Distinct Spatial Configurations Research Articles

The evolution of spatial codes in informal urbanism: analysis of residential patterns in Palestinian-Israeli towns

ABSTRACT This research explores the impact of urbanization on familial spatial codes within informal settings and sheds light on their adaptation to contemporary processes. Through comparing residential patterns between traditionally clan-based neighbourhoods alongside urbanized mixed-familial ones in the Palestinian-Israeli town of Sakhnin, the study seeks to scrutinize the socio-economic and political influences on the conduct of traditional code-based systems. Employing GIS analysis, the study examines a two-decade development period of residential patterns in both types of neighbourhoods and uncovers distinct spatial configurations. However, comprehensive interviews with residents reveal that despite urbanization constraints, the familial code continues to guide bottom-up development.

Sonotope patterns within a mountain beech forest of Northern Italy: a methodological and empirical approach

According to the Sonotope Hypothesis, the heterogenous nature of the acoustically sensed, but not yet interpreted, environmental sounds (i.e., sonoscape) is created by the spatial and temporal conformation of sonic patches (sonotopes) as recently been described in a Mediterranean rural landscape. We investigated the Sonotope Hypothesis in a mountain beech forest of the Northern Apennines, Italy that is notoriously poor in soniferous species. Our aim was to test whether sonotopes were temporally distinct over seasonal and astronomical timeframes and spatially configured in relation to vegetation variables. We used the Acoustic Complexity Index (ACItf) to analyze the heterogeneity of sonic information gathered from an array of 11 sound recorders deployed within a lattice of eleven 4-ha hexagonal sample sites distributed throughout a 48-ha managed beech forest. We visualized and described the temporal patterns of ACItf between seasons (May–June and July–August 2021), across six astronomical periods (Night I, Morning Twilight, Morning, Afternoon, Evening Twilight, and Night II), and according to two aggregated frequency classes (≤2000 and >2000 Hz). We introduced Spectral Sonic Signature (SSS) calculated from the sequence of ACItf values along frequency bins as a descriptor of the dynamic production of sounds across spatial and temporal scales. We calculated Mean Spectral Dissimilarity to compare SSS values across temporal periods and between sample sites. We identified sonotopes by grouping similar SSS for each sample site generated from cluster analyses and visualized their spatial arrangements. Frequencies ≤2000 Hz (mainly geophonies from wind and rain) were more prevalent than frequencies >2000 Hz (mainly biophonies from songbirds). Despite there being no strong relationship to vegetation variables and minimal biophony and anthropophony, distinct sonotopes still emerged for every astronomical and seasonal period. This suggests that the sonoscape expresses distinct spatial and temporal sonotope configurations associated with the temporal and spatial patterns of geophysical events that generate geophonies with minimal animal or anthropogenic occurrences. A new strategy based on the reintroduction of indigenous trees and shrubs in managed clearings should be considered for enhancing local biodiversity conservation along with ecoacoustic monitoring based on the Sonotope Hypothesis.

Developing a 15-minute city: A comparative study of four Italian Cities-Cagliari, Perugia, Pisa, and Trieste

The pandemic and the environmental crisis raise the question of a radical transformation of cities to foster inclusion, sustainability, participation, and quality of life. The 15-minute city concept prefigures a reorganization of urban spaces, structures, and functions aimed at increasing residents’ access to essential services, favoring sustainable modes of transportation, and transforming public urban spaces into multifunctional places. The proposed study develops a set of indicators derived from the spatial and configurational analysis to evaluate the compliance of urban systems with the 15-minute city concept. The selected areas of study are the cities of Cagliari, Perugia, Pisa, and Trieste, in Italy. The study investigates four issues: i) defining a set of relevant, reproducible, and comparable indicators for measuring density, proximity, and diversity; ii) investigating the influence of distinct urban planning concepts, manifested by distinct spatial configurations, on density, proximity, and diversity; iii) defining urban scale metrics to measure levels of spatial injustice in terms of unequal conditions of access to essential services and iv) measuring the correlation between configurational factors and access to services. The analysis underlines the gap in access to essential services among central compact districts and dispersed outer areas, thus enabling the identification of inequalities in the distribution of spatial capital. Moreover, the study underlines the relationship between the urban environment structure and the location of functions. As a result, the study emphasizes that the proposed set of indicators is instrumental to understanding the urban environment's potential to meet urban populations' needs and facilitating informed decisions in urban planning.

