Expression of the Hox gene complex in the indirect development of a sea urchin

Hox complex genes control spatial patterning mechanisms in the development of arthropod and vertebrate body plans. Hox genes are all expressed during embryogenesis in these groups, which are all directly developing organisms in that embryogenesis leads at once to formation of major elements of the respective adult body plans. In the maximally indirect development of a large variety of invertebrates, the process of embryogenesis leads only to a free-living, bilaterally organized feeding larva. Maximal indirect development is exemplified in sea urchins. The 5-fold radially symmetric adult body plan of the sea urchin is generated long after embryogenesis is complete, by a separate process occurring within imaginal tissues set aside in the larva. The single Hox gene complex of Strongylocentrotus purpuratus contains 10 genes, and expression of eight of these genes was measured by quantitative methods during both embryonic and larval developmental stages and also in adult tissues. Only two of these genes are used significantly during the entire process of embryogenesis per se, although all are copiously expressed during the stages when the adult body plan is forming in the imaginal rudiment. They are also all expressed in various combinations in adult tissues. Thus, development of a microscopic, free-living organism of bilaterian grade, the larva, does not appear to require expression of the Hox gene cluster as such, whereas development of the adult body plan does. These observations reflect on mechanisms by which bilaterian metazoans might have arisen in Precambrian evolution.

Multi-Scaled Grassland-Woody Plant Dynamics in the Heterogeneous Marl Prairies of the Southern Everglades

The Everglades freshwater marl prairie is a dynamic and spatially heterogeneous landscape, containing thousands of tree islands nested within a marsh matrix. Spatial processes underlie population and community dynamics across the mosaic, especially the balance between woody and graminoid components, and landscape patterns reflect interactions among multiple biotic and abiotic drivers. To better understand these complex, multi-scaled relationships we employed a three-tiered hierarchical design to investigate the effects of seed source, hydrology, and more indirectly fire on the establishment of new woody recruits in the marsh, and to assess current tree island patterning across the landscape. Our analyses were conducted at the ground level at two scales, which we term the micro- and meso-scapes, and results were related to remotely detected tree island distributions assessed in the broader landscape, that is, the macro-scape. Seed source and hydrologic effects on recruitment in the micro- and meso-scapes were analyzed via logistic regression, and spatial aggregation in the macro-scape was evaluated using a grid-based univariate O-ring function. Results varied among regions and scales but several general trends were observed. The patterning of adult populations was the strongest driver of recruitment in the micro- and meso-scape prairies, with recruits frequently aggregating around adults or tree islands. However in the macro-scape biologically associated (second order) aggregation was rare, suggesting that emergent woody patches are heavily controlled by underlying physical and environmental factors such as topography, hydrology, and fire.

The Monitoring and Assessment Plan (MAP) Greater Everglades Wetlands Module- Landscape Pattern- Ridge, Slough, and Tree Island Mosaics: Year 1 Annual Report

In the current managed Everglades system, the pre-drainage, patterned mosaic of sawgrass ridges, sloughs and tree islands has been substantially altered or reduced largely as a result of human alterations to historic ecological and hydrological processes that sustained landscape patterns. The pre-compartmentalization ridge and slough landscape was a mosaic of sloughs, elongated sawgrass ridges (50-200m wide), and tree islands. The ridges and sloughs and tree islands were elongated in the direction of the water flow, with roughly equal area of ridge and slough. Over the past decades, the ridge-slough topographic relief and spatial patterning have degraded in many areas of the Everglades. Nutrient enriched areas have become dominated by Typha with little topographic relief; areas of reduced flow have lost the elongated ridge-slough topography; and ponded areas with excessively long hydroperiods have experienced a decline in ridge prevalence and shape, and in the number of tree islands (Sklar et al. 2004, Ogden 2005).

