Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

NASA Astrophysics Data System (ADS)

Vize, Peter D.; Gerth, Victor E.

2007-01-01

Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture

PubMed Central

Baumann, Kim; Venail, Julien; Berbel, Ana; Domenech, Maria Jose; Money, Tracy; Conti, Lucio; Hanzawa, Yoshie; Madueno, Francisco; Bradley, Desmond

2015-01-01

Models for the control of above-ground plant architectures show how meristems can be programmed to be either shoots or flowers. Molecular, genetic, transgenic, and mathematical studies have greatly refined these models, suggesting that the phase of the shoot reflects different genes contributing to its repression of flowering, its vegetativeness (‘veg’), before activators promote flower development. Key elements of how the repressor of flowering and shoot meristem gene TFL1 acts have now been tested, by changing its spatiotemporal pattern. It is shown that TFL1 can act outside of its normal expression domain in leaf primordia or floral meristems to repress flower identity. These data show how the timing and spatial pattern of TFL1 expression affect overall plant architecture. This reveals that the underlying pattern of TFL1 interactors is complex and that they may be spatially more widespread than TFL1 itself, which is confined to shoots. However, the data show that while TFL1 and floral genes can both act and compete in the same meristem, it appears that the main shoot meristem is more sensitive to TFL1 rather than floral genes. This spatial analysis therefore reveals how a difference in response helps maintain the ‘veg’ state of the shoot meristem. PMID:26019254

larvalign: Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster.

PubMed

Muenzing, Sascha E A; Strauch, Martin; Truman, James W; Bühler, Katja; Thum, Andreas S; Merhof, Dorit

2018-01-01

The larval brain of the fruit fly Drosophila melanogaster is a small, tractable model system for neuroscience. Genes for fluorescent marker proteins can be expressed in defined, spatially restricted neuron populations. Here, we introduce the methods for 1) generating a standard template of the larval central nervous system (CNS), 2) spatial mapping of expression patterns from different larvae into a reference space defined by the standard template. We provide a manually annotated gold standard that serves for evaluation of the registration framework involved in template generation and mapping. A method for registration quality assessment enables the automatic detection of registration errors, and a semi-automatic registration method allows one to correct registrations, which is a prerequisite for a high-quality, curated database of expression patterns. All computational methods are available within the larvalign software package: https://github.com/larvalign/larvalign/releases/tag/v1.0.

Local neighborhood transition probability estimation and its use in contextual classification

NASA Technical Reports Server (NTRS)

Chittineni, C. B.

1979-01-01

The problem of incorporating spatial or contextual information into classifications is considered. A simple model that describes the spatial dependencies between the neighboring pixels with a single parameter, Theta, is presented. Expressions are derived for updating the posteriori probabilities of the states of nature of the pattern under consideration using information from the neighboring patterns, both for spatially uniform context and for Markov dependencies in terms of Theta. Techniques for obtaining the optimal value of the parameter Theta as a maximum likelihood estimate from the local neighborhood of the pattern under consideration are developed.

What Does Children's Spatial Language Reveal about Spatial Concepts? Evidence from the Use of Containment Expressions

ERIC Educational Resources Information Center

Johanson, Megan; Papafragou, Anna

2014-01-01

Children's overextensions of spatial language are often taken to reveal spatial biases. However, it is unclear whether extension patterns should be attributed to children's overly general spatial concepts or to a narrower notion of conceptual similarity allowing metaphor-like extensions. We describe a previously unnoticed extension of…

Design and implementation of spatial knowledge grid for integrated spatial analysis

NASA Astrophysics Data System (ADS)

Liu, Xiangnan; Guan, Li; Wang, Ping

2006-10-01

Supported by spatial information grid(SIG), the spatial knowledge grid (SKG) for integrated spatial analysis utilizes the middleware technology in constructing the spatial information grid computation environment and spatial information service system, develops spatial entity oriented spatial data organization technology, carries out the profound computation of the spatial structure and spatial process pattern on the basis of Grid GIS infrastructure, spatial data grid and spatial information grid (specialized definition). At the same time, it realizes the complex spatial pattern expression and the spatial function process simulation by taking the spatial intelligent agent as the core to establish space initiative computation. Moreover through the establishment of virtual geographical environment with man-machine interactivity and blending, complex spatial modeling, network cooperation work and spatial community decision knowledge driven are achieved. The framework of SKG is discussed systematically in this paper. Its implement flow and the key technology with examples of overlay analysis are proposed as well.

Identification of unique cis-element pattern on simulated microgravity treated Arabidopsis by in silico and gene expression

NASA Astrophysics Data System (ADS)

Soh, Hyuncheol; Choi, Yongsang; Lee, Taek-Kyun; Yeo, Up-Dong; Han, Kyeongsik; Auh, Chungkyun; Lee, Sukchan

2012-08-01

Arabidopsis gene expression microarray (44 K) was used to detect genes highly induced under simulated microgravity stress (SMS). Ten SMS-inducible genes were selected from the microarray data and these 10 genes were found to be abundantly expressed in 3-week-old plants. Nine out of the 10 SMS-inducible genes were also expressed in response to the three abiotic stresses of drought, touch, and wounding in 3-week-old Arabidopsis plants respectively. However, WRKY46 was elevated only in response to SMS. Six other WRKY genes did not respond to SMS. To clarify the characteristics of the genes expressed at high levels in response to SMS, 20 cis-elements in the promoters of the 40 selected genes including the 10 SMS-inducible genes, the 6 WRKY genes, and abiotic stress-inducible genes were analyzed and their spatial positions on each promoter were determined. Four cis-elements (M/T-G-T-P from MYB1AT or TATABOX5, GT1CONSENSUS, TATABOX5, and POLASIG1) showed a unique spatial arrangement in most SMS-inducible genes including WRKY46. Therefore the M/T-G-T-P cis-element patterns identified in the promoter of WRKY46 may play important roles in regulating gene expression in response to SMS. The presences of the cis-element patterns suggest that the order or spatial positioning of certain groups of cis-elements is more important than the existence or numbers of specific cis-elements. Taken together, our data indicate that WRKY46 is a novel SMS inducible transcription factor and the unique spatial arrangement of cis-elements shown in WRKY46 promoter may play an important role for its response to SMS.

Spatial distribution and expression of intracellular and extracellular acid phosphatases of cluster roots at different developmental stages in white lupin.

PubMed

Tang, Hongliang; Li, Xiaoqing; Zu, Chao; Zhang, Fusuo; Shen, Jianbo

2013-09-15

Acid phosphatases (APases) play a key role in phosphorus (P) acquisition and recycling in plants. White lupin (Lupinus albus L.) forms cluster roots (CRs) and produces large amounts of APases under P deficiency. However, the relationships between the activity of intracellular and extracellular APases (EC 3.1.3.2) and CR development are not fully understood. Here, comparative studies were conducted to examine the spatial variation pattern of APase activity during CR development using the enzyme-labelled fluorescence-97 (ELF-97) and the p-nitrophenyl phosphate methods. The activity of intracellular and extracellular APases was significantly enhanced under P deficiency in the non-CRs and CRs at different developmental stages. These two APases exhibited different spatial distribution patterns during CR development, and these distribution patterns were highly modified by P deficiency. The activity of extracellular APase increased steadily with CR development from meristematic, juvenile, mature to senescent stages under P deficiency. In comparison, P deficiency-induced increase in the activity of intracellular APase remained relatively constant during CR development. Increased activity of intracellular and extracellular APases was associated with enhanced expression of LaSAP1 encoding intracellular APase and LaSAP2 encoding extracellular APase. The expression levels of these two genes were significantly higher at transcriptional level in both mature and senescent CRs. Taken together, these findings demonstrate that both activity and gene expression of intracellular or extracellular APases exhibit a differential response pattern during CR development, depending on root types, CR developmental stages and P supply. Simultaneous in situ determination of intracellular and extracellular APase activity has proved to be an effective approach for studying spatial variation of APases during CR development. Copyright © 2013 Elsevier GmbH. All rights reserved.

Sex-specific effects of prenatal chronic mild stress on adult spatial learning capacity and regional glutamate receptor expression profiles.

PubMed

Wang, Yan; Ma, Yuchao; Hu, Jingmin; Zhang, Xinxin; Cheng, Wenwen; Jiang, Han; Li, Min; Ren, Jintao; Zhang, Xiaosong; Liu, Mengxi; Sun, Anji; Wang, Qi; Li, Xiaobai

2016-07-01

Both animal experiments and clinical studies have demonstrated that prenatal stress can cause cognitive disorders in offspring. To explore the scope of these deficits and identify potential underlying mechanisms, we examined the spatial learning and memory performance and glutamate receptor (GluR) expression patterns of adult rats exposed to prenatal chronic mild stress (PCMS). Principal component analysis (PCA) was employed to reveal the interrelationships among spatial learning indices and GluR expression changes. Female PCMS-exposed offspring exhibited markedly impaired spatial learning and memory in the Morris water maze (MWM) task compared to control females, while PCMS-exposed males showed better initial spatial learning in the MWM compared to control males. PCMS also altered basal and post-MWM glutamate receptor expression patterns, but these effects differed markedly between sexes. Male PCMS-exposed offspring exhibited elevated basal expression of NR1, mGluR5, and mGluR2/3 in the prefrontal cortex (PFC), whereas females showed no basal expression changes. Following MWM training, PCMS-exposed males expressed higher NR1 in the PFC and mammillary body (MB), higher mGluR2/3 in PFC, and lower NR2B in the hippocampus (HIP), PFC, and MB compared to unstressed MWM-trained males. Female PCMS-exposed offspring showed strongly reduced NR1 in MB and NR2B in the HIP, PFC, and MB, and increased mGluR2/3 in PFC compared to unstressed MWM-trained females. This is the first report suggesting that NMDA subunits in the MB are involved in spatial learning. Additionally, PCA further suggests that the NR1-NR2B form is the most important for spatial memory formation. These results reveal long-term sex-specific effects of PCMS on spatial learning and memory performance in adulthood and implicate GluR expression changes within HIP, PFC, and MB as possible molecular mechanisms underlying cognitive dysfunction in offspring exposed to prenatal stress. Copyright © 2016 Elsevier Inc. All rights reserved.

The fin-to-limb transition as the re-organization of a Turing pattern

PubMed Central

Onimaru, Koh; Marcon, Luciano; Musy, Marco; Tanaka, Mikiko; Sharpe, James

2016-01-01

A Turing mechanism implemented by BMP, SOX9 and WNT has been proposed to control mouse digit patterning. However, its generality and contribution to the morphological diversity of fins and limbs has not been explored. Here we provide evidence that the skeletal patterning of the catshark Scyliorhinus canicula pectoral fin is likely driven by a deeply conserved Bmp–Sox9–Wnt Turing network. In catshark fins, the distal nodular elements arise from a periodic spot pattern of Sox9 expression, in contrast to the stripe pattern in mouse digit patterning. However, our computer model shows that the Bmp–Sox9–Wnt network with altered spatial modulation can explain the Sox9 expression in catshark fins. Finally, experimental perturbation of Bmp or Wnt signalling in catshark embryos produces skeletal alterations which match in silico predictions. Together, our results suggest that the broad morphological diversity of the distal fin and limb elements arose from the spatial re-organization of a deeply conserved Turing mechanism. PMID:27211489

Regulatory analysis of the mouse Hoxb3 gene: multiple elements work in concert to direct temporal and spatial patterns of expression.

PubMed

Kwan, C T; Tsang, S L; Krumlauf, R; Sham, M H

2001-04-01

The expression pattern of the mouse Hoxb3 gene is exceptionally complex and dynamic compared with that of other members of the Hoxb cluster. There are multiple types of transcripts for Hoxb3 gene, and the anterior boundaries of its expression vary at different stages of development. Two enhancers flanking Hoxb3 on the 3' and 5' sides regulate Hoxb2 and Hoxb4, respectively, and these control regions define the two ends of a 28-kb interval in and around the Hoxb3 locus. To assay the regulatory potential of DNA fragments in this interval we have used transgenic analysis with a lacZ reporter gene to locate cis-elements for directing the dynamic patterns of Hoxb3 expression. Our detailed analysis has identified four new and widely spaced cis-acting regulatory regions that can together account for major aspects of the Hoxb3 expression pattern. Elements Ib, IIIa, and IVb control gene expression in neural and mesodermal tissues; element Va controls mesoderm-specific gene expression. The most anterior neural expression domain of Hoxb3 is controlled by an r5 enhancer (element IVa); element IIIa directs reporter expression in the anterior spinal cord and hindbrain up to r6, and the region A enhancer (in element I) mediates posterior neural expression. Hence, the regulation of segmental expression of Hoxb3 in the hindbrain is different from that of Hoxa3, as two separate enhancer elements contribute to expression in r5 and r6. The mesoderm-specific element (Va) directs reporter expression to prevertebra C1 at 12.5 dpc, which is the anterior limit of paraxial mesoderm expression for Hoxb3. When tested in combinations, these cis-elements appear to work as modules in an additive manner to recapitulate the major endogenous expression patterns of Hoxb3 during embryogenesis. Together our study shows that multiple control elements direct reporter gene expression in diverse tissue-, temporal-, and spatially restricted subset of the endogenous Hoxb3 expression domains and work in concert to control the neural and mesodermal patterns of expression. Copyright 2001 Academic Press.