Networks, space and belonging: the Marwaris in Manipur

ABSTRACT This article aims to supplement existing economic analyses of the Marwari mercantile network by exploring how the network is both grounded spatially and reproduced culturally in Manipur. It discusses some of the economic and socio-cultural practices adopted by the Marwari merchants in Manipur including their business activities, marriage patterns and temple construction. In so doing, it highlights the nature of relationships between these practices and how they are connected to their mercantile network at large. The article also illustrates how merchant communities such as the Marwaris carve out their own space through cultural processes of place-making in a contested place like Manipur. Elucidating how the Marwari mercantile network gets reproduced culturally, it reveals the ways in which networks of capital relate to distinct spatial configurations – in this case, borderland. In turn, the above process also delineates how the idea of belonging for the Marwari merchants is emplaced and shaped at the same time by their mercantile network. Based primarily on interviews, observation and some documents, the materials used in this article stem mainly from Imphal and some from Churachandpur.

Chemical topology molecular engineering of CO2-philic membranes toward highly efficient carbon capture

Membrane gas separation processes represent a crucial platform for achieving carbon neutral climate goals. CO2-philic membranes offer excellent solubility selectivity due to their high affinity, thereby allowing the separation of gas fractions with similar molecular sizes or smaller than CO2 molecules. This level of separation is difficult to achieve with conventional diffusion-dominated separation membranes. However, the gas permeability of PEO membranes is often hampered by dense chain packing and crystallization behavior. To overcome this challenge, we employed a molecular engineering approach to develop a unique PEO membrane with a hyperbranched chemical topology connection. The packing density of the polymer chains was effectively regulated by employing cross-linker molecules with distinct spatial configurations, while the free volume fraction was successfully reinforced. This unique molecular engineering strategy led to the creation of a PEO membrane exhibiting superior performance that surpassed the limit of the 2019 upper-bound line. This work demonstrated a molecular design strategy for the precise control of structural attributes in crosslinked PEO networks, offering an alternative solution for developing CO2 capture membranes and enabling further opportunities for rational membrane material design.

Local Commitment and Global Reach: Advancing Sustainable Capacity Building in Higher Education

Universities play a crucial role in building the economic development capacity for their communities and regions. Their capacity building role is typically defined by contributions to the economic bottom line of the community and region where a university is located. This kind of capacity building may find itself in conflict with the long-term sustainable development needs of the region and with the responsibility of the university itself. Sustainable capacity building may require strategies that focus on the specific social, cultural, environmental, and physical context of a university’s location beyond purely economic capacity goals. To achieve sustainable development outcomes, universities must advance an understanding of the context conditions within which they are located. At least three context systems are relevant to this view of development: the economy, society and culture, and the environment with its physical, biological, and ecological context conditions. Each of these context systems is characterized by distinct time frames, spatial configurations, rules, and success measures. A focus on economic development outcomes reflects only one subsystem’s rules, behaviors, and success measures. By analyzing two case study examples from the United States and South Africa, we offer a framework for universities to advance sustainability objectives that correspond to their broader responsibilities. We argue that in order to meet these broader responsibilities, universities must first commit to giving expression to their own local context through the voices and lived realities of students and residents. Since universities build the brain trust of communities and regions around the world, they play an essential role in strengthening global sustainability goals by building the local capacity of their communities and regions.

Spatial Organization and Prognostic Significance of NK and NKT-like Cells via Multimarker Analysis of the Colorectal Cancer Microenvironment.