Cell-cell communication in three dimensional microenvironments

Cellular behavior is dependent on a variety of extracellular cues required for normal tissue function, wound healing, and activation of the immune system. Removed from their in vivo microenvironment and cultured in vitro, cells lose many environmental cues and that may result in abberant behavior, making it difficult to study cellular processes. In order to mimic native tissue environments, optical tweezer and microfluidic technologies were used to place cells within defined areas of the culture environment. To provide three dimensional supports found in natural tissues, hydrogel scaffolds of poly (ethylene glycol) diacrylate and the basement membrane matrix Matrigel were used. Optical tweezer technology allowed precision placement and formation of homotypic and heterotypic arrays of human U937, HEK 293, and porcine mesenchymal stem cells. Alternatively, two microfluidic devices were designed to pattern Matrigel scaffolds. The first microfluidic device utilized laminar flow to spatially pattern multiple cell types within the device. Gradients of soluble molecules were then be formed and manipulated across the Matrigel scaffolds. Patterning Matrigel using laminar flow techniques require microfluidic expertise and do not produce consistent patterning conditions, limiting their use difficult in most cell culture laboratories. Thus, a buried Matrigel polydimethylsiloxane (PDMS) device was developed for spatial patterning of biological scaffolds. Matrigel is injected into micron sized channels of PDMS fabricated by soft lithography and allowed to thermally cure. Following curing, a second PDMS device was placed on top of the buried Matrigel channels to support media flow. In order to validate these systems, a cell-cell communication model system was developed utilizing LPS and TNFα signaling with fluorescent reporter systems to monitor communication in real time. We demonstrated the utility of microfluidic devices to support the cell-cell communication model system by co culturing three cell types within Matrigel scaffolds and monitoring signaling activity via fluorescent reporters.

Synthetic Circuits for Feedback and Detection in Bacteria

Synthetic biology, by co-opting molecular machinery from existing organisms, can be used as a tool for building new genetic systems from scratch, for understanding natural networks through perturbation, or for hybrid circuits that piggy-back on existing cellular infrastructure. Although the toolbox for genetic circuits has greatly expanded in recent years, it is still difficult to separate the circuit function from its specific molecular implementation. In this thesis, we discuss the function-driven design of two synthetic circuit modules, and use mathematical models to understand the fundamental limits of circuit topology versus operating regimes as determined by the specific molecular implementation. First, we describe a protein concentration tracker circuit that sets the concentration of an output protein relative to the concentration of a reference protein. The functionality of this circuit relies on a single negative feedback loop that is implemented via small programmable protein scaffold domains. We build a mass-action model to understand the relevant timescales of the tracking behavior and how the input/output ratios and circuit gain might be tuned with circuit components. Second, we design an event detector circuit with permanent genetic memory that can record order and timing between two chemical events. This circuit was implemented using bacteriophage integrases that recombine specific segments of DNA in response to chemical inputs. We simulate expected population-level outcomes using a stochastic Markov-chain model, and investigate how inferences on past events can be made from differences between single-cell and population-level responses. Additionally, we present some preliminary investigations on spatial patterning using the event detector circuit as well as the design of stationary phase promoters for growth-phase dependent activation. These results advance our understanding of synthetic gene circuits, and contribute towards the use of circuit modules as building blocks for larger and more complex synthetic networks.

Landscape structure shapes carnivore-mediated seed dispersal kernels

Context Seed dispersal is recognized as having profound effects on the distribution, dynamics and structure of plant populations and communities. However, knowledge of how landscape structure shapes carnivore-mediated seed dispersal patterns is still scarce, thereby limiting our understanding of large-scale plant population processes. Objectives We aim to determine how the amount and spatial configuration of forest cover impacted the relative abundance of carnivorous mammals, and how these effects cascaded through the seed dispersal kernels they generated. Methods Camera traps activated by animal movement were used for carnivore sampling. Colour-coded seed mimics embedded in common figs were used to know the exact origin of the dispersed seed mimics later found in carnivore scats. We applied this procedure in two sites differing in landscape structure. Results We did not find between-site differences in the relative abundance of the principal carnivore species contributing to seed dispersal patterns, Martes foina. Mean dispersal distance and the probability of long dispersal events were higher in the site with spatially continuous and abundant forest cover, compared to the site with spatially aggregated and scarcer forest cover. Seed deposition closely matched the spatial patterning of forest cover in both study sites, suggesting behaviour-based mechanisms underpinning seed dispersal patterns generated by individual frugivore species. Conclusions Our results provide the first empirical evidence of the impact of landscape structure on carnivore-mediated seed dispersal kernels. They also indicate that seed dispersal kernels generated strongly depend on the effect that landscape structure exerts on carnivore populations, particularly on habitat-use preferences.