Unique Temporal Expression of Triplicated Long-Wavelength Opsins in Developing Butterfly Eyes

PubMed Central

Arikawa, Kentaro; Iwanaga, Tomoyuki; Wakakuwa, Motohiro; Kinoshita, Michiyo

2017-01-01

Following gene duplication events, the expression patterns of the resulting gene copies can often diverge both spatially and temporally. Here we report on gene duplicates that are expressed in distinct but overlapping patterns, and which exhibit temporally divergent expression. Butterflies have sophisticated color vision and spectrally complex eyes, typically with three types of heterogeneous ommatidia. The eyes of the butterfly Papilio xuthus express two green- and one red-absorbing visual pigment, which came about via gene duplication events, in addition to one ultraviolet (UV)- and one blue-absorbing visual pigment. We localized mRNAs encoding opsins of these visual pigments in developing eye disks throughout the pupal stage. The mRNAs of the UV and blue opsin are expressed early in pupal development (pd), specifying the type of the ommatidium in which they appear. Red sensitive photoreceptors first express a green opsin mRNA, which is replaced later by the red opsin mRNA. Broadband photoreceptors (that coexpress the green and red opsins) first express the green opsin mRNA, later change to red opsin mRNA and finally re-express the green opsin mRNA in addition to the red mRNA. Such a unique temporal and spatial expression pattern of opsin mRNAs may reflect the evolution of visual pigments and provide clues toward understanding how the spectrally complex eyes of butterflies evolved. PMID:29238294

ULTRAPETALA trxG genes interact with KANADI transcription factor genes to regulate Aradopsis Gynoecium patterning

USDA-ARS?s Scientific Manuscript database

Organ formation relies upon precise patterns of gene expression that are under tight spatial and temporal regulation. Transcription patterns are specified by several cellular processes during development, including chromatin remodeling, but little is known about how chromatin remodeling factors cont...

Selective memory generalization by spatial patterning of protein synthesis

PubMed Central

O’Donnell, Cian; Sejnowski, Terrence J.

2014-01-01

Summary Protein synthesis is crucial for both persistent synaptic plasticity and long-term memory. De novo protein expression can be restricted to specific neurons within a population, and to specific dendrites within a single neuron. Despite its ubiquity, the functional benefits of spatial protein regulation for learning are unknown. We used computational modeling to study this problem. We found that spatially patterned protein synthesis can enable selective consolidation of some memories but forgetting of others, even for simultaneous events that are represented by the same neural population. Key factors regulating selectivity include the functional clustering of synapses on dendrites, and the sparsity and overlap of neural activity patterns at the circuit level. Based on these findings we proposed a novel two-step model for selective memory generalization during REM and slow-wave sleep. The pattern-matching framework we propose may be broadly applicable to spatial protein signaling throughout cortex and hippocampus. PMID:24742462

Selective memory generalization by spatial patterning of protein synthesis.

PubMed

O'Donnell, Cian; Sejnowski, Terrence J

2014-04-16

Protein synthesis is crucial for both persistent synaptic plasticity and long-term memory. De novo protein expression can be restricted to specific neurons within a population, and to specific dendrites within a single neuron. Despite its ubiquity, the functional benefits of spatial protein regulation for learning are unknown. We used computational modeling to study this problem. We found that spatially patterned protein synthesis can enable selective consolidation of some memories but forgetting of others, even for simultaneous events that are represented by the same neural population. Key factors regulating selectivity include the functional clustering of synapses on dendrites, and the sparsity and overlap of neural activity patterns at the circuit level. Based on these findings, we proposed a two-step model for selective memory generalization during REM and slow-wave sleep. The pattern-matching framework we propose may be broadly applicable to spatial protein signaling throughout cortex and hippocampus. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Data Analysis and Visualization; nternational Research Training Group ``Visualization of Large and Unstructured Data Sets,'' University of Kaiserslautern, Germany; Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA

2008-05-12

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss (i) integration of data clustering and visualization into one framework; (ii) application of data clustering to 3D gene expression data; (iii)more » evaluation of the number of clusters k in the context of 3D gene expression clustering; and (iv) improvement of overall analysis quality via dedicated post-processing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.« less

High cell density suppresses BMP4-induced differentiation of human pluripotent stem cells to produce macroscopic spatial patterning in a unidirectional perfusion culture chamber.

PubMed

Tashiro, Shota; Le, Minh Nguyen Tuyet; Kusama, Yuta; Nakatani, Eri; Suga, Mika; Furue, Miho K; Satoh, Taku; Sugiura, Shinji; Kanamori, Toshiyuki; Ohnuma, Kiyoshi

2018-04-19

Spatial pattern formation is a critical step in embryogenesis. Bone morphogenetic protein 4 (BMP4) and its inhibitors are major factors for the formation of spatial patterns during embryogenesis. However, spatial patterning of the human embryo is unclear because of ethical issues and isotropic culture environments resulting from conventional culture dishes. Here, we utilized human pluripotent stem cells (hiPSCs) and a simple anisotropic (unidirectional perfusion) culture chamber, which creates unidirectional conditions, to measure the cell community effect. The influence of cell density on BMP4-induced differentiation was explored during static culture using a conventional culture dish. Immunostaining of the early differentiation marker SSEA-1 and the mesendoderm marker BRACHYURY revealed that high cell density suppressed differentiation, with small clusters of differentiated and undifferentiated cells formed. Addition of five-fold higher concentration of BMP4 showed similar results, suggesting that suppression was not caused by depletion of BMP4 but rather by high cell density. Quantitative RT-PCR array analysis showed that BMP4 induced multi-lineage differentiation, which was also suppressed under high-density conditions. We fabricated an elongated perfusion culture chamber, in which proteins were transported unidirectionally, and hiPSCs were cultured with BMP4. At low density, the expression was the same throughout the chamber. However, at high density, SSEA-1 and BRACHYURY were expressed only in upstream cells, suggesting that some autocrine/paracrine factors inhibited the action of BMP4 in downstream cells to form the spatial pattern. Human iPSCs cultured in a perfusion culture chamber might be useful for studying in vitro macroscopic pattern formation in human embryogenesis. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

ROOT HAIR DEFECTIVE SIX-LIKE Class I Genes Promote Root Hair Development in the Grass Brachypodium distachyon

PubMed Central

Kim, Chul Min

2016-01-01

Genes encoding ROOT HAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix loop helix proteins are expressed in future root hair cells of the Arabidopsis thaliana root meristem where they positively regulate root hair cell development. Here we show that there are three RSL class I protein coding genes in the Brachypodium distachyon genome, BdRSL1, BdRSL2 and BdRSL3, and each is expressed in developing root hair cells after the asymmetric cell division that forms root hair cells and hairless epidermal cells. Expression of BdRSL class I genes is sufficient for root hair cell development: ectopic overexpression of any of the three RSL class I genes induces the development of root hairs in every cell of the root epidermis. Expression of BdRSL class I genes in root hairless Arabidopsis thaliana root hair defective 6 (Atrhd6) Atrsl1 double mutants, devoid of RSL class I function, restores root hair development indicating that the function of these proteins has been conserved. However, neither AtRSL nor BdRSL class I genes is sufficient for root hair development in A. thaliana. These data demonstrate that the spatial pattern of class I RSL activity can account for the pattern of root hair cell differentiation in B. distachyon. However, the spatial pattern of class I RSL activity cannot account for the spatial pattern of root hair cells in A. thaliana. Taken together these data indicate that that the functions of RSL class I proteins have been conserved among most angiosperms—monocots and eudicots—despite the dramatically different patterns of root hair cell development. PMID:27494519

Identification of a spatially specific enhancer element in the chicken Msx-2 gene that regulates its expression in the apical ectodermal ridge of the developing limb buds of transgenic mice.

PubMed

Sumoy, L; Wang, C K; Lichtler, A C; Pierro, L J; Kosher, R A; Upholt, W B

1995-07-01

Msx-2 is a member of the Msx family of homeobox-containing genes expressed in a variety of embryonic tissues involved in epithelial-mesenchymal interactions and pattern formation. In the developing chick limb bud, Msx-2 is expressed in the apical ectodermal ridge, which plays a crucial role in directing the growth and patterning of limb mesoderm. In addition, Msx-2 is expressed in the anterior nonskeletal-forming mesoderm of the limb bud, in the posterior necrotic zone, and in the interdigital mesenchyme. Studies of the altered expression patterns of Msx-2 in amelic and polydactylous mutant chick limbs have suggested that the apical ectodermal ridge and mesodermal domains of Msx-2 expression are independently regulated and that there might be separate cis-regulatory elements in the Msx-2 gene controlling its spatially distinct domains of expression. To test this hypothesis, we have isolated the chicken Msx-2 gene and have tested the ability of various regions of the gene to target expression of LacZ reporter gene to specific regions of the limbs of transgenic mice. A variety of these constructs are consistently expressed only in the apical ectodermal ridge and the ectoderm of the genital tubercle and are not expressed in the mesoderm of the limb bud or in other regions of the embryo where the endogenous Msx-2 gene is expressed. These results suggest the presence of spatially specific cis-regulatory elements in the Msx-2 gene. We identified a 348-bp region in the 5' flanking region of the Msx-2 gene which can act as an apical ectodermal ridge enhancer element when placed in reverse orientation in front of the reporter gene with transcription initiation directed by the minimal hsp68 promoter.

Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms

PubMed Central

van Gestel, Jordi; Weissing, Franz J; Kuipers, Oscar P; Kovács, Ákos T

2014-01-01

In nature, most bacteria live in surface-attached sedentary communities known as biofilms. Biofilms are often studied with respect to bacterial interactions. Many cells inhabiting biofilms are assumed to express ‘cooperative traits', like the secretion of extracellular polysaccharides (EPS). These traits can enhance biofilm-related properties, such as stress resilience or colony expansion, while being costly to the cells that express them. In well-mixed populations cooperation is difficult to achieve, because non-cooperative individuals can reap the benefits of cooperation without having to pay the costs. The physical process of biofilm growth can, however, result in the spatial segregation of cooperative from non-cooperative individuals. This segregation can prevent non-cooperative cells from exploiting cooperative neighbors. Here we examine the interaction between spatial pattern formation and cooperation in Bacillus subtilis biofilms. We show, experimentally and by mathematical modeling, that the density of cells at the onset of biofilm growth affects pattern formation during biofilm growth. At low initial cell densities, co-cultured strains strongly segregate in space, whereas spatial segregation does not occur at high initial cell densities. As a consequence, EPS-producing cells have a competitive advantage over non-cooperative mutants when biofilms are initiated at a low density of founder cells, whereas EPS-deficient cells have an advantage at high cell densities. These results underline the importance of spatial pattern formation for competition among bacterial strains and the evolution of microbial cooperation. PMID:24694715

Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms.

PubMed

van Gestel, Jordi; Weissing, Franz J; Kuipers, Oscar P; Kovács, Akos T

2014-10-01

In nature, most bacteria live in surface-attached sedentary communities known as biofilms. Biofilms are often studied with respect to bacterial interactions. Many cells inhabiting biofilms are assumed to express 'cooperative traits', like the secretion of extracellular polysaccharides (EPS). These traits can enhance biofilm-related properties, such as stress resilience or colony expansion, while being costly to the cells that express them. In well-mixed populations cooperation is difficult to achieve, because non-cooperative individuals can reap the benefits of cooperation without having to pay the costs. The physical process of biofilm growth can, however, result in the spatial segregation of cooperative from non-cooperative individuals. This segregation can prevent non-cooperative cells from exploiting cooperative neighbors. Here we examine the interaction between spatial pattern formation and cooperation in Bacillus subtilis biofilms. We show, experimentally and by mathematical modeling, that the density of cells at the onset of biofilm growth affects pattern formation during biofilm growth. At low initial cell densities, co-cultured strains strongly segregate in space, whereas spatial segregation does not occur at high initial cell densities. As a consequence, EPS-producing cells have a competitive advantage over non-cooperative mutants when biofilms are initiated at a low density of founder cells, whereas EPS-deficient cells have an advantage at high cell densities. These results underline the importance of spatial pattern formation for competition among bacterial strains and the evolution of microbial cooperation.

Solid perception mechanism by a shading pattern: spatial frequency components in a corrugated wave pattern.

PubMed

Nameda, N

1988-01-01

Illumination allows solid object perception to be obtained and depicted by a shading pattern produced by lighting. The shading cue, as one of solid perception cues (Gibson 1979), was investigated in regard to a white corrugated wave shape, using computer graphic device: Tospix-2. The reason the corrugated wave was chosen, is that an alternately bright and dark pattern, produced by shading, can be conveniently analyzed into contained spatial frequencies. This paper reports spatial frequency properties contained in the shading pattern. The shading patterns, input into the computer graphic device, are analyzed by Fourier Transformation by the same device. After the filtration by various spatial frequency low and high pass filters, Inverse Fourier Transformation is carried out for the residual components. The result of the analysis indicates that the third through higher harmonics components are important in regard to presenting a solid reality feeling in solid perception. Sakata (1983) also reported that an edged pattern, superimposed onto a lower sinusoidal pattern, was important in solid perception. The third through higher harmonics components express the changing position of luminance on the pattern, and a slanted plane relating to the light direction. Detection of a solid shape, constructed with flat planes, is assumed to be on the bottom of the perfect curved solid perception mechanism. Apparent evidence for this assumption, in difficult visual conditions, is that a flat paneled solid is seen before the curved solid. This mechanism is explained by two spatial frequency neural network systems, assumed as having correspondence with higher spatial frequency detection and lower spatial frequency detection.