Although tumor-infiltrating T cells hold a beneficial prognostic role in colorectal cancer, other lymphocytic populations are less characterized. We developed a multiplexed immunofluorescence assay coupled with digital image analysis and machine learning to identify natural killer (NK) cells (NCAM1+CD3-), natural killer T-like (NKT-like) cells (NCAM1+CD3+), and T cells (NCAM1-CD3+) within the PTPRC+ (CD45+) cell population and to measure their granzyme B (GZMB; cytotoxicity marker) and FCGR3A (CD16a; NK-cell maturity marker) expression. We evaluated immune cell densities and spatial configuration in 907 incident colorectal carcinoma cases within two prospective cohort studies. We found that T cells were approximately 100 times more abundant than NK and NKT-like cells. Overall, NK cells showed high GZMB expression and were located closer to tumor cells than T and NKT-like cells. In T and NKT-like cells, GZMB expression was enriched in cells in closer proximity to tumor cells. Higher densities of both T and NKT-like cells associated with longer cancer-specific survival, independent of potential confounders (P trend < 0.0007). Higher stromal GZMB+ and FCGR3A+ NK-cell densities associated with longer cancer-specific survival (P trend < 0.003). For T and NKT-like cells, greater proximity to tumor cells associated with longer cancer-specific survival (P trend < 0.0001). These findings indicate that cytotoxic NCAM1+CD3-GZMB+ NK cells and NCAM1+CD3+ NKT-like cells are relatively rare lymphocytic populations within the colorectal cancer microenvironment and show distinct spatial configuration and associations with patient outcome. The results highlight the utility of a quantitative multimarker assay for in situ, single-cell immune biomarker evaluation and underscore the importance of spatial context for tumor microenvironment characterization.

In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence

SummaryTumors are dynamic ecosystems comprising localized niches (microdomains), possessing distinct compositions and spatial configurations of cancer and non-cancer cell populations. Microdomain-specific network signaling coevolves with a continuum of cell states and functional plasticity associated with disease progression and therapeutic responses. We present LEAPH, an unsupervised machine learning algorithm for identifying cell phenotypes, which applies recursive steps of probabilistic clustering and spatial regularization to derive functional phenotypes (FPs) along a continuum. Combining LEAPH with pointwise mutual information and network biology analyses enables the discovery of outcome-associated microdomains visualized as distinct spatial configurations of heterogeneous FPs. Utilization of an immunofluorescence-based (51 biomarkers) image dataset of colorectal carcinoma primary tumors (n = 213) revealed microdomain-specific network dysregulation supporting cancer stem cell maintenance and immunosuppression that associated selectively with the recurrence phenotype. LEAPH enables an explainable artificial intelligence platform providing insights into pathophysiological mechanisms and novel drug targets to inform personalized therapeutic strategies.

Rheology of capsule suspensions in plane Poiseuille flows

The rheology of a capsule suspension in two-dimensional confined Poiseuille flow is studied numerically using an immersed-boundary lattice Boltzmann method. The effects of capsule volume fraction ϕ and bending stiffness Eb on the rheology of the suspension are investigated first. The apparent viscosity does not monotonically increase with ϕ: the variation curve can be divided into four flow regimes. In each regime, there is a distinct equilibrium spatial configuration. The overall lateral position of the capsules is directly connected with the apparent viscosity. Then, we propose to investigate the effect of inertia on the capsule configuration in dilute cases and the capsule transport in concentrated cases. For dilute cases, phase diagrams of flow regimes on the (ϕ, Eb) plane are plotted. It is found that, as the Reynolds number (Re) increases, the range of values for regime I, with a single-line configuration, reduces, while the range for regime II (transition configuration) increases. It is highly correlated with the equilibrium lateral position of a single capsule. For even larger Re, the range for regime IV (random configuration) increases rapidly and dominates because the larger inertia makes the arrangement more random. For concentrated cases, we observe that the optimal volume fraction, at which the transport of capsules is a maximum, increases with Re. This study may help to understand the collective behavior of capsules in Poiseuille flows.

