individual gene trees in several recent phylogenomic studies from diverse lineages has revealed a surprising amount of topological conflict or incongruence, but we still know relatively little about its distribution across the tree of life. To further our understanding of incongruence, the factors that contribute to it and how it can be ameliorated, we examined its distribution in a clade of 20 Culicidae mosquito species through the reconstruction and analysis of the phylogenetic histories of 2,007 groups of orthologous genes. Levels of incongruence were generally low, the three exceptions being the internodes concerned with the branching of Anopheles christyi, with the branching of the subgenus Anopheles as well as the already reported incongruence within the Anopheles gambiae species complex. Two of these incongruence events (A. gambiae species complex and A. christyi) are likely due to biological factors, whereas the third (subgenus Anopheles) is likely due to analytical factors. Similar to previous studies, the use of genes or internodes with high bootstrap support or internode certainty values, both of which were positively correlated with gene alignment length, substantially reduced the observed incongruence. However, the clade support values of the internodes concerned with the branching of the subgenus Anopheles as well as within the A. gambiae species complex remained very low. Based on these results, we infer that the prevalence of incongruence in Culicidae mosquitoes is generally low, that it likely stems from both analytical and biological factors, and that it can be ameliorated through the selection of genes with strong phylogenetic signal. More generally, selection of genes with strong phylogenetic signal may be a general empirical solution for reducing incongruence and increasing the robustness of inference in phylogenomic studies.
| S-EPMC4700963 | biostudies-literature
Project description:The understanding of microbial compositions in different dimensions is essential to achieve the successful design and operation of the partial nitritation/anammox (PN/A) process. This study investigated the microbial communities of different sludge morphologies and spatial distribution in the one-stage PN/A process of treating real coal to ethylene glycol (CtEG) wastewater at a pilot-scale integrated fixed-film activated sludge (IFAS) reactor. The results showed that ammonia-oxidizing bacteria (AOB) was mainly distributed in flocs (13.56 ± 3.16%), whereas anammox bacteria (AnAOB) was dominated in the biofilms (17.88 ± 8.05%). Furthermore, the dominant AnAOB genus in biofilms among the first three chambers was Candidatus Brocadia (6.46 ± 2.14% to 11.82 ± 6.33%), whereas it was unexpectedly transformed to Candidatus Kuenenia (9.47 ± 1.70%) and Candidatus Anammoxoglobus (8.56 ± 4.69%) in the last chamber. This demonstrated that the niche differentiation resulting from morphological (dissolved oxygen) and spatial heterogeneity (gradient distribution of nutrients and toxins) was the main reason for dominant bacterial distribution. Overall, this study presents more comprehensive information on the heterogeneous distribution and transformation of communities in PN/A processes, providing a theoretical basis for targeted culture and selection of microbial communities in practical engineering.
| S-EPMC9201488 | biostudies-literature
Project description:IntroductionKnowledge of species richness patterns and their relation with climate is required to develop various forest management actions including habitat management, biodiversity and risk assessment, restoration and ecosystem modelling. In practice, the pattern of the data might not be spatially constant and cannot be well addressed by ordinary least square (OLS) regression. This study uses GWR to deal with spatial non-stationarity and to identify the spatial correlation between the plant richness distribution and the climate variables (i.e., the temperature and precipitation) in a 1° grid in different biogeographic zones of India.MethodologyWe utilized the species richness data collected using 0.04 ha nested quadrats in an Indian study. The data from this national study, titled 'Biodiversity Characterization at Landscape Level', were aggregated at the 1° grid level and adjudged for sampling sufficiency. The performances of OLS and GWR models were compared in terms of the coefficient of determination (R2) and the corrected Akaike Information Criterion (AICc).Results and discussionA comparative study of the R2 and AICc values of the models showed that all the GWR models performed better compared with the analogous OLS models. The climate variables were found to significantly influence the distribution of plant richness in India. The minimum precipitation (Pmin) consistently dominated individually (R2 = 0.69; AICc = 2608) and in combinations. Among the shared models, the one with a combination of Pmin and Tmin had the best model fits (R2 = 0.72 and AICc = 2619), and variation partitioning revealed that the influence of these parameters on the species richness distribution was dominant in the arid and the semi-arid zones and in the Deccan peninsula zone.ConclusionThe shift in climate variables and their power to explain the species richness of biogeographic zones suggests that the climate-diversity relationships of plants species vary spatially. In particular, the dominant influence of Tmin and Pmin could be closely linked to the climate tolerance hypothesis (CTH). We found that the climate variables had a significant influence in defining species richness patterns in India; however, various other environmental and non-environmental (edaphic, topographic and anthropogenic) variables need to be integrated in the models to understand climate-species richness relationships better at a finer scale.
| S-EPMC6586307 | biostudies-literature
Project description:Sympatric predators are predicted to partition resources, especially under conditions of food limitation. Spatial heterogeneity that influences prey availability might play an important role in the scales at which potential competitors select habitat. We assessed potential mechanisms for coexistence by examining the role of heterogeneity in resource partitioning between sympatric raptors overwintering in the southern Great Plains. We conducted surveys for wintering Red-tailed hawk (Buteo jamaicensis) and Northern Harrier (Circus cyanea) at two state wildlife management areas in Oklahoma, USA. We used information from repeated distance sampling to project use locations in a GIS. We applied resource selection functions to model habitat selection at three scales and analyzed for niche partitioning using the outlying mean index. Habitat selection of the two predators was mediated by spatial heterogeneity. The two predators demonstrated significant fine-scale discrimination in habitat selection in homogeneous landscapes, but were more sympatric in heterogeneous landscapes. Red-tailed hawk used a variety of cover types in heterogeneous landscapes but specialized on riparian forest in homogeneous landscapes. Northern Harrier specialized on upland grasslands in homogeneous landscapes but selected more cover types in heterogeneous landscapes. Our study supports the growing body of evidence that landscapes can affect animal behaviors. In the system we studied, larger patches of primary land cover types were associated with greater allopatry in habitat selection between two potentially competing predators. Heterogeneity within the scale of raptor home ranges was associated with greater sympatry in use and less specialization in land cover types selected.
| S-EPMC5574806 | biostudies-other
Project description:The building of large-scale Digital Elevation Models (DEMs) using various interpolation algorithms is one of the key issues in geographic information science. Different choices of interpolation algorithms may trigger significant differences in interpolation accuracy and computational efficiency, and a proper interpolation algorithm needs to be carefully used based on the specific characteristics of the scene of interpolation. In this paper, we comparatively investigate the performance of parallel Radial Basis Function (RBF)-based, Moving Least Square (MLS)-based, and Shepard's interpolation algorithms for building DEMs by evaluating the influence of terrain type, raw data density, and distribution patterns on the interpolation accuracy and computational efficiency. The drawn conclusions may help select a suitable interpolation algorithm in a specific scene to build large-scale DEMs.
| S-EPMC7924418 | biostudies-literature
Project description:Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.
| S-EPMC6276595 | biostudies-literature