Quantify spatial relations to discover handwritten graphical symbols

NASA Astrophysics Data System (ADS)

Li, Jinpeng; Mouchère, Harold; Viard-Gaudin, Christian

2012-01-01

To model a handwritten graphical language, spatial relations describe how the strokes are positioned in the 2-dimensional space. Most of existing handwriting recognition systems make use of some predefined spatial relations. However, considering a complex graphical language, it is hard to express manually all the spatial relations. Another possibility would be to use a clustering technique to discover the spatial relations. In this paper, we discuss how to create a relational graph between strokes (nodes) labeled with graphemes in a graphical language. Then we vectorize spatial relations (edges) for clustering and quantization. As the targeted application, we extract the repetitive sub-graphs (graphical symbols) composed of graphemes and learned spatial relations. On two handwriting databases, a simple mathematical expression database and a complex flowchart database, the unsupervised spatial relations outperform the predefined spatial relations. In addition, we visualize the frequent patterns on two text-lines containing Chinese characters.

Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

PubMed

Kohsokabe, Takahiro; Kaneko, Kunihiko

2016-01-01

Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Evolution‐development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures

PubMed Central

Kohsokabe, Takahiro

2016-01-01

ABSTRACT Search for possible relationships between phylogeny and ontogeny is important in evolutionary‐developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell‐to‐cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi‐stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical‐systems theory, which lead to the evolution‐development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. J. Exp. Zool. (Mol. Dev. Evol.) 326B:61–84, 2016. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc. PMID:26678220

Local accumulation times for spatial difference in morphogen concentration

NASA Astrophysics Data System (ADS)

Wen, Xiaoqing; Yin, Hongwei

During development of multicellular organisms, spatial patterns of cells and tissue organizations rely on the action of morphogens, which are signaling molecules and act as dose-dependent regulators of gene expression and cellular differentiation. Since some experimental evidences have indicated that the spatial difference in morphogen concentration regulates cellular proliferation rather than this concentration profile in developing tissues, we propose spatially discrete models to describe this difference for a synthesis-diffusion-degradation process of morphogen in infinite and finite development fields, respectively. For both of models, we respectively derive analytical expressions of local accumulation times, which are required to form the steady state of the spatial difference in morphogen concentration. Our results show that the local accumulation times for the spatial difference in morphogen concentrations are different from the ones for morphogen concentration profiles.

Dynamic CRM occupancy reflects a temporal map of developmental progression.

PubMed

Wilczyński, Bartek; Furlong, Eileen E M

2010-06-22

Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.

The tailless Ortholog nhr-67 Regulates Patterning of Gene Expression and Morphogenesis in the C. elegans Vulva

PubMed Central

Fernandes, Jolene S; Sternberg, Paul W

2007-01-01

Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown. Dissection of the gene regulatory networks involved in vulval patterning and differentiation would help us understand how cells generate a spatially defined pattern of cell fates during organogenesis. We disrupted the activity of 508 transcription factors via RNAi and assayed the expression of ceh-2, a marker for vulB fate during the L4 stage. From this screen, we identified the tailless ortholog nhr-67 as a novel regulator of gene expression in multiple vulval cell types. We find that one way in which nhr-67 maintains cell identity is by restricting inappropriate cell fusion events in specific vulval cells, namely vulE and vulF. nhr-67 exhibits a dynamic expression pattern in the vulval cells and interacts with three other transcriptional regulators cog-1 (Nkx6.1/6.2), lin-11 (LIM), and egl-38 (Pax2/5/8) to generate the composite expression patterns of their downstream targets. We provide evidence that egl-38 regulates gene expression in vulB1, vulC, vulD, vulE, as well as vulF cells. We demonstrate that the pairwise interactions between these regulatory genes are complex and vary among the seven cell types. We also discovered a striking regulatory circuit that affects a subset of the vulval lineages: cog-1 and nhr-67 inhibit both one another and themselves. We postulate that the differential levels and combinatorial patterns of lin-11, cog-1, and nhr-67 expression are a part of a regulatory code for the mature vulval cell types. PMID:17465684

Gene expression underlying adaptive variation in Heliconius wing patterns: non-modular regulation of overlapping cinnabar and vermilion prepatterns.

PubMed

Reed, Robert D; McMillan, W Owen; Nagy, Lisa M

2008-01-07

Geographical variation in the mimetic wing patterns of the butterfly Heliconius erato is a textbook example of adaptive polymorphism; however, little is known about how this variation is controlled developmentally. Using microarrays and qPCR, we identified and compared expression of candidate genes potentially involved with a red/yellow forewing band polymorphism in H. erato. We found that transcripts encoding the pigment synthesis enzymes cinnabar and vermilion showed pattern- and polymorphism-related expression patterns, respectively. cinnabar expression was associated with the forewing band regardless of pigment colour, providing the first gene expression pattern known to be correlated with a major Heliconius colour pattern. In contrast, vermilion expression changed spatially over time in red-banded butterflies, but was not expressed at detectable levels in yellow-banded butterflies, suggesting that regulation of this gene may be involved with the red/yellow polymorphism. Furthermore, we found that the yellow pigment, 3-hydroxykynurenine, is incorporated into wing scales from the haemolymph rather than being synthesized in situ. We propose that some aspects of Heliconius colour patterns are determined by spatio-temporal overlap of pigment gene transcription prepatterns and speculate that evolutionary changes in vermilion regulation may in part underlie an adaptive colour pattern polymorphism.

Effects of nitrogen nutrition on the synthesis and deposition of the ω-gliadins of wheat.

PubMed

Wan, Yongfang; Gritsch, Cristina Sanchis; Hawkesford, Malcolm J; Shewry, Peter R

2014-03-01

The ω-gliadin storage proteins of wheat are of interest in relation to their impact on grain processing properties and their role in food allergy, particularly the ω-5 sub-group and wheat-dependent exercise-induced anaphylaxis. The ω-gliadins are also known to be responsive to nitrogen application. This study therefore compares the effects of cultivar and nitrogen availability on the synthesis and deposition of ω-gliadins in wheat grown under field conditions in the UK, including temporal and spatial analyses at the protein and transcript levels. SDS-PAGE, western blotting and N-terminal amino acid sequencing were used to compare the patterns of ω-gliadin components in mature grain of six British wheat (Triticum aestivum) cultivars and their accumulation during the development of grain grown in field plots with varying nitrogen supply. Changes in gene expression during development were determined using real-time reverse transcription-PCR (RT-PCR). Spatial patterns of gene expression and protein accumulation were determined by in situ hybridization and immunofluorescence microscopy, respectively. Two patterns of ω-gliadins were identified in the six cultivars, including both monomeric 'gliadin' proteins and subunits present in polymeric 'glutenin' fractions. Increasing the level of nitrogen fertilizer in field plots resulted in increased expression of ω-gliadin transcripts and increased proportions of ω-5 gliadins. Nitrogen supply also affected the spatial patterns of ω-gliadin synthesis and deposition, which were differentially increased in the outer layers of the starchy endosperm with high levels of nitrogen. Wheat ω-gliadins vary in amount and composition between cultivars, and in their response to nitrogen supply. Their spatial distribution is also affected by nitrogen supply, being most highly concentrated in the sub-aleurone cells of the starchy endosperm under higher nitrogen availability.

Usability and potential of geostatistics for spatial discrimination of multiple sclerosis lesion patterns.

PubMed

Marschallinger, Robert; Golaszewski, Stefan M; Kunz, Alexander B; Kronbichler, Martin; Ladurner, Gunther; Hofmann, Peter; Trinka, Eugen; McCoy, Mark; Kraus, Jörg

2014-01-01

In multiple sclerosis (MS) the individual disease courses are very heterogeneous among patients and biomarkers for setting the diagnosis and the estimation of the prognosis for individual patients would be very helpful. For this purpose, we are developing a multidisciplinary method and workflow for the quantitative, spatial, and spatiotemporal analysis and characterization of MS lesion patterns from MRI with geostatistics. We worked on a small data set involving three synthetic and three real-world MS lesion patterns, covering a wide range of possible MS lesion configurations. After brain normalization, MS lesions were extracted and the resulting binary 3-dimensional models of MS lesion patterns were subject to geostatistical indicator variography in three orthogonal directions. By applying geostatistical indicator variography, we were able to describe the 3-dimensional spatial structure of MS lesion patterns in a standardized manner. Fitting a model function to the empirical variograms, spatial characteristics of the MS lesion patterns could be expressed and quantified by two parameters. An orthogonal plot of these parameters enabled a well-arranged comparison of the involved MS lesion patterns. This method in development is a promising candidate to complement standard image-based statistics by incorporating spatial quantification. The work flow is generic and not limited to analyzing MS lesion patterns. It can be completely automated for the screening of radiological archives. Copyright © 2013 by the American Society of Neuroimaging.

Evolution and inheritance of early embryonic patterning in D. simulans and D. sechellia

PubMed Central

Lott, Susan E.; Ludwig, Michael Z.; Kreitman, Martin

2010-01-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation which selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth ‘stripe allometry’) in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species D. simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the “margin of error” for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness PMID:21121913

Spatial Control of Cell Transfection Using Soluble or Solid-Phase Redox Agents and a Redox-Active Ferrocenyl Lipid

PubMed Central

Aytar, Burcu S.; Muller, John P. E.; Kondo, Yukishige; Abbott, Nicholas L.; Lynn, David M.

2013-01-01

We report principles for active, user-defined control over the locations and timing with which DNA is expressed in cells. Our approach exploits unique properties of a ferrocenyl cationic lipid that is inactive when oxidized, but active when chemically reduced. We show that methods that exert spatial control over the administration of reducing agents can lead to local activation of lipoplexes and spatial control over gene expression. The versatility of this approach is demonstrated using both soluble and solid-phase reducing agents. These methods provide control over cell transfection, including methods for remote activation and the patterning of expression using solid-phase redox agents, that are difficult to achieve using conventional lipoplexes. PMID:23965341

Spatial control of cell transfection using soluble or solid-phase redox agents and a redox-active ferrocenyl lipid.

PubMed

Aytar, Burcu S; Muller, John P E; Kondo, Yukishige; Abbott, Nicholas L; Lynn, David M

2013-09-11

We report principles for active, user-defined control over the locations and timing with which DNA is expressed in cells. Our approach exploits unique properties of a ferrocenyl cationic lipid that is inactive when oxidized, but active when chemically reduced. We show that methods that exert spatial control over the administration of reducing agents can lead to local activation of lipoplexes and spatial control over gene expression. The versatility of this approach is demonstrated using both soluble and solid-phase reducing agents. These methods provide control over cell transfection, including methods for remote activation and the patterning of expression using solid-phase redox agents, that are difficult to achieve using conventional lipoplexes.

Nodal patterning without Lefty inhibitory feedback is functional but fragile

PubMed Central

Gagnon, James A; Pauli, Andrea; Zimmerman, Steven; Aksel, Deniz C; Reyon, Deepak; Tsai, Shengdar Q; Joung, J Keith

2017-01-01

Developmental signaling pathways often activate their own inhibitors. Such inhibitory feedback has been suggested to restrict the spatial and temporal extent of signaling or mitigate signaling fluctuations, but these models are difficult to rigorously test. Here, we determine whether the ability of the mesendoderm inducer Nodal to activate its inhibitor Lefty is required for development. We find that zebrafish lefty mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality. Strikingly, development can be fully restored without feedback: Lethal patterning defects in lefty mutants can be rescued by ectopic expression of lefty far from its normal expression domain or by spatially and temporally uniform exposure to a Nodal inhibitor drug. While drug-treated mutants are less tolerant of mild perturbations to Nodal signaling levels than wild type embryos, they can develop into healthy adults. These results indicate that patterning without inhibitory feedback is functional but fragile. PMID:29215332

Multicellular regulation of entropy, spatial order, and information

NASA Astrophysics Data System (ADS)

Youk, Hyun

Many multicellular systems such as tissues and microbial biofilms consist of cells that secrete and sense signalling molecules. Understanding how collective behaviours of secrete-and-sense cells is an important challenge. We combined experimental and theoretical approaches to understand multicellular coordination of gene expression and spatial pattern formation among secrete-and-sense cells. We engineered secrete-and-sense yeast cells to show that cells can collectively and permanently remember a past event by reminding each other with their secreted signalling molecule. If one cell ``forgets'' then another cell can remind it. Cell-cell communication ensures a long-term (permanent) memory by overcoming common limitations of intracellular memory. We also established a new theoretical framework inspired by statistical mechanics to understand how fields of secrete-and-sense cells form spatial patterns. We introduce new metrics - cellular entropy, cellular Hamiltonian, and spatial order index - for dynamics of cellular automata that form spatial patterns. Our theory predicts how fast any spatial patterns form, how ordered they are, and establishes cellular Hamiltonian that, like energy for non-living systems, monotonically decreases towards a minimum over time. ERC Starting Grant (MultiCellSysBio), NWO VIDI, NWO NanoFront.