A simple method for determination of fine resolution urban form patterns with distinct thermal properties using class-level landscape metrics

ContextRelationships between land surface temperature (LST) and spatial configuration of urban form described by landscape metrics so far have been investigated with coarse resolution LST imagery within artificially superimposed land divisions. Citywide micro-scale observations are needed to better inform urban design and help mitigate urban heat island effects in warming climates.ObjectivesThe primary objective was to sub-divide an existing high-resolution land cover (LC) map into groups of patches with distinct spatial and thermal properties suitable for urban LST studies relevant to micro-scales. The secondary objective was to provide insights into the optimal analytical unit size to calculate class-level landscape metrics strongly correlated with LST at 2 m spatial resolution.MethodsA two-tiered unsupervised k-means clustering analysis was deployed to derive spatially distinct groups of patches of each major LC class followed by further subdivisions into hottest, coldest and intermediary sub-classes, making use of high resolution class-level landscape metrics strongly correlated with LST.ResultsAggregation class-level landscape metrics were consistently correlated with LST for green and grey LC classes and the optimal search window size for their calculations was 100 m for LST at 2 m resolution. ANOVA indicated that all Tier 1 and most of Tier 2 subdivisions were thermally and spatially different.ConclusionsThe two-tiered k-means clustering approach was successful at depicting subdivisions of major LC classes with distinct spatial configuration and thermal properties, especially at a broader Tier 1 level. Further research into spatial configuration of LC patches with similar spatial but different thermal properties is required.

Deep learning derived tumor infiltration maps for personalized target definition in Glioblastoma radiotherapy

PurposeGlioblastoma is routinely treated by concomitant radiochemotherapy. Current target definition guidelines use anatomic MRI (magnetic resonance imaging) scans, taking into account contrast enhancement and the rather unspecific hyperintensity on the fluid-attenuated inversion recovery (FLAIR) sequence. Methods and materialsWe applied deep learning based free water correction of diffusion tensor imaging (DTI) scans to estimate the infiltrative gross tumor volume (iGTV) inside of the FLAIR hyperintense region. We analyzed the resulting iGTVs and their impact on target volume definition in a retrospective cohort of 33 GBM patients. ResultsiGTVs were significantly smaller compared to standard pre- and post-operative gross tumor volume (GTV) definitions. Two novel infiltrative tumor GTVs (nGTVPRE-OP and nGTVPOST-OP) defined as the conjunction volume of the standard GTV and the iGTV showed only a moderate increase in size compared to standard GTV definitions. On postoperative scans, the iGTV was predominantly covered by the two clinical target volume (CTV) concepts CTVEORTC and CTVROTG1. A novel infiltrative tumor CTV (nCTV) [nGTVPOST-OP + 2 cm margin] was significantly smaller compared to CTVROTG1 but larger than CTVEORTC. The overlap volume and conformity index demonstrated a distinct spatial configuration of the nCTV. Tumor recurrences overlapped with the iGTV in all but one patients and were completely covered by the nCTV in all patients. After reducing the margin to 1 cm recurrences coverage was at least in-field in all patients. ConclusionTo conclude, free water corrected DTI scans may help to define infiltrative tumor areas of GBM that could ultimately be used to individualize RT treatment planning in terms of dose sparing or dose escalation.

A Gold‐Nanoparticle‐Based SERS Reporter that Rolls on DNA Origami Templates

AbstractPlasmonic nanostructures with distinct spatial configuration and geometry are of considerable significance because of their desired optical response. These optical responses have close relationship with the inter‐particle parameters in plasmonic nanostructures. However, the precise control of the consecutive variation of these parameters remains a formidable challenge. Here, we demonstrate a gold nanoparticle (AuNP) ‐based plasmonic nano‐reporter, in which a AuNP performs as a walker to stepwise roll directionally and progressively on DNA origami. Using another AuNP as a stator, the rolling of the AuNP reporter could generate the inter‐particle distance variation, which would be monitored by surface‐enhanced Raman scattering (SERS). Our method opens up a door to develop an optical reporter that monitors inter‐particle variations in plasmonic nanostructures.