Plant β-diversity i in human-altered forest ecosystems: the importance of the structural, spatial, and topographical characteristics of stands in patterning plant species assemblages

An understanding of spatial patterns of plant species diversity and the factors that drive those patterns is critical for the development of appropriate biodiversity management in forest ecosystems. We studied the spatial organization of plants species in human- modified and managed oak forests (primarily, Quercus faginea) in the Central Pre- Pyrenees, Spain. To test whether plant community assemblages varied non-randomly across the spatial scales, we used multiplicative diversity partitioning based on a nested hierarchical design of three increasingly coarser spatial scales (transect, stand, region). To quantify the importance of the structural, spatial, and topographical characteristics of stands in patterning plant species assemblages and identify the determinants of plant diversity patterns, we used canonical ordination. We observed a high contribution of ˟-diversity to total -diversity and found ˟-diversity to be higher and ˞-diversity to be lower than expected by random distributions of individuals at different spatial scales. Results, however, partly depended on the weighting of rare and abundant species. Variables expressing the historical management intensities of the stand such as mean stand age, the abundance of the dominant tree species (Q. faginea), age structure of the stand, and stand size were the main factors that explained the compositional variation in plant communities. The results indicate that (1) the structural, spatial, and topographical characteristics of the forest stands have the greatest effect on diversity patterns, (2) forests in landscapes that have different land use histories are environmentally heterogeneous and, therefore, can experience high levels of compositional differentiation, even at local scales (e.g., within the same stand). Maintaining habitat heterogeneity at multiple spatial scales should be considered in the development of management plans for enhancing plant diversity and related functions in human-altered forests

Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions

We define a pair-correlation function that can be used to characterize spatiotemporal patterning in experimental images and snapshots from discrete simulations. Unlike previous pair-correlation functions, the pair-correlation functions developed here depend on the location and size of objects. The pair-correlation function can be used to indicate complete spatial randomness, aggregation or segregation over a range of length scales, and quantifies spatial structures such as the shape, size and distribution of clusters. Comparing pair-correlation data for various experimental and simulation images illustrates their potential use as a summary statistic for calibrating discrete models of various physical processes.

Phenotyping cotton ovule fibre initiation with spatial statistics

Yield in cultivated cotton (Gossypium spp.) is affected by the number and distribution of fibres initiated on the seed surface but, apart from simple statistical summaries, little has been done to assess this phenotype quantitatively. Here we use two types of spatial statistics to describe and quantify differences in patterning of cotton ovule fibre initials (FI). The following five different species of Gossypium were analysed: G. hirsutum L., G. barbadense L., G. arboreum, G. raimondii Ulbrich. and G. trilobum (DC.) Skovsted. Scanning electron micrographs of FIs were taken on the day of anthesis. Cell centres for fibre and epidermal cells were digitised and analysed by spatial statistics methods appropriate for marked point processes and tessellations. Results were consistent with previously published reports of fibre number and spacing. However, it was shown that the spatial distributions of FIs in all of species examined exhibit regularity, and are not completely random as previously implied. The regular arrangement indicates FIs do not appear independently of each other and we surmise there may be some form of mutual inhibition specifying fibre-initial development. It is concluded that genetic control of FIs differs from that of stomata, another well studied plant idioblast. Since spatial statistics show clear species differences in the distribution of FIs within this genus, they provide a useful method for phenotyping cotton. © CSIRO 2007.

Sostdc1 Plays an Essential Role in Mammalian Tooth Patterning : Insight into the Rodent Dental Evolution