Correlated tuning of the speckle pattern in an interferometer based on a multimode fiber-optic waveguide

NASA Astrophysics Data System (ADS)

Bykovskii, Iu. A.; Kul'Chin, Iu. N.; Obukh, V. F.; Smirnov, V. L.

1990-08-01

The correlated tuning of the speckle pattern in the radiation field of a single-fiber multimode interferometer is investigated experimentally and analytically in the presence of external action. It is found that correlated changes in the speckle pattern are observed in both the near and the far emission fields of the waveguide. An expression is obtained which provides a way to determine the maximum size of the speckle correlation region. The use of spatial filtering for isolating the effect of correlated speckle pattern tuning is suggested. It is shown that the use of a spatial filter makes it possible to increase the efficiency of fiber-optic transducers.

EMAP and EMAGE: a framework for understanding spatially organized data.

PubMed

Baldock, Richard A; Bard, Jonathan B L; Burger, Albert; Burton, Nicolas; Christiansen, Jeff; Feng, Guanjie; Hill, Bill; Houghton, Derek; Kaufman, Matthew; Rao, Jianguo; Sharpe, James; Ross, Allyson; Stevenson, Peter; Venkataraman, Shanmugasundaram; Waterhouse, Andrew; Yang, Yiya; Davidson, Duncan R

2003-01-01

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

Characterization of Disease-Related Covariance Topographies with SSMPCA Toolbox: Effects of Spatial Normalization and PET Scanners

PubMed Central

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2013-01-01

In order to generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [18F]fluorodeoxyglucose PET scans from PD patients and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5 and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in PD patients imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. PMID:23671030

Characterization of disease-related covariance topographies with SSMPCA toolbox: effects of spatial normalization and PET scanners.

PubMed

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2014-05-01

To generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [(18) F]fluorodeoxyglucose PET scans from patients with PD and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5, and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in patients with PD imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. Copyright © 2013 Wiley Periodicals, Inc.

Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns.

PubMed

Norred, S Elizabeth; Caveney, Patrick M; Chauhan, Gaurav; Collier, Lauren K; Collier, C Patrick; Abel, Steven M; Simpson, Michael L

2018-05-18

Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting-the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increase in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA ("spatial noise") that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. These results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.

Optimizing information flow in small genetic networks. IV. Spatial coupling

NASA Astrophysics Data System (ADS)

Sokolowski, Thomas R.; Tkačik, Gašper

2015-06-01

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the input) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively different regulatory strategy emerges where individual cells respond to the input in a nearly steplike fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.

Spatial pattern of receptor expression in the olfactory epithelium.

PubMed Central

Nef, P; Hermans-Borgmeyer, I; Artières-Pin, H; Beasley, L; Dionne, V E; Heinemann, S F

1992-01-01

A PCR-based strategy for amplifying putative receptors involved in murine olfaction was employed to isolate a member (OR3) of the seven-transmembrane-domain receptor superfamily. During development, the first cells that express OR3 appear adjacent to the wall of the telencephalic vesicle at embryonic day 10. The OR3 receptor is uniquely expressed in a subset of olfactory cells that have a characteristic bilateral symmetry in the adult olfactory epithelium. This receptor and its specific pattern of expression may serve a functional role in odor coding or, alternatively, may play a role in the development of the olfactory system. Images PMID:1384038

Two cis elements collaborate to spatially repress transcription from a sea urchin promoter

NASA Technical Reports Server (NTRS)

Frudakis, T. N.; Wilt, F.

1995-01-01

The expression pattern of many territory-specific genes in metazoan embryos is maintained by an active process of negative spatial regulation. However, the mechanism of this strategy of gene regulation is not well understood in any system. Here we show that reporter constructs containing regulatory sequence for the SM30-alpha gene of Stronglyocentrotus purpuratus are expressed in a pattern congruent with that of the endogenous SM30 gene(s), largely as a result of active transcriptional repression in cell lineages in which the gene is not normally expressed. Chloramphenicol acetyl transferase assays of deletion constructs from the 2600-bp upstream region showed that repressive elements were present in the region from -1628 to -300. In situ hybridization analysis showed that the spatial fidelity of expression was severely compromised when the region from -1628 to -300 was deleted. Two highly repetitive sequence motifs, (G/A/C)CCCCT and (T/C)(T/A/C)CTTTT(T/A/C), are present in the -1628 to -300 region. Representatives of these elements were analyzed by gel mobility shift experiments and were found to interact specifically with protein in crude nuclear extracts. When oligonucleotides containing either sequence element were co-injected with a correctly regulated reporter as potential competitors, the reporter was expressed in inappropriate cells. When composite oligonucleotides, containing both sequence elements, were fused to a misregulated reporter, the expression of the reporter in inappropriate cells was suppressed. Comparison of composite oligonucleotides with oligonucleotides containing single constituent elements show that both sequence elements are required for effective spatial regulation. Thus, both individual elements are required, but only a composite element containing both elements is sufficient to function as a tissue-specific repressive element.

Cell-type- and tissue-specific transcriptomes of the white spruce (Picea glauca) bark unmask fine-scale spatial patterns of constitutive and induced conifer defense.

PubMed

Celedon, Jose M; Yuen, Macaire M S; Chiang, Angela; Henderson, Hannah; Reid, Karen E; Bohlmann, Jörg

2017-11-01

Plant defenses often involve specialized cells and tissues. In conifers, specialized cells of the bark are important for defense against insects and pathogens. Using laser microdissection, we characterized the transcriptomes of cortical resin duct cells, phenolic cells and phloem of white spruce (Picea glauca) bark under constitutive and methyl jasmonate (MeJa)-induced conditions, and we compared these transcriptomes with the transcriptome of the bark tissue complex. Overall, ~3700 bark transcripts were differentially expressed in response to MeJa. Approximately 25% of transcripts were expressed in only one cell type, revealing cell specialization at the transcriptome level. MeJa caused cell-type-specific transcriptome responses and changed the overall patterns of cell-type-specific transcript accumulation. Comparison of transcriptomes of the conifer bark tissue complex and specialized cells resolved a masking effect inherent to transcriptome analysis of complex tissues, and showed the actual cell-type-specific transcriptome signatures. Characterization of cell-type-specific transcriptomes is critical to reveal the dynamic patterns of spatial and temporal display of constitutive and induced defense systems in a complex plant tissue or organ. This was demonstrated with the improved resolution of spatially restricted expression of sets of genes of secondary metabolism in the specialized cell types. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Honey Bee Aggression Supports a Link Between Gene Regulation and Behavioral Evolution

USDA-ARS?s Scientific Manuscript database

A prominent theory holds that animal phenotypes arise by evolutionary changes in the regulation of gene expression. Emerging from studies of animal development, evidence for this theory consists largely of differences in temporal or spatial patterns of gene expression that are related to morphologi...

New insights into roles of cell wall invertase in early seed development revealed by comprehensive spatial and temporal expression patterns of GhCWIN1 in cotton.

PubMed

Wang, Lu; Ruan, Yong-Ling

2012-10-01

Despite substantial evidence on the essential roles of cell wall invertase (CWIN) in seed filling, it remains largely unknown how CWIN exerts its regulation early in seed development, a critical stage that sets yield potential. To fill this knowledge gap, we systematically examined the spatial and temporal expression patterns of a major CWIN gene, GhCWIN1, in cotton (Gossypium hirsutum) seeds from prefertilization to prestorage phase. GhCWIN1 messenger RNA was abundant at the innermost seed coat cell layer at 5 d after anthesis but became undetectable at 10 d after anthesis, at the onset of its differentiation into transfer cells characterized by wall ingrowths, suggesting that CWIN may negatively regulate transfer cell differentiation. Within the filial tissues, GhCWIN1 transcript was detected in endosperm cells undergoing nuclear division but not in those cells at the cellularization stage, with similar results observed in Arabidopsis (Arabidopsis thaliana) endosperm for CWIN, AtCWIN4. These findings indicate a function of CWIN in nuclear division but not cell wall biosynthesis in endosperm, contrasting to the role proposed for sucrose synthase (Sus). Further analyses revealed a preferential expression pattern of GhCWIN1 and AtCWIN4 in the provascular region of the torpedo embryos in cotton and Arabidopsis seed, respectively, indicating a role of CWIN in vascular initiation. Together, these novel findings provide insights into the roles of CWIN in regulating early seed development spatially and temporally. By comparing with previous studies on Sus expression and in conjunction with the expression of other related genes, we propose models of CWIN- and Sus-mediated regulation of early seed development.

Evolution and inheritance of early embryonic patterning in Drosophila simulans and D. sechellia.

PubMed

Lott, Susan E; Ludwig, Michael Z; Kreitman, Martin

2011-05-01

Pattern formation in Drosophila is a widely studied example of a robust developmental system. Such robust systems pose a challenge to adaptive evolution, as they mask variation that selection may otherwise act upon. Yet we find variation in the localization of expression domains (henceforth "stripe allometry") in the pattern formation pathway. Specifically, we characterize differences in the gap genes giant and Kruppel, and the pair-rule gene even-skipped, which differ between the sibling species Drosophila simulans and D. sechellia. In a double-backcross experiment, stripe allometry is consistent with maternal inheritance of stripe positioning and multiple genetic factors, with a distinct genetic basis from embryo length. Embryos produced by F1 and F2 backcross mothers exhibit novel spatial patterns of gene expression relative to the parental species, with no measurable increase in positional variance among individuals. Buffering of novel spatial patterns in the backcross genotypes suggests that robustness need not be disrupted in order for the trait to evolve, and perhaps the system is incapable of evolving to prevent the expression of all genetic variation. This limitation, and the ability of natural selection to act on minute genetic differences that are within the "margin of error" for the buffering mechanism, indicates that developmentally buffered traits can evolve without disruption of robustness. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Three urocortins in medaka: identification and spatial expression in the central nervous system.

PubMed

Hosono, K; Yamashita, J; Kikuchi, Y; Hiraki-Kajiyama, T; Okubo, K

2017-05-01

The urocortin (UCN) group of neuropeptides includes urocortin 1/sauvagine/urotensin 1 (UTS1), urocortin 2 (UCN2) and urocortin 3 (UCN3). In recent years, evidence has accumulated showing that UCNs play pivotal roles in mediating stress response and anxiety in mammals. Evidence has also emerged regarding the evolutionary conservation of UCNs in vertebrates, but very little information is available about UCNs in non-mammalian vertebrates. Indeed, at present, there are no reports of the empirical identification of ucn2 in non-mammalian vertebrates or of the distribution of ucn2 and ucn3 expression in the adult central nervous system (CNS) of these animals. To gain insight into the evolutionary nature of UCNs in vertebrates, we cloned uts1, ucn2 and ucn3 in a teleost fish, medaka and examined the spatial expression of these genes in the adult brain and spinal cord. Although all known UCN2 genes except those in rodents have been reported to likely lack the necessary structural features to produce a functional pre-pro-protein, all three UCN genes in medaka, including ucn2, displayed all of these features, suggesting their functionality. The three UCN genes exhibited distinct spatial expression patterns in the medaka brain: uts1 was primarily expressed in broad regions of the dorsal telencephalon, ucn2 was expressed in restricted regions of the thalamus and brainstem and ucn3 was expressed in discrete nuclei throughout many regions of the brain. We also found that these genes were all expressed throughout the medaka spinal cord, each with a distinct spatial pattern. Given that many of these regions have been implicated in stress responses and anxiety, the three UCNs may serve distinct physiological roles in the medaka CNS, including those involved in stress and anxiety, as shown in the mammalian CNS. © 2017 British Society for Neuroendocrinology.

A simulation study of hardwood rootstock populations in young loblolly pine plantations

Treesearch

David R. Weise; Glenn R. Glover

1988-01-01

A computer program to simulate spatial distribution of hardwood rootstock populations is presented. Nineteen 3 to 6 yearold loblolly pine (Pinus taeda L.) plantations in Alabama and Georgia were measured to provide information for the simulator. Spatial pattern, expressed as Pielou's nonrandomness index (PNI), ranged from 0.47 to 2.45. Scatterplots illustrated no...

Spatial distributions of Kv4 channels and KChip2 isoforms in the murine heart based on laser capture microdissection.

PubMed

Teutsch, Christine; Kondo, Richard P; Dederko, Dorothy A; Chrast, Jacqueline; Chien, Kenneth R; Giles, Wayne R

2007-03-01

Regional differences in repolarizing K(+) current densities and expression levels of their molecular components are important for coordinating the pattern of electrical excitation and repolarization of the heart. The small size of hearts from mice may obscure these interventricular and/or transmural expression differences of K(+) channels. We have examined this possibility in adult mouse ventricle using a technology that provides very high spatial resolution of tissue collection. Conventional manual dissection and laser capture microdissection (LCM) were utilized to dissect tissue from distinct ventricular regions. RNA was isolated from epicardial, mid-myocardial and endocardial layers of both the right and left ventricles. Real-time RT-PCR was used to quantify the transcript expression in these different regions. LCM revealed significant interventricular and transmural gradients for both Kv4.2 and the alpha-subunit of KChIP2. The expression profile of a second K(+) channel transcript, Kir2.1, which is responsible for the inwardly rectifying K(+) current I(k1), showed no interventricular or transmural gradients and therefore served as a negative control. Our findings are in contrast to previous reports of a relatively uniform left ventricular transmural pattern of expression of Kv4.2, Kv4.3 and KChIP2 in adult mouse heart, which appear to be different than that in larger mammals. Specifically, our results demonstrate significant epi- to endocardial differences in the patterns of expression of both Kv4.2 and KChIP2.