Using space syntax and Q-analysis for investigating movement patterns in buildings: The case of shopping malls

In this study, we present the potential of the conjunction between space syntax and Q-analysis methodologies for investigating patterns of movement flows in buildings. This potential is illustrated by an implementation of the two methodologies by comparing between two shopping malls in Israel, which are characterized by distinct spatial configurations. Q-analysis was used to identify the spread of individuals’ movement paths and their conjunction into movement areas, while space syntax enabled to examine how these aspects of movement flow are affected by the malls’ spatial configuration. The results indicate that high spatial integration and intelligibility levels not only promote intensive movement in accessible and central areas (as found in previous studies) but also the spread of movement paths and their formation to integrated circulation systems. The combined implementation of space syntax and Q-analysis improves our understanding about the role of building’ spatial configuration in shaping movement flows. We discuss the potential of this implementation for monitoring and improving movement flow and usability of spaces in buildings.

Daily States of the March–April East Pacific ITCZ in Three Decades of High-Resolution Satellite Data

Abstract Zonally elongated areas of cloudiness that make up the east Pacific intertropical convergence zone (ITCZ) can take on several configurations in instantaneous observations. A novel statistical model is used to automatically assess the daily state of the east Pacific ITCZ using infrared satellite images from 1980 to 2012. Four ITCZ states are defined based on ITCZ location relative to the equator: north (nITCZ) and south (sITCZ) of the equator, simultaneously north and south of the equator (dITCZ, for double ITCZ), and over the equator (eITCZ). A fifth ITCZ state is used to classify days when no zonally elongated area of cloudiness is present (aITCZ, for absent ITCZ). The ITCZ states can occur throughout the year (except for the eITCZ, which is not present during June–October), with the nITCZ state dominating in terms of frequency of occurrence. Interannual variability of the state distribution is large. The most striking variability in ITCZ states is observed in spring. During March–April, the dITCZ state occurs on average 34% of the time, second only to the nITCZ state (39%). Composites of observed infrared temperature and precipitation by ITCZ state reveal distinct spatial configurations of cloudiness and rainfall. Strong sea surface temperature anomalies are associated only with eITCZ and sITCZ and they correspond to El Niño and La Niña, respectively. However, all five ITCZ states are associated with distinct atmospheric circulation patterns. A connection is found between the ITCZ and the South Pacific convergence zone (SPCZ), such that activity in the SPCZ is enhanced when the ITCZ is absent in the east Pacific.

A spectral–structural bag-of-features scene classifier for very high spatial resolution remote sensing imagery

Land-use classification of very high spatial resolution remote sensing (VHSR) imagery is one of the most challenging tasks in the field of remote sensing image processing. However, the land-use classification is hard to be addressed by the land-cover classification techniques, due to the complexity of the land-use scenes. Scene classification is considered to be one of the expected ways to address the land-use classification issue. The commonly used scene classification methods of VHSR imagery are all derived from the computer vision community that mainly deal with terrestrial image recognition. Differing from terrestrial images, VHSR images are taken by looking down with airborne and spaceborne sensors, which leads to the distinct light conditions and spatial configuration of land cover in VHSR imagery. Considering the distinct characteristics, two questions should be answered: (1) Which type or combination of information is suitable for the VHSR imagery scene classification? (2) Which scene classification algorithm is best for VHSR imagery? In this paper, an efficient spectral–structural bag-of-features scene classifier (SSBFC) is proposed to combine the spectral and structural information of VHSR imagery. SSBFC utilizes the first- and second-order statistics (the mean and standard deviation values, MeanStd) as the statistical spectral descriptor for the spectral information of the VHSR imagery, and uses dense scale-invariant feature transform (SIFT) as the structural feature descriptor. From the experimental results, the spectral information works better than the structural information, while the combination of the spectral and structural information is better than any single type of information. Taking the characteristic of the spatial configuration into consideration, SSBFC uses the whole image scene as the scope of the pooling operator, instead of the scope generated by a spatial pyramid (SP) commonly used in terrestrial image classification. The experimental results show that the whole image as the scope of the pooling operator performs better than the scope generated by SP. In addition, SSBFC codes and pools the spectral and structural features separately to avoid mutual interruption between the spectral and structural features. The coding vectors of spectral and structural features are then concatenated into a final coding vector. Finally, SSBFC classifies the final coding vector by support vector machine (SVM) with a histogram intersection kernel (HIK). Compared with the latest scene classification methods, the experimental results with three VHSR datasets demonstrate that the proposed SSBFC performs better than the other classification methods for VHSR image scenes.