This thesis work focuses on the role of TGF-beta family antagonists during the development of mouse dentition. Tooth develops through an interaction between the dental epithelium and underlying neural crest derived mesenchyme. The reciprocal signaling between these tissues is mediated by soluble signaling molecules and the balance between activatory and inhibitory signals appears to be essential for the pattern formation. We showed the importance of Sostdc1 in the regulation of tooth shape and number. The absence of Sostdc1 altered the molar cusp patterning and led to supernumerary tooth formation both in the molar and incisor region. We showed that initially, Sostdc1 expression is in the mesenchyme, suggesting that dental mesenchyme may limit supernumerary tooth induction. We tested this in wild-type incisors by minimizing the amount of mesenchymal tissue surrounding the incisor tooth germs prior to culture in vitro. The cultured teeth phenocopied the extra incisor phenotype of the Sostdc1-deficient mice. Furthermore, we showed that minimizing the amount of dental mesenchyme in cultured Sostdc1-deficient incisors caused the formation of additional de novo incisors that resembled the successional incisor development resulting from activated Wnt signaling. Sostdc1 seemed to be able to inhibit both mesenchymal BMP4 and epithelial canonical Wnt signaling, which thus allows Sostdc1 to restrict the enamel knot size and regulate the tooth shape and number. Our work emphasizes the dual role for the tooth mesenchyme as a suppressor as well as an activator during tooth development. We found that the placode, forming the thick mouse incisor, is prone to disintegration during initiation of tooth development. The balance between two mesenchymal TGF-beta family signals, BMP4 and Activin is essential in this regulation. The inhibition of BMP4 or increase in Activin signaling led to the splitting of the large incisor placode into two smaller placodes resulting in thin incisors. These two signals appeared to have different effects on tooth epithelium and the analysis of the double null mutant mice lacking Sostdc1 and Follistatin indicated that these TGF-beta inhibitors regulate the mutual balance of BMP and Activin in vivo. In addition, this work provides an alternative explanation for the issue of incisor identity published in Science by Tucker et al. in 1998 and proposes that the molar like morphology that can be obtained by inhibiting BMP signaling is due to partial splitting of the incisor placodes and not due to change in tooth identity from the incisor to the molar. This thesis work presents possible molecular mechanisms that may have modified the mouse dental pattern during evolution leading to the typical rodent dentition of modern mouse. The rodent dentition is specialized for gnawing and consists of two large continuously growing incisors and toothless diastema region separating the molars and incisors. The ancestors of rodents had higher number of more slender incisors together with canines and premolars. Additionally, murine rodents, which include the mouse, have lost their ability for tooth replacement. This work has revealed that the inhibitory molecules appear to play a role in the tooth number suppression by delineating the spatial and temporal action of the inductive signals. The results suggest that Sostdc1 plays an essential role in several stages of tooth development through the regulation of both the BMP and Wnt pathway. The work shows a dormant sequential tooth forming potential present in wild type mouse incisor region and gives a new perspective on tooth suppression by dental mesenchyme. It reveals as well a novel mechanism to create a large mouse incisor through the regulation of mesenchymal balance between inductive and inhibitory signals.

The determination of spatial pattern in Dictyostelium discoideum

Free-living amoebae of the cellular slime mould Dictyostelium discoideum aggregate when starved and give rise to a long and thin multicellular structure, the slug. The slug resembles a metazoan embryo, and as with other embryos it is possible to specify a fate map. In the case of Dictyostelium discoideum the map is especially simple: cells in the anterior fifth of the slug die and form a stalk while the majority of those in the posterior differentiate into spores. The genesis of this anterior-posterior distinction is the subject of our review. In particular, we ask: what are the relative roles of individual pre-aggregative predispositions and post-aggregative position in determining cell fate? We review the literature on the subject and conclude that both factors are important. Variations in nutritional status, or in cell cycle phase at starvation, can bias the probability that an amoeba differentiates into a stalk cell or a spore. On the other hand, isolates, or slug fragments, consisting of only prestalk cells or only prespore cells can regulate so as to result in a normal range of both cell types. We identify three levels of control, each being responsible for guiding patterning in normal development: (i) 'coin tossing', whereby a cell autonomously exhibits a preference for developing along either the stalk or the spore pathway with relative probabilities that can be influenced by the environment; (ii) 'chemical kinetics', whereby prestalk and prespore cells originate from undifferentiated amoebae on a probabilistic basis but, having originated, interact (e.g. via positive and negative feedbacks), and the interaction influences the possibility of conversion of one cell type into the other, and (iii) 'positional information', in which the spatial distribution of morphogens in the slug influences the pathway of differentiation. In the case of possibilities (i) and (ii), sorting out of like cell types leads to the final spatial pattern. In the case of possibility (iii), the pattern arises in situ.

Spatial filter based light-sheet laser interference technique for three-dimensional nanolithography

We propose a laser interference technique for the fabrication of 3D nano-structures. This is possible with the introduction of specialized spatial filter in a 2 pi cylindrical lens system (consists of two opposing cylindrical lens sharing a common geometrical focus). The spatial filter at the back-aperture of a cylindrical lens gives rise to multiple light-sheet patterns. Two such interfering counter-propagating light-sheet pattern result in periodic 3D nano-pillar structure. This technique overcomes the existing slow point-by-point scanning, and has the ability to pattern selectively over a large volume. The proposed technique allows large-scale fabrication of periodic structures. Computational study shows a field-of-view (patterning volume) of approximately 12: 2mm(3) with the pillar-size of 80 nm and inter-pillar separation of 180 nm. Applications are in nano-waveguides, 3D nano-electronics, photonic crystals, and optical microscopy. (C) 2015 AIP Publishing LLC.