Differential expression pattern of UBX family genes in Caenorhabditis elegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamauchi, Seiji; Sasagawa, Yohei; Ogura, Teru

2007-06-29

UBX (ubiquitin regulatory X)-containing proteins belong to an evolutionary conserved protein family and determine the specificity of p97/VCP/Cdc48p function by binding as its adaptors. Caenorhabditis elegans was found to possess six UBX-containing proteins, named UBXN-1 to -6. However, no general or specific function of them has been revealed. During the course of understanding not only their function but also specified function of p97, we investigated spatial and temporal expression patterns of six ubxn genes in this study. Transcript analyses showed that the expression pattern of each ubxn gene was different throughout worm's development and may show potential developmental dynamics inmore » their function, especially ubxn-5 was expressed specifically in the spermatogenic germline, suggesting a crucial role in spermatogenesis. In addition, as ubxn-4 expression was induced by ER stress, it would function as an ERAD factor in C. elegans. In vivo expression analysis by using GFP translational fusion constructs revealed that six ubxn genes show distinct expression patterns. These results altogether demonstrate that the expression of all six ubxn genes of C. elegans is differently regulated.« less

The spatial and temporal expression of Ch-en, the engrailed gene in the polychaete Chaetopterus, does not support a role in body axis segmentation

NASA Technical Reports Server (NTRS)

Seaver, E. C.; Paulson, D. A.; Irvine, S. Q.; Martindale, M. Q.

2001-01-01

We are interested in understanding whether the annelids and arthropods shared a common segmented ancestor and have approached this question by characterizing the expression pattern of the segment polarity gene engrailed (en) in a basal annelid, the polychaete Chaetopterus. We have isolated an en gene, Ch-en, from a Chaetopterus cDNA library. Genomic Southern blotting suggests that this is the only en class gene in this animal. The predicted protein sequence of the 1.2-kb cDNA clone contains all five domains characteristic of en proteins in other taxa, including the en class homeobox. Whole-mount in situ hybridization reveals that Ch-en is expressed throughout larval life in a complex spatial and temporal pattern. The Ch-en transcript is initially detected in a small number of neurons associated with the apical organ and in the posterior portion of the prototrochophore. At later stages, Ch-en is expressed in distinct patterns in the three segmented body regions (A, B, and C) of Chaetopterus. In all segments, Ch-en is expressed in a small set of segmentally iterated cells in the CNS. In the A region, Ch-en is also expressed in a small group of mesodermal cells at the base of the chaetal sacs. In the B region, Ch-en is initially expressed broadly in the mesoderm that then resolves into one band/segment coincident with morphological segmentation. The mesodermal expression in the B region is located in the anterior region of each segment, as defined by the position of ganglia in the ventral nerve cord, and is involved in the morphogenesis of segment-specific feeding structures late in larval life. We observe banded mesodermal and ectodermal staining in an anterior-posterior sequence in the C region. We do not observe a segment polarity pattern of expression of Ch-en in the ectoderm, as is observed in arthropods. Copyright 2001 Academic Press.

Competition between anthocyanin and flavonol biosynthesis produces spatial pattern variation of floral pigments between Mimulus species

PubMed Central

Yuan, Yao-Wu; Rebocho, Alexandra B.; Sagawa, Janelle M.; Stanley, Lauren E.; Bradshaw, Harvey D.

2016-01-01

Flower color patterns have long served as a model for developmental genetics because pigment phenotypes are visually striking, yet generally not required for plant viability, facilitating the genetic analysis of color and pattern mutants. The evolution of novel flower colors and patterns has played a key role in the adaptive radiation of flowering plants via their specialized interactions with different pollinator guilds (e.g., bees, butterflies, birds), motivating the search for allelic differences affecting flower color pattern in closely related plant species with different pollinators. We have identified LIGHT AREAS1 (LAR1), encoding an R2R3-MYB transcription factor, as the causal gene underlying the spatial pattern variation of floral anthocyanin pigmentation between two sister species of monkeyflower: the bumblebee-pollinated Mimulus lewisii and the hummingbird-pollinated Mimulus cardinalis. We demonstrated that LAR1 positively regulates FLAVONOL SYNTHASE (FLS), essentially eliminating anthocyanin biosynthesis in the white region (i.e., light areas) around the corolla throat of M. lewisii flowers by diverting dihydroflavonol into flavonol biosynthesis from the anthocyanin pigment pathway. FLS is preferentially expressed in the light areas of the M. lewisii flower, thus prepatterning the corolla. LAR1 expression in M. cardinalis flowers is much lower than in M. lewisii, explaining the unpatterned phenotype and recessive inheritance of the M. cardinalis allele. Furthermore, our gene-expression analysis and genetic mapping results suggest that cis-regulatory change at the LAR1 gene played a critical role in the evolution of different pigmentation patterns between the two species. PMID:26884205

Competition between anthocyanin and flavonol biosynthesis produces spatial pattern variation of floral pigments between Mimulus species.

PubMed

Yuan, Yao-Wu; Rebocho, Alexandra B; Sagawa, Janelle M; Stanley, Lauren E; Bradshaw, Harvey D

2016-03-01

Flower color patterns have long served as a model for developmental genetics because pigment phenotypes are visually striking, yet generally not required for plant viability, facilitating the genetic analysis of color and pattern mutants. The evolution of novel flower colors and patterns has played a key role in the adaptive radiation of flowering plants via their specialized interactions with different pollinator guilds (e.g., bees, butterflies, birds), motivating the search for allelic differences affecting flower color pattern in closely related plant species with different pollinators. We have identified LIGHT AREAS1 (LAR1), encoding an R2R3-MYB transcription factor, as the causal gene underlying the spatial pattern variation of floral anthocyanin pigmentation between two sister species of monkeyflower: the bumblebee-pollinated Mimulus lewisii and the hummingbird-pollinated Mimulus cardinalis. We demonstrated that LAR1 positively regulates FLAVONOL SYNTHASE (FLS), essentially eliminating anthocyanin biosynthesis in the white region (i.e., light areas) around the corolla throat of M. lewisii flowers by diverting dihydroflavonol into flavonol biosynthesis from the anthocyanin pigment pathway. FLS is preferentially expressed in the light areas of the M. lewisii flower, thus prepatterning the corolla. LAR1 expression in M. cardinalis flowers is much lower than in M. lewisii, explaining the unpatterned phenotype and recessive inheritance of the M. cardinalis allele. Furthermore, our gene-expression analysis and genetic mapping results suggest that cis-regulatory change at the LAR1 gene played a critical role in the evolution of different pigmentation patterns between the two species.

Happiness and the patterns of life: a study of geolocated tweets.

PubMed

Frank, Morgan R; Mitchell, Lewis; Dodds, Peter Sheridan; Danforth, Christopher M

2013-01-01

The patterns of life exhibited by large populations have been described and modeled both as a basic science exercise and for a range of applied goals such as reducing automotive congestion, improving disaster response, and even predicting the location of individuals. However, these studies have had limited access to conversation content, rendering changes in expression as a function of movement invisible. In addition, they typically use the communication between a mobile phone and its nearest antenna tower to infer position, limiting the spatial resolution of the data to the geographical region serviced by each cellphone tower. We use a collection of 37 million geolocated tweets to characterize the movement patterns of 180,000 individuals, taking advantage of several orders of magnitude of increased spatial accuracy relative to previous work. Employing the recently developed sentiment analysis instrument known as the hedonometer, we characterize changes in word usage as a function of movement, and find that expressed happiness increases logarithmically with distance from an individual's average location.

Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns

DOE PAGES

Norred, Sarah Elizabeth; Caveney, Patrick M.; Chauhan, Gaurav; ...

2018-04-24

Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting—the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increasemore » in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA (“spatial noise”) that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. Furthermore, these results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.« less

Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norred, Sarah Elizabeth; Caveney, Patrick M.; Chauhan, Gaurav

Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting—the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increasemore » in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA (“spatial noise”) that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. Furthermore, these results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.« less

Microenvironments engineered by inkjet bioprinting spatially direct adult stem cells toward muscle- and bone-like subpopulations.

PubMed

Phillippi, Julie A; Miller, Eric; Weiss, Lee; Huard, Johnny; Waggoner, Alan; Campbell, Phil

2008-01-01

In vivo, growth factors exist both as soluble and as solid-phase molecules, immobilized to cell surfaces and within the extracellular matrix. We used this rationale to develop more biologically relevant approaches to study stem cell behaviors. We engineered stem cell microenvironments using inkjet bioprinting technology to create spatially defined patterns of immobilized growth factors. Using this approach, we engineered cell fate toward the osteogenic lineage in register to printed patterns of bone morphogenetic protein (BMP) 2 contained within a population of primary muscle-derived stem cells (MDSCs) isolated from adult mice. This patterning approach was conducive to patterning the MDSCs into subpopulations of osteogenic or myogenic cells simultaneously on the same chip. When cells were cultured under myogenic conditions on BMP-2 patterns, cells on pattern differentiated toward the osteogenic lineage, whereas cells off pattern differentiated toward the myogenic lineage. Time-lapse microscopy was used to visualize the formation of multinucleated myotubes, and immunocytochemistry was used to demonstrate expression of myosin heavy chain (fast) in cells off BMP-2 pattern. This work provides proof-of-concept for engineering spatially controlled multilineage differentiation of stem cells using patterns of immobilized growth factors. This approach may be useful for understanding cell behaviors to immobilized biological patterns and could have potential applications for regenerative medicine.

Three members of the iodothyronine deiodinase family, dio1, dio2 and dio3, are expressed in spatially and temporally specific patterns during metamorphosis of the flounder, Paralichthys olivaceus.

PubMed

Itoh, Kae; Watanabe, Kohei; Wu, Xiaoming; Suzuki, Tohru

2010-07-01

Flounder metamorphosis, marked by eye migration, lateralized pigmentation, and tissue differentiation in the stomach and skeletal muscle, is stimulated by thyroid hormone (TH). It is known that tri-iodothyronine (T3) produced by iodothyronine deiodinase type-1 (Dio1) from thyroxine (T4) enters the blood, whereas T3 produced by Dio2 penetrates into the nucleus of the Dio2-expressing cells, and then Dio3 inactivates both T4 and T3. To better understand the distinct functions of these three deiodinases in T3 regulation during flounder metamorphosis, we examined the tissue expression patterns of dio1, dio2, and dio3 in larvae of the Japanese flounder, Paralichthys olivaceus, by section in situ hybridization (SISH). We found that each deiodinase is expressed in a spatially and temporally specific pattern. dio1 is expressed in liver parenchymal cells from pro-metamorphosis to early climax, while dio2 is expressed in limited regions of the eyes, tectum, and skeletal muscles from pro-metamorphosis to post-climax. Considering these findings together with reports on other vertebrates, we predict that the liver cells expressing dio1 supply T3 to the blood, and that this systemic T3 synchronizes metamorphosis of differentiating tissues throughout the larval body, whereas the eyes, tectum, and skeletal muscles autonomously produce additional T3 for local tissue differentiation. Finally, dio3 expression is detected in skeletal muscle and gastric gland blastemas, which both undergo marked tissue differentiation at metamorphic climax. We hypothesize that dio3 expression protects these tissues from basal T3 levels early in metamorphosis, ensuring, together with the T3 surge from the liver, the synchronization of tissue differentiation at metamorphic climax.

Gene expression in spider appendages reveals reversal of exd/hth spatial specificity, altered leg gap gene dynamics, and suggests divergent distal morphogen signaling.

PubMed

Prpic, Nikola-Michael; Janssen, Ralf; Wigand, Barbara; Klingler, Martin; Damen, Wim G M

2003-12-01

Leg development in Drosophila has been studied in much detail. However, Drosophila limbs form in the larva as imaginal discs and not during embryogenesis as in most other arthropods. Here, we analyze appendage genes in the spider Cupiennius salei and the beetle Tribolium castaneum. Differences in decapentaplegic (dpp) expression suggest a different mode of distal morphogen signaling suitable for the specific geometry of growing limb buds. Also, expression of the proximal genes homothorax (hth) and extradenticle (exd) is significantly altered: in the spider, exd is restricted to the proximal leg and hth expression extends distally, while in insects, exd is expressed in the entire leg and hth is restricted to proximal parts. This reversal of spatial specificity demonstrates an evolutionary shift, which is nevertheless compatible with a conserved role of this gene pair as instructor of proximal fate. Different expression dynamics of dachshund and Distal-less point to modifications in the regulation of the leg gap gene system. We comment on the significance of this finding for attempts to homologize leg segments in different arthropod classes. Comparison of the expression profiles of H15 and optomotor-blind to the Drosophila patterns suggests modifications also in the dorsal-ventral patterning system of the legs. Together, our results suggest alterations in many components of the leg developmental system, namely proximal-distal and dorsal-ventral patterning, and leg segmentation. Thus, the leg developmental system exhibits a propensity to evolutionary change, which probably forms the basis for the impressive diversity of arthropod leg morphologies.

b-FGF induces corneal blood and lymphatic vessel growth in a spatially distinct pattern.