Towards a Spatial Understanding of Trade-Offs in Sustainable Development: A Meso-Scale Analysis of the Nexus between Land Use, Poverty, and Environment in the Lao PDR.

In land systems, equitably managing trade-offs between planetary boundaries and human development needs represents a grand challenge in sustainability oriented initiatives. Informing such initiatives requires knowledge about the nexus between land use, poverty, and environment. This paper presents results from Lao PDR, where we combined nationwide spatial data on land use types and the environmental state of landscapes with village-level poverty indicators. Our analysis reveals two general but contrasting trends. First, landscapes with paddy or permanent agriculture allow a greater number of people to live in less poverty but come at the price of a decrease in natural vegetation cover. Second, people practising extensive swidden agriculture and living in intact environments are often better off than people in degraded paddy or permanent agriculture. As poverty rates within different landscape types vary more than between landscape types, we cannot stipulate a land use–poverty–environment nexus. However, the distinct spatial patterns or configurations of these rates point to other important factors at play. Drawing on ethnicity as a proximate factor for endogenous development potentials and accessibility as a proximate factor for external influences, we further explore these linkages. Ethnicity is strongly related to poverty in all land use types almost independently of accessibility, implying that social distance outweighs geographic or physical distance. In turn, accessibility, almost a precondition for poverty alleviation, is mainly beneficial to ethnic majority groups and people living in paddy or permanent agriculture. These groups are able to translate improved accessibility into poverty alleviation. Our results show that the concurrence of external influences with local—highly contextual—development potentials is key to shaping outcomes of the land use–poverty–environment nexus. By addressing such leverage points, these findings help guide more effective development interventions. At the same time, they point to the need in land change science to better integrate the understanding of place-based land indicators with process-based drivers of land use change.

A historic neighbourhood as arts space: the little india experience

Many cities around the world are redeveloping their neighbourhoods as arts and cultural precincts. Urban industrial zones and lower‐income residential areas have taken on new life as arts neighbourhoods in a bid to attract high‐yield visitors, propel their creative industry and brand themselves as attractive to investors and residents. This article has two aims. Conceptually it explores the notion of arts urbanization – the creation of arts spaces in cities and the socio‐spatial dynamics which they embody. Empirically, the concept is tested using the case of Singapore's Arts Housing Scheme. Under this scheme, historic ethnic precincts take on new roles as arts and creative belts. While the scheme has yielded some success by way of fostering spaces of identity and inspiration for artists, it has also generated social concerns and spatial challenges. Singapore's Little India offers an empirical setting to explore this concept. The paper argues that geography matters to the arts and that arts‐led urbanization creates distinct spatial configurations in cities. For this reason, a greater understanding of and research into arts neighbourhoods and their socio‐spatial dynamics are essential if we are to aspire to sustainable and sensitive development of cities and their creative communities.

Biological Invasions in Heterogeneous Environments: The Coupled Map Lattice Framework

Spatial heterogeneity greatly affects the population spread. Although the theory for biological invasion in heterogeneous spatially continuous habitats have received considerable attention, spatially discrete models have remained outside of the mainstream. In this study, we formulate and analyze a Coupled Map Lattice model for a single species population invading a two dimensional heterogeneous environment. The population growth rate and dispersal coefficient depend on the site quality. We first find an analytical criterium for the spread success in terms of the population growth rate and the dispersal coefficient in unfavorable regions. We then implemented our model for two distinct spatial configurations: periodical stripe-like and randomized environments. The spread rate is computed numerically and it shows a decrease with an increase of the fraction of the hostile sites. However, we observed that invasion success does not depend on the fraction of favorable sites but crucially depends on the connectivity of favorable regions.