Self-organized vegetation patterning as a fingerprint of climate and human impact on semi-arid ecosystems

Spatially periodic vegetation patterns are well known in arid and semi-arid regions around the world. Mathematical models have been developed that attribute this phenomenon to a symmetry-breaking instability. Such models are based on the interplay between competitive and facilitative influences that the vegetation exerts on its own dynamics when it is constrained by arid conditions, but evidence for these predictions is still lacking. Moreover, not all models can account for the development of regularly spaced spots of bare ground in the absence of a soil prepattern. We applied Fourier analysis to high-resolution, remotely sensed data taken at either end of a 40-year interval in southern Niger. Statistical comparisons based on this textural characterization gave us broad-scale evidence that the decrease in rainfall over recent decades in the sub-Saharan Sahel has been accompanied by a detectable shift from homogeneous vegetation cover to spotted patterns marked by a spatial frequency of about 20 cycles km-1. Wood cutting and grazing by domestic animals have led to a much more marked transition in unprotected areas than in a protected reserve. Field measurements demonstrated that the dominant spatial frequency was endogenous rather than reflecting the spatial variation of any pre-existing heterogeneity in soil properties. All these results support the use of models that can account for periodic vegetation patterns without invoking substrate heterogeneity or anisotropy, and provide new elements for further developments, refinements and tests. This study underlines the potential of studying vegetation pattern properties for monitoring climatic and human impacts on the extensive fragile areas bordering hot deserts. Explicit consideration of vegetation self-patterning may also improve our understanding of vegetation and climate interactions in arid areas. © 2006 The Authors.

Disentangling the Harrisson Archive to Interpret the Spatial and Temporal Distribution of Vertebrate Remains at Niah Caves, Sarawak

During the 1950s and 1960s, excavations by the Sarawak Museum at Niah Cave in northwest Borneo produced an enormous archive of records and artefacts, including in excess of 750,000 macro- and micro-vertebrate remains. The excellent state of preservation of the animal bone, dating from the Late Pleistocene (c. 40 kya) to as recently as c. 500 years ago had the potential to provide unparalleled zooarchaeological information about early hunter-gatherer resource procurement, temporal changes in subsistence patterning, and the impact of peoples on the local and regional environment in Island Southeast Asia. However, the coarse-grained methods of excavation employed during the original investigations and the sheer scale of the archaeological record and bone assemblages dissuaded many researchers from attempting to tackle the Niah archives. This paper outlines how important information on the nature of the archaeological record at Niah has now finally been extracted from the archive using a combination of zooarchaeological analysis and reference to the extensive archaeological records from the site. Copyright (C) 2009 John Wiley & Sons, Ltd.

Ultrabithorax Confers Spatial Identity in a Context-Specific Manner in the Drosophila Postembryonic Ventral Nervous System

In holometabolous insects such as Drosophila melanogaster, neuroblasts produce an initial population of diverse neurons during embryogenesis and a much larger set of adult-specific neurons during larval life. In the ventral CNS, many of these secondary neuronal lineages differ significantly from one body segment to another, suggesting a role for anteroposterior patterning genes. Here we systematically characterize the expression pattern and function of the Hox gene Ultrabithorax (Ubx) in all 25 postembryonic lineages. We find that Ubx is expressed in a segment-, lineage-, and hemilineage-specific manner in the thoracic and anterior abdominal segments. When Ubx is removed from neuroblasts via mitotic recombination, neurons in these segments exhibit the morphologies and survival patterns of their anterior thoracic counterparts. Conversely, when Ubx is ectopically expressed in anterior thoracic segments, neurons exhibit complementary posterior transformation phenotypes. Our findings demonstrate that Ubx plays a critical role in conferring segment-appropriate morphology and survival on individual neurons in the adult-specific ventral CNS. Moreover, while always conferring spatial identity in some sense, Ubx has been co-opted during evolution for distinct and even opposite functions in different neuronal hemilineages.