PubMed

Hajrasouliha, Amir R; Sadrai, Zahra; Chauhan, Sunil K; Dana, Reza

2012-07-01

To study the spatial variances in ligand expression and angiogenic effect in response to the inflammatory response induced by basic fibroblast growth factor (b-FGF). b-FGF micropellets (80 ng) were implanted in the temporal side of the cornea of Balb/c mice. On days 1, 3, and 7, blood (heme-) and lymphangiogenesis were observed by immunofluorescence staining of corneal flat mounts with LYVE-1 and CD31 to identify lymphatic and blood vessels, respectively. A second group of corneas were harvested for quantitative real-time polymerase chain reaction. Each cornea was divided into 2 different areas: (1) pre-pellet area and (2) opposite-pellet area. Expression of vascular endothelial growth factor (VEGF) ligands was evaluated using real-time polymerase chain reaction in each respective zone. Blood vessels grew into the cornea from the pre-pellet area, whereas corneal lymphatic vessels grew from the opposite-pellet area toward the center of the cornea. VEGF-A was upregulated in the pre-pellet, whereas VEGF-D expression was mostly observed in the opposite-pellet area. VEGF-C level increased simultaneously in both areas. A single inducing factor, that is, b-FGF, may simultaneously provoke hemangiogenesis and lymphangiogenesis in different locations of the cornea through differential expression of VEGF ligands. This distinctive spatial pattern should be considered while evaluating the corneal predilection for inflammation beyond that which is directly visible by slit lamp examination.

The landscape context of forest and grassland in the United States

Treesearch

Kurt H. Riitters

2011-01-01

As development introduces competing land uses into forest and grassland landscapes, the public expresses concern for landscape patterns through headline issues such as urban sprawl and fragmentation. Resource managers need a deeper understanding of the causes and consequences of landscape patterns to know if, where, and how to take any needed actions. The spatial...

Spatiotemporal pattern in somitogenesis: a non-Turing scenario with wave propagation.

PubMed

Nagahara, Hiroki; Ma, Yue; Takenaka, Yoshiko; Kageyama, Ryoichiro; Yoshikawa, Kenichi

2009-08-01

Living organisms maintain their lives under far-from-equilibrium conditions by creating a rich variety of spatiotemporal structures in a self-organized manner, such as temporal rhythms, switching phenomena, and development of the body. In this paper, we focus on the dynamical process of morphogens in somitogenesis in mice where propagation of the gene expression level plays an essential role in creating the spatially periodic patterns of the vertebral columns. We present a simple discrete reaction-diffusion model which includes neighboring interaction through an activator, but not diffusion of an inhibitor. We can produce stationary periodic patterns by introducing the effect of spatial discreteness to the field. Based on the present model, we discuss the underlying physical principles that are independent of the details of biomolecular reactions. We also discuss the framework of spatial discreteness based on the reaction-diffusion model in relation to a cellular array, by comparison with an actual experimental observation.

Zic3 is required in the migrating primitive streak for node morphogenesis and left–right patterning

PubMed Central

Sutherland, Mardi J.; Wang, Shuyun; Quinn, Malgorzata E.; Haaning, Allison; Ware, Stephanie M.

2013-01-01

In humans, loss-of-function mutations in ZIC3 cause isolated cardiovascular malformations and X-linked heterotaxy, a disorder with abnormal left–right asymmetry of organs. Zic3 null mice recapitulate the human heterotaxy phenotype but also have early gastrulation defects, axial patterning defects and neural tube defects complicating an assessment of the role of Zic3 in cardiac development. Zic3 is expressed ubiquitously during critical stages of left–right patterning but its later expression in the developing heart remains controversial and the molecular mechanism(s) by which it causes heterotaxy are unknown. To define the temporal and spatial requirements, for Zic3 in left–right patterning, we generated conditional Zic3 mice and Zic3-LacZ-BAC reporter mice. The latter provide compelling evidence that Zic3 is expressed in the mouse node and absent in the heart. Conditional deletion using T-Cre identifies a requirement for Zic3 in the primitive streak and migrating mesoderm for proper left–right patterning and cardiac development. In contrast, Zic3 is not required in heart progenitors or the cardiac compartment. In addition, the data demonstrate abnormal node morphogenesis in Zic3 null mice and identify similar node dysplasia when Zic3 was specifically deleted from the migrating mesoderm and primitive streak. These results define the temporal and spatial requirements for Zic3 in node morphogenesis, left–right patterning and cardiac development and suggest the possibility that a requirement for Zic3 in node ultrastructure underlies its role in heterotaxy and laterality disorders. PMID:23303524

Mono-2-ethylhexyl phthalate disrupts neurulation and modifies the embryonic redox environment and gene expression

PubMed Central

Sant, Karilyn E.; Dolinoy, Dana C.; Jilek, Joseph L.; Sartor, Maureen A.; Harris, Craig

2016-01-01

Mono-2-ethylhexl phthalate (MEHP) is the primary metabolite of di-2-ethylhexyl phthalate (DEHP), a ubiquitous contaminant in plastics. This study sought to determine how structural defects caused by MEHP in mouse whole embryo culture were related to temporal and spatial patterns of redox state and gene expression. MEHP reduced morphology scores along with increased incidence of neural tube defects. Glutathione (GSH) and cysteine (Cys) concentrations fluctuated spatially and temporally in embryo (EMB) and visceral yolk sac (VYS) across the 24h culture. Redox potentials (Eh) for GSSG/GSH were increased by MEHP in EMB (12h) but not in VYS. CySS/CyS Eh in EMB and VYS were significantly increased at 3h and 24h, respectively. Gene expression at 6h showed that MEHP induced selective alterations in EMB and VYS for oxidative phosphorylation and energy metabolism pathways. Overall, MEHP affects neurulation, alters Eh, and spatially alters the expression of metabolic genes in the early organogenesis-stage mouse conceptus. PMID:27167697

Solving Large-scale Spatial Optimization Problems in Water Resources Management through Spatial Evolutionary Algorithms

NASA Astrophysics Data System (ADS)

Wang, J.; Cai, X.

2007-12-01

A water resources system can be defined as a large-scale spatial system, within which distributed ecological system interacts with the stream network and ground water system. Water resources management, the causative factors and hence the solutions to be developed have a significant spatial dimension. This motivates a modeling analysis of water resources management within a spatial analytical framework, where data is usually geo- referenced and in the form of a map. One of the important functions of Geographic information systems (GIS) is to identify spatial patterns of environmental variables. The role of spatial patterns in water resources management has been well established in the literature particularly regarding how to design better spatial patterns for satisfying the designated objectives of water resources management. Evolutionary algorithms (EA) have been demonstrated to be successful in solving complex optimization models for water resources management due to its flexibility to incorporate complex simulation models in the optimal search procedure. The idea of combining GIS and EA motivates the development and application of spatial evolutionary algorithms (SEA). SEA assimilates spatial information into EA, and even changes the representation and operators of EA. In an EA used for water resources management, the mathematical optimization model should be modified to account the spatial patterns; however, spatial patterns are usually implicit, and it is difficult to impose appropriate patterns to spatial data. Also it is difficult to express complex spatial patterns by explicit constraints included in the EA. The GIS can help identify the spatial linkages and correlations based on the spatial knowledge of the problem. These linkages are incorporated in the fitness function for the preference of the compatible vegetation distribution. Unlike a regular GA for spatial models, the SEA employs a special hierarchical hyper-population and spatial genetic operators to represent spatial variables in a more efficient way. The hyper-population consists of a set of populations, which correspond to the spatial distributions of the individual agents (organisms). Furthermore spatial crossover and mutation operators are designed in accordance with the tree representation and then applied to both organisms and populations. This study applies the SEA to a specific problem of water resources management- maximizing the riparian vegetation coverage in accordance with the distributed groundwater system in an arid region. The vegetation coverage is impacted greatly by the nonlinear feedbacks and interactions between vegetation and groundwater and the spatial variability of groundwater. The SEA is applied to search for an optimal vegetation configuration compatible to the groundwater flow. The results from this example demonstrate the effectiveness of the SEA. Extension of the algorithm for other water resources management problems is discussed.

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development.

PubMed

Johansson, Martin M; Lundin, Elin; Qian, Xiaoyan; Mirzazadeh, Mohammadreza; Halvardson, Jonatan; Darj, Elisabeth; Feuk, Lars; Nilsson, Mats; Jazin, Elena

2016-01-01

Renewed attention has been directed to the functions of the Y chromosome in the central nervous system during early human male development, due to the recent proposed involvement in neurodevelopmental diseases. PCDH11Y and NLGN4Y are of special interest because they belong to gene families involved in cell fate determination and formation of dendrites and axon. We used RNA sequencing, immunocytochemistry and a padlock probing and rolling circle amplification strategy, to distinguish the expression of X and Y homologs in situ in the human brain for the first time. To minimize influence of androgens on the sex differences in the brain, we focused our investigation to human embryos at 8-11 weeks post-gestation. We found that the X- and Y-encoded genes are expressed in specific and heterogeneous cellular sub-populations of both glial and neuronal origins. More importantly, we found differential distribution patterns of X and Y homologs in the male developing central nervous system. This study has visualized the spatial distribution of PCDH11X/Y and NLGN4X/Y in human developing nervous tissue. The observed spatial distribution patterns suggest the existence of an additional layer of complexity in the development of the male CNS.

A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas

PubMed Central

Davis, Fred P.; Eddy, Sean R.

2009-01-01

Motivation: Gene expression patterns can be useful in understanding the structural organization of the brain and the regulatory logic that governs its myriad cell types. A particularly rich source of spatial expression data is the Allen Brain Atlas (ABA), a comprehensive genome-wide in situ hybridization study of the adult mouse brain. Here, we present an open-source program, ALLENMINER, that searches the ABA for genes that are expressed, enriched, patterned or graded in a user-specified region of interest. Results: Regionally enriched genes identified by ALLENMINER accurately reflect the in situ data (95–99% concordance with manual curation) and compare with regional microarray studies as expected from previous comparisons (61–80% concordance). We demonstrate the utility of ALLENMINER by identifying genes that exhibit patterned expression in the caudoputamen and neocortex. We discuss general characteristics of gene expression in the mouse brain and the potential application of ALLENMINER to design strategies for specific genetic access to brain regions and cell types. Availability: ALLENMINER is freely available on the Internet at http://research.janelia.org/davis/allenminer. Contact: davisf@janelia.hhmi.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19414530

Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

PubMed Central

Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

2013-01-01

The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

Spatially Restricted and Developmentally Dynamic Expression of Engrailed Genes in Multiple Cerebellar Cell Types

PubMed Central

Wilson, Sandra L.; Kalinovsky, Anna; Orvis, Grant D.

2011-01-01

The cerebellum is a highly organized structure partitioned into lobules along the anterior–posterior (A-P) axis and into striped molecular domains along the medial–lateral (M-L) axis. The Engrailed (En) homeobox genes are required for patterning the morphological and molecular domains along both axes, as well as for the establishment of the normal afferent topography required to generate a fully functional cerebellum. As a means to understand how the En genes regulate multiple levels of cerebellum construction, we characterized En1 and En2 expression around birth and at postnatal day (P)21 during the period when the cerebellum undergoes a remarkable transformation from a smooth ovoid structure to a highly foliated structure. We show that both En1 and En2 are expressed in many neuronal cell types in the cerebellum, and expression persists until at least P21. En1 and En2 expression, however, undergoes profound changes in their cellular and spatial distributions between embryonic stages and P21, and their expression domains become largely distinct. Comparison of the distribution of En-expressing Purkinje cells relative to early- and late-onset Purkinje cell M-L stripe proteins revealed that although En1- and En2-expressing Purkinje cell domains do not strictly align with those of ZEBRINII at P21, a clear pattern exists that is most evident at E17.5 by an inverse correlation between the level of En2 expression and PLCβ4 and EPHA4. PMID:21431469

An optimized ERP brain-computer interface based on facial expression changes.