Species-area relationships in coral communities: evaluating mechanisms for a commonly observed pattern

Landscape-scale attributes of patch size, spatial isolation, and topographic complexity are known to influence diversity and abundance in terrestrial and marine systems, but remain collectively untested for reef-building corals. To investigate the relationship between the coral assemblage and seascape variation in reef habitats, we took advantage of the distinct boundaries, spatial configurations, and topographic complexities among artificial reef patches to overcome the difficulties of manipulating natural reefs. Reef size (m2) was found to be the foremost predictor of coral richness in accordance with species-area relationship predictions. Larger reefs were also found to support significantly higher colony densities, enabling us to reject the null hypothesis of random placement (a sampling artifact) in favor of target area predictions that suggest greater rates of immigration on larger reefs. Unlike the pattern previously documented for reef fishes, topographic complexity was not a significant predictor of any coral assemblage response variable, despite the range of complexity values sampled. Lastly, coral colony density was best explained by both increasing reef size and decreasing reef spatial isolation, a pattern found exclusively among brooding species with shorter larval dispersal distances. We conclude that seascape attributes of reef size and spatial configuration within the seascape can influence the species richness and abundance of the coral community at relatively small spatial scales (<1 km). Specifically, we demonstrate how patterns in the coral communities that have naturally established on these manipulated reefs agree with the target area and island biogeography mechanisms to drive species-area relationships in reef-building corals. Based on the patterns documented in artificial reefs, habitat degradation that results in smaller, more isolated natural reefs may compromise coral diversity.

Completing the set of h/ E(spl) cyclic genes in zebrafish: her12 and her15 reveal novel modes of expression and contribute to the segmentation clock

Somitogenesis is the key developmental process that lays down the framework for a metameric body in vertebrates. Somites are generated from the un-segmented presomitic mesoderm (PSM) by a pre-patterning process driven by a molecular oscillator termed the segmentation clock. The Delta–Notch intercellular signaling pathway and genes belonging to the hairy ( h) and Enhancer of split ( E(spl))-related ( h/E(spl)) family of transcriptional repressors are conserved components of this oscillator. A subset of these genes, called cyclic genes, is characterized by oscillating mRNA expression that sweeps anteriorly like a wave through the embryonic PSM. Periodic transcriptional repression by H/E(spl) proteins is thought to provide a critical part of a negative feedback loop in the oscillatory process, but it is an open question how many cyclic h/E(spl) genes are involved in the somitogenesis clock in any species, and what distinct roles they might play. From a genome-wide search for h/E(spl) genes in the zebrafish, we previously estimated a total of five cyclic members. Here we report that one of these, the m Hes5 homologue her15 actually exists as a very recently duplicated gene pair. We investigate the expression of this gene pair and analyse its regulation and activity in comparison to the paralogous her12 gene, and the other cyclic h/E(spl) genes in the zebrafish. The her15 gene pair and her12 display novel and distinct expression features, including a caudally restricted oscillatory domain and dynamic stripes of expression in the rostral PSM that occur at the future segmental borders. her15 expression stripes demarcate a unique two-segment interval in the rostral PSM. Mutant, morpholino, and inhibitor studies show that her12 and her15 expression in the PSM is regulated by Delta–Notch signaling in a complex manner, and is dependent on her7, but not her1 function. Morpholino-mediated her12 knockdown disrupts cyclic gene expression, indicating that it is a non-redundant core component of the segmentation clock. Over-expression of her12, her15 or her7 disrupts cyclic gene expression and somite border formation, and structure function analysis of Her7 indicates that DNA binding, but not Groucho-recruitment seems to be important in this process. Thus, the zebrafish has five functional cyclic h/E(spl) genes, which are expressed in a distinct spatial configuration. We propose that this creates a segmentation oscillator that varies in biochemical composition depending on position in the PSM.