PubMed

Jin, Jing; Daly, Ian; Zhang, Yu; Wang, Xingyu; Cichocki, Andrzej

2014-06-01

Interferences from spatially adjacent non-target stimuli are known to evoke event-related potentials (ERPs) during non-target flashes and, therefore, lead to false positives. This phenomenon was commonly seen in visual attention-based brain-computer interfaces (BCIs) using conspicuous stimuli and is known to adversely affect the performance of BCI systems. Although users try to focus on the target stimulus, they cannot help but be affected by conspicuous changes of the stimuli (such as flashes or presenting images) which were adjacent to the target stimulus. Furthermore, subjects have reported that conspicuous stimuli made them tired and annoyed. In view of this, the aim of this study was to reduce adjacent interference, annoyance and fatigue using a new stimulus presentation pattern based upon facial expression changes. Our goal was not to design a new pattern which could evoke larger ERPs than the face pattern, but to design a new pattern which could reduce adjacent interference, annoyance and fatigue, and evoke ERPs as good as those observed during the face pattern. Positive facial expressions could be changed to negative facial expressions by minor changes to the original facial image. Although the changes are minor, the contrast is big enough to evoke strong ERPs. In this paper, a facial expression change pattern between positive and negative facial expressions was used to attempt to minimize interference effects. This was compared against two different conditions, a shuffled pattern containing the same shapes and colours as the facial expression change pattern, but without the semantic content associated with a change in expression, and a face versus no face pattern. Comparisons were made in terms of classification accuracy and information transfer rate as well as user supplied subjective measures. The results showed that interferences from adjacent stimuli, annoyance and the fatigue experienced by the subjects could be reduced significantly (p < 0.05) by using the facial expression change patterns in comparison with the face pattern. The offline results show that the classification accuracy of the facial expression change pattern was significantly better than that of the shuffled pattern (p < 0.05) and the face pattern (p < 0.05). The facial expression change pattern presented in this paper reduced interference from adjacent stimuli and decreased the fatigue and annoyance experienced by BCI users significantly (p < 0.05) compared to the face pattern.

An optimized ERP brain-computer interface based on facial expression changes

NASA Astrophysics Data System (ADS)

Jin, Jing; Daly, Ian; Zhang, Yu; Wang, Xingyu; Cichocki, Andrzej

2014-06-01

Objective. Interferences from spatially adjacent non-target stimuli are known to evoke event-related potentials (ERPs) during non-target flashes and, therefore, lead to false positives. This phenomenon was commonly seen in visual attention-based brain-computer interfaces (BCIs) using conspicuous stimuli and is known to adversely affect the performance of BCI systems. Although users try to focus on the target stimulus, they cannot help but be affected by conspicuous changes of the stimuli (such as flashes or presenting images) which were adjacent to the target stimulus. Furthermore, subjects have reported that conspicuous stimuli made them tired and annoyed. In view of this, the aim of this study was to reduce adjacent interference, annoyance and fatigue using a new stimulus presentation pattern based upon facial expression changes. Our goal was not to design a new pattern which could evoke larger ERPs than the face pattern, but to design a new pattern which could reduce adjacent interference, annoyance and fatigue, and evoke ERPs as good as those observed during the face pattern. Approach. Positive facial expressions could be changed to negative facial expressions by minor changes to the original facial image. Although the changes are minor, the contrast is big enough to evoke strong ERPs. In this paper, a facial expression change pattern between positive and negative facial expressions was used to attempt to minimize interference effects. This was compared against two different conditions, a shuffled pattern containing the same shapes and colours as the facial expression change pattern, but without the semantic content associated with a change in expression, and a face versus no face pattern. Comparisons were made in terms of classification accuracy and information transfer rate as well as user supplied subjective measures. Main results. The results showed that interferences from adjacent stimuli, annoyance and the fatigue experienced by the subjects could be reduced significantly (p < 0.05) by using the facial expression change patterns in comparison with the face pattern. The offline results show that the classification accuracy of the facial expression change pattern was significantly better than that of the shuffled pattern (p < 0.05) and the face pattern (p < 0.05). Significance. The facial expression change pattern presented in this paper reduced interference from adjacent stimuli and decreased the fatigue and annoyance experienced by BCI users significantly (p < 0.05) compared to the face pattern.

Correct Hox gene expression established independently of position in Caenorhabditis elegans.

PubMed

Cowing, D; Kenyon, C

1996-07-25

The Hox genes are expressed in a conserved sequence of spatial domains along the anteroposterior (A/P) body axes of many organisms. In Drosophila, position-specific signals located along the A/P axis establish the pattern of Hox gene expression. In the nematode Caenorhabditis elegans, it is not known how the pattern of Hox gene expression is established. C. elegans uses lineal control mechanisms and local cell interactions to specify early blastomere identities. However, many cells expressing the same Hox gene are unrelated by lineage, suggesting that, as in Drosophila, domains of Hox gene expression may be defined by cell-extrinsic A/P positional signals. To test this, we have investigated whether posterior mesodermal and ectodermal cells will express their normal posterior Hox gene when they are mispositioned in the anterior. Surprisingly, we find that correct Hox gene expression does not depend on cell position, but is highly correlated with cell lineage. Thus, although the most striking feature of Hox gene expression is its positional specificity, in C. elegans the pattern is achieved, at least in part, by a lineage-specific control system that operates without regard to A/P position.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Molecular characterization of cDNAs encoding G protein alpha and beta subunits and study of their temporal and spatial expression patterns in Nicotiana plumbaginifolia Viv.

PubMed

Kaydamov, C; Tewes, A; Adler, K; Manteuffel, R

2000-04-25

We have isolated cDNA sequences encoding alpha and beta subunits of potential G proteins from a cDNA library prepared from somatic embryos of Nicotiana plumbaginifolia Viv. at early developmental stages. The predicted NPGPA1 and NPGPB1 gene products are 75-98% identical to the known respective plant alpha and beta subunits. Southern hybridizations indicate that NPGPA1 is probably a single-copy gene, whereas at least two copies of NPGPB1 exist in the N. plumbaginifolia genome. Northern analyses reveal that both NPGPA1 and NPGPB1 mRNA are expressed in all embryogenic stages and plant tissues examined and their expression is obviously regulated by the plant hormone auxin. Immunohistological localization of NPGPalpha1 and NPGPbeta1 preferentially on plasma and endoplasmic reticulum membranes and their immunochemical detection exclusively in microsomal cell fractions implicate membrane association of both proteins. The temporal and spatial expression patterns of NPGPA1 and NPGPB1 show conformity as well as differences. This could account for not only cooperative, but also individual activities of both subunits during embryogenesis and plant development.

The development of wing shape in Lepidoptera: mitotic density, not orientation, is the primary determinant of shape.

PubMed

Nijhout, H Frederik; Cinderella, Margaret; Grunert, Laura W

2014-03-01

The wings of butterflies and moths develop from imaginal disks whose structure is always congruent with the final adult wing. It is therefore possible to map every point on the imaginal disk to a location on the adult wing throughout ontogeny. We studied the growth patterns of the wings of two distantly related species with very different adult wing shapes, Junonia coenia and Manduca sexta. The shape of the wing disks change throughout their growth phase in a species-specific pattern. We measured mitotic densities and mitotic orientation in successive stages of wing development approximately one cell division apart. Cell proliferation was spatially patterned, and the density of mitoses was highly correlated with local growth. Unlike other systems in which the direction of mitoses has been viewed as the primary determinant of directional growth, we found that in these two species the direction of growth was only weakly correlated with the orientation of mitoses. Directional growth appears to be imposed by a constantly changing spatial pattern of cell division coupled with a weak bias in the orientation of cell division. Because growth and cell division in imaginal disk require ecdysone and insulin signaling, the changing spatial pattern of cell division may due to a changing pattern of expression of receptors or downstream elements in the signaling pathways for one or both of these hormones. Evolution of wing shape comes about by changes in the progression of spatial patterns of cell division. © 2014 Wiley Periodicals, Inc.

Interactions between Bmp-4 and Msx-1 act to restrict gene expression to odontogenic mesenchyme.

PubMed

Tucker, A S; Al Khamis, A; Sharpe, P T

1998-08-01

Tooth development is regulated by a reciprocal series of epithelial-mesenchymal interactions. Bmp4 has been identified as a candidate signalling molecule in these interactions, initially as an epithelial signal and then later at the bud stage as a mesenchymal signal (Vainio et al. [1993] Cell 75:45-58). A target gene for Bmp4 signalling is the homeobox gene Msx-1, identified by the ability of recombinant Bmp4 protein to induce expression in mesenchyme. There is, however, no evidence that Bmp4 is the endogenous inducer of Msx-1 expression. Msx-1 and Bmp-4 show dynamic, interactive patterns of expression in oral epithelium and ectomesenchyme during the early stages of tooth development. In this study, we compare the temporal and spatial expression of these two genes to determine whether the changing expression patterns of these genes are consistent with interactions between the two molecules. We show that changes in Bmp-4 expression precede changes in Msx-1 expression. At embryonic day (E)10.5-E11.0, expression patterns are consistent with BMP4 from the epithelium, inducing or maintaining Msx-1 in underlying mesenchyme. At E11.5, Bmp-4 expression shifts from epithelium to mesenchyme and is rapidly followed by localised up-regulation of Msx-1 expression at the sites of Bmp-4 expression. Using cultured explants of developing mandibles, we confirm that exogenous BMP4 is capable of replacing the endogenous source in epithelium and inducing Msx-1 gene expression in mesenchyme. By using noggin, a BMP inhibitor, we show that endogenous Msx-1 expression can be inhibited at E10.5 and E11.5, providing the first evidence that endogenous Bmp-4 from the epithelium is responsible for regulating the early spatial expression of Msx-1. We also show that the mesenchymal shift in Bmp-4 is responsible for up-regulating Msx-1 specifically at the sites of future tooth formation. Thus, we establish that a reciprocal series of interactions act to restrict expression of both genes to future sites of tooth formation, creating a positive feedback loop that maintains expression of both genes in tooth mesenchymal cells.

Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.

PubMed

Wai, Ching M; VanBuren, Robert; Zhang, Jisen; Huang, Lixian; Miao, Wenjing; Edger, Patrick P; Yim, Won C; Priest, Henry D; Meyers, Blake C; Mockler, Todd; Smith, J Andrew C; Cushman, John C; Ming, Ray

2017-10-01

The altered carbon assimilation pathway of crassulacean acid metabolism (CAM) photosynthesis results in an up to 80% higher water-use efficiency than C 3 photosynthesis in plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA (miRNA) expression patterns in the obligate CAM plant pineapple [Ananas comosus (L.) Merr.]. The high-resolution transcriptome atlas allowed us to distinguish between CAM-related and non-CAM gene copies. A differential gene co-expression network across green and white leaf diel datasets identified genes with circadian oscillation, CAM-related functions, and source-sink relations. Gene co-expression clusters containing CAM pathway genes are enriched with clock-associated cis-elements, suggesting circadian regulation of CAM. About 20% of pineapple microRNAs have diel expression patterns, with several that target key CAM-related genes. Expression and physiology data provide a model for CAM-specific carbohydrate flux and long-distance hexose transport. Together these resources provide a list of candidate genes for targeted engineering of CAM into C 3 photosynthesis crop species. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity

PubMed Central

Jackson, Daniel J.; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M.; Fleck, Claudia

2017-01-01

Abstract Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent “GS” domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. PMID:28961798

Spatial and temporal expression patterns of auxin response transcription factors in the syncytium induced by the beet cyst nematode Heterodera schachtii in Arabidopsis.

PubMed

Hewezi, Tarek; Piya, Sarbottam; Richard, Geoffrey; Rice, J Hollis

2014-09-01

Plant-parasitic cyst nematodes induce the formation of a multinucleated feeding site in the infected root, termed the syncytium. Recent studies point to key roles of the phytohormone auxin in the regulation of gene expression and establishment of the syncytium. Nevertheless, information about the spatiotemporal expression patterns of the transcription factors that mediate auxin transcriptional responses during syncytium formation is limited. Here, we provide a gene expression map of 22 auxin response factors (ARFs) during the initiation, formation and maintenance stages of the syncytium induced by the cyst nematode Heterodera schachtii in Arabidopsis. We observed distinct and overlapping expression patterns of ARFs throughout syncytium development phases. We identified a set of ARFs whose expression is predominantly located inside the developing syncytium, whereas others are expressed in the neighbouring cells, presumably to initiate specific transcriptional programmes required for their incorporation within the developing syncytium. Our analyses also point to a role of certain ARFs in determining the maximum size of the syncytium. In addition, several ARFs were found to be highly expressed in fully developed syncytia, suggesting a role in maintaining the functional phenotype of mature syncytia. The dynamic distribution and overlapping expression patterns of various ARFs seem to be essential characteristics of ARF activity during syncytium development. © 2014 BSPP AND JOHN WILEY & SONS LTD.

The human footprint in Mexico: physical geography and historical legacies.

PubMed

González-Abraham, Charlotte; Ezcurra, Exequiel; Garcillán, Pedro P; Ortega-Rubio, Alfredo; Kolb, Melanie; Bezaury Creel, Juan E

2015-01-01

Using publicly available data on land use and transportation corridors we calculated the human footprint index for the whole of Mexico to identify large-scale spatial patterns in the anthropogenic transformation of the land surface. We developed a map of the human footprint for the whole country and identified the ecological regions that have most transformed by human action. Additionally, we analyzed the extent to which (a) physical geography, expressed spatially in the form of biomes and ecoregions, compared to (b) historical geography, expressed as the spatial distribution of past human settlements, have driven the patterns of human modification of the land. Overall Mexico still has 56% of its land surface with low impact from human activities, but these areas are not evenly distributed. The lowest values are on the arid north and northwest, and the tropical southeast, while the highest values run along the coast of the Gulf of Mexico and from there inland along an east-to-west corridor that follows the Mexican transversal volcanic ranges and the associated upland plateau. The distribution of low- and high footprint areas within ecoregions forms a complex mosaic: the generally well-conserved Mexican deserts have some highly transformed agro-industrial areas, while many well-conserved, low footprint areas still persist in the highly-transformed ecoregions of central Mexico. We conclude that the spatial spread of the human footprint in Mexico is both the result of the limitations imposed by physical geography to human development at the biome level, and, within different biomes, of a complex history of past civilizations and technologies, including the 20th Century demographic explosion but also the spatial pattern of ancient settlements that were occupied by the Spanish Colony.

The Human Footprint in Mexico: Physical Geography and Historical Legacies

PubMed Central

Ortega-Rubio, Alfredo; Kolb, Melanie; Bezaury Creel, Juan E.

2015-01-01

Using publicly available data on land use and transportation corridors we calculated the human footprint index for the whole of Mexico to identify large-scale spatial patterns in the anthropogenic transformation of the land surface. We developed a map of the human footprint for the whole country and identified the ecological regions that have most transformed by human action. Additionally, we analyzed the extent to which (a) physical geography, expressed spatially in the form of biomes and ecoregions, compared to (b) historical geography, expressed as the spatial distribution of past human settlements, have driven the patterns of human modification of the land. Overall Mexico still has 56% of its land surface with low impact from human activities, but these areas are not evenly distributed. The lowest values are on the arid north and northwest, and the tropical southeast, while the highest values run along the coast of the Gulf of Mexico and from there inland along an east-to-west corridor that follows the Mexican transversal volcanic ranges and the associated upland plateau. The distribution of low- and high footprint areas within ecoregions forms a complex mosaic: the generally well-conserved Mexican deserts have some highly transformed agro-industrial areas, while many well-conserved, low footprint areas still persist in the highly-transformed ecoregions of central Mexico. We conclude that the spatial spread of the human footprint in Mexico is both the result of the limitations imposed by physical geography to human development at the biome level, and, within different biomes, of a complex history of past civilizations and technologies, including the 20th Century demographic explosion but also the spatial pattern of ancient settlements that were occupied by the Spanish Colony. PMID:25803839

Activation patterns in superficial layers of neocortex change between experiences independent of behavior, environment, or the hippocampus.

PubMed

Takehara-Nishiuchi, Kaori; Insel, Nathan; Hoang, Lan T; Wagner, Zachary; Olson, Kathy; Chawla, Monica K; Burke, Sara N; Barnes, Carol A

2013-09-01

Previous work suggests that activation patterns of neurons in superficial layers of the neocortex are more sensitive to spatial context than activation patterns in deep cortical layers. A possible source of this laminar difference is the distribution of contextual information to the superficial cortical layers carried by hippocampal efferents that travel through the entorhinal cortex and subiculum. To evaluate the role that the hippocampus plays in determining context sensitivity in superficial cortical layers, behavior-induced expression of the immediate early gene Arc was examined in hippocampus-lesioned and control rats after exposing them to 2 distinct contexts. Contrary to expectations, hippocampal lesions had no observable effect on Arc expression in any neocortical layer relative to controls. Furthermore, another group of intact animals was exposed to the same environment twice, to determine the reliability of Arc-expression patterns across identical contextual and behavioral episodes. Although this condition included no difference in external input between 2 epochs, the significant layer differences in Arc expression still remained. Thus, laminar differences in activation or plasticity patterns are not likely to arise from hippocampal sources or differences in external inputs, but are more likely to be an intrinsic property of the neocortex.

Spatially patterned matrix elasticity directs stem cell fate

NASA Astrophysics Data System (ADS)

Yang, Chun; DelRio, Frank W.; Ma, Hao; Killaars, Anouk R.; Basta, Lena P.; Kyburz, Kyle A.; Anseth, Kristi S.

2016-08-01

There is a growing appreciation for the functional role of matrix mechanics in regulating stem cell self-renewal and differentiation processes. However, it is largely unknown how subcellular, spatial mechanical variations in the local extracellular environment mediate intracellular signal transduction and direct cell fate. Here, the effect of spatial distribution, magnitude, and organization of subcellular matrix mechanical properties on human mesenchymal stem cell (hMSCs) function was investigated. Exploiting a photodegradation reaction, a hydrogel cell culture substrate was fabricated with regions of spatially varied and distinct mechanical properties, which were subsequently mapped and quantified by atomic force microscopy (AFM). The variations in the underlying matrix mechanics were found to regulate cellular adhesion and transcriptional events. Highly spread, elongated morphologies and higher Yes-associated protein (YAP) activation were observed in hMSCs seeded on hydrogels with higher concentrations of stiff regions in a dose-dependent manner. However, when the spatial organization of the mechanically stiff regions was altered from a regular to randomized pattern, lower levels of YAP activation with smaller and more rounded cell morphologies were induced in hMSCs. We infer from these results that irregular, disorganized variations in matrix mechanics, compared with regular patterns, appear to disrupt actin organization, and lead to different cell fates; this was verified by observations of lower alkaline phosphatase (ALP) activity and higher expression of CD105, a stem cell marker, in hMSCs in random versus regular patterns of mechanical properties. Collectively, this material platform has allowed innovative experiments to elucidate a novel spatial mechanical dosing mechanism that correlates to both the magnitude and organization of spatial stiffness.

Temporal and spatial expression patterns of Hedgehog receptors in the developing inner and middle ear.

PubMed

Shin, Jeong-Oh; Ankamreddy, Harinarayana; Jakka, Naga Mahesh; Lee, Seokwon; Kim, Un-Kyung; Bok, Jinwoong

2017-01-01

The mammalian inner ear is a complex organ responsible for balance and hearing. Sonic hedgehog (Shh), a member of the Hedgehog (Hh) family of secreted proteins, has been shown to play important roles in several aspects of inner ear development, including dorsoventral axial specification, cochlear elongation, tonotopic patterning, and hair cell differentiation. Hh proteins initiate a downstream signaling cascade by binding to the Patched 1 (Ptch1) receptor. Recent studies have revealed that other types of co-receptors can also mediate Hh signaling, including growth arrest-specific 1 (Gas1), cell-adhesion molecules-related/down-regulated by oncogenes (Cdon), and biregional Cdon binding protein (Boc). However, little is known about the role of these Hh co-receptors in inner ear development. In this study, we examined the expression patterns of Gas1, Cdon, and Boc, as well as that of Ptch1, in the developing mouse inner ear from otocyst (embryonic day (E) 9.5) until birth and in the developing middle ear at E15.5. Ptch1, a readout of Hh signaling, was expressed in a graded pattern in response to Shh signaling throughout development. Expression patterns of Gas1, Cdon, and Boc differed from that of Ptch1, and each Hh co-receptor was expressed in specific cells and domains in the developing inner and middle ear. These unique and differential expression patterns of Hh co-receptors suggest their roles in mediating various time- and space-specific functions of Shh during ear development.

Prenatal Loud Music and Noise: Differential Impact on Physiological Arousal, Hippocampal Synaptogenesis and Spatial Behavior in One Day-Old Chicks

PubMed Central

Sanyal, Tania; Kumar, Vivek; Nag, Tapas Chandra; Jain, Suman; Sreenivas, Vishnu; Wadhwa, Shashi

2013-01-01

Prenatal auditory stimulation in chicks with species-specific sound and music at 65 dB facilitates spatial orientation and learning and is associated with significant morphological and biochemical changes in the hippocampus and brainstem auditory nuclei. Increased noradrenaline level due to physiological arousal is suggested as a possible mediator for the observed beneficial effects following patterned and rhythmic sound exposure. However, studies regarding the effects of prenatal high decibel sound (110 dB; music and noise) exposure on the plasma noradrenaline level, synaptic protein expression in the hippocampus and spatial behavior of neonatal chicks remained unexplored. Here, we report that high decibel music stimulation moderately increases plasma noradrenaline level and positively modulates spatial orientation, learning and memory of one day-old chicks. In contrast, noise at the same sound pressure level results in excessive increase of plasma noradrenaline level and impairs the spatial behavior. Further, to assess the changes at the molecular level, we have quantified the expression of functional synapse markers: synaptophysin and PSD-95 in the hippocampus. Compared to the controls, both proteins show significantly increased expressions in the music stimulated group but decrease in expressions in the noise group. We propose that the differential increase of plasma noradrenaline level and altered expression of synaptic proteins in the hippocampus are responsible for the observed behavioral consequences following prenatal 110 dB music and noise stimulation. PMID:23861759

HLA-C expression pattern is spatially different between psoriasis and eczema skin lesions.

PubMed

Carlén, Lina; Sakuraba, Kazuko; Ståhle, Mona; Sánchez, Fabio

2007-02-01

Interactions between genetic and environmental factors underlie the immune dysregulation and keratinocyte abnormalities that characterize psoriasis. Among known psoriasis susceptibility loci (PSORS), PSORS1 on chromosome 6 has the strongest association to disease. Altered expression of some PSORS1 candidate genes has been reported but little is known about HLA-C expression in psoriasis. This study compared expression of major histocompatibility complex class Ia and HLA-C in psoriasis, allergic contact eczema, and normal skin. Although HLA-C was abundant in protein extracts from both eczema and psoriasis, a consistent and intriguing difference in the expression pattern was observed; strong immunoreactivity in the basal cell layer, polarized towards the basement membrane in psoriasis, whereas in eczema lesions HLA-C immunostaining was present mostly in suprabasal cells. Inflammatory cells in the dermis were strongly stained in both diseases. Normal skin epithelium showed less intense but similar HLA-C staining as eczema lesions. HLA class Ia expression overall resembled that of HLA-C in all samples. The distinct HLA-C expression patterns in psoriasis and eczema suggest a functional role in the specific psoriasis immune response and not only a general feature of inflammation.

Upregulation of the β-form of 14-3-3 protein in telencephalon of goldfish (Carassius auratus): its possible role in spatial learning.

PubMed

Subramanian, Dharaneedharan; Ramalingam, Rajkumar; Karuppasamy, Radhakrishnan; Subramanian, Thanga Leela; Chellam, Balasundaram; Rajan, Koilmani Emmanuvel

2012-10-03

In the present study, we observed variations in the expression pattern of proteins isolated from the telencephalon of goldfish (Carassius auratus). The expression of a 28 kDa protein was elevated in the individuals trained in a spatial task when compared with the untrained individuals. The ∼28 kDa protein was analyzed using liquid chromatography and mass spectrometry; further, the data were analyzed using the MASCOT search engine. The analysis showed that the ∼28 kDa protein is a β form of 14-3-3 protein with 35.1% identity. In addition, the semiquantitative PCR confirmed the variation in the expression of 14-3-3 between the trained and the untrained groups. Subsequently, we examined the effect of upregulation of 14-3-3 (β) in the neurotransmitters; that is, serotonin (5-hydroxytryptamine, 5-HT) and dopamine (DA). Notably, the level of 5-HT and DA was found to be significantly elevated in the telencephalon of individuals trained in the spatial task than in the untrained individuals. Our results suggest that the spatial learning increases the expression of 14-3-3 (β), which in turn leads to an increase in the level of 5-HT and DA. The upregulated 5-HT and DA may facilitate synapse formation during spatial learning in a novel environment.

Complex genomic rearrangement in CCS-LacZ transgenic mice.

PubMed

Stroud, Dina Myers; Darrow, Bruce J; Kim, Sang Do; Zhang, Jie; Jongbloed, Monique R M; Rentschler, Stacey; Moskowitz, Ivan P G; Seidman, Jonathan; Fishman, Glenn I

2007-02-01

The cardiac conduction system (CCS)-lacZ insertional mouse mutant strain genetically labels the developing and mature CCS. This pattern of expression is presumed to reflect the site of transgene integration rather than regulatory elements within the transgene proper. We sought to characterize the genomic structure of the integration locus and identify nearby gene(s) that might potentially confer the observed CCS-specific transcription. We found rearrangement of chromosome 7 between regions D1 and E1 with altered transcription of multiple genes in the D1 region. Several lines of evidence suggested that regulatory elements from at least one gene, Slco3A1, influenced CCS-restricted reporter gene expression. In embryonic hearts, Slco3A1 was expressed in a spatial pattern similar to the CCS-lacZ transgene and was similarly neuregulin-responsive. At later stages, however, expression patterns of the transgene and Slco3A1 diverged, suggesting that the Slco3A1 locus may be necessary, but not sufficient to confer CCS-specific transgene expression in the CCS-lacZ line. (c) 2007 Wiley-Liss, Inc.

MAEWEST expression in flower development of two petunia species.

PubMed

Segatto, Ana Lúcia A; Turchetto-Zolet, Andreia Carina; Aizza, Lilian Cristina B; Monte-Bello, Carolina C; Dornelas, Marcelo C; Margis, Rogerio; Freitas, Loreta B

2013-07-03

Changes in flower morphology may influence the frequency and specificity of animal visitors. In Petunia (Solanaceae), adaptation to different pollinators is one of the factors leading to species diversification within the genus. This study provides evidence that differential expression patterns of MAWEWEST (MAW) homologs in different Petunia species may be associated with adaptive changes in floral morphology. The Petunia × hybrida MAW gene belongs to the WOX (WUSCHEL-related homeobox) transcription factor family and has been identified as a controller of petal fusion during corolla formation. We analyzed the expression patterns of P. inflata and P. axillaris MAW orthologs (PiMAW and PaMAW, respectively) by reverse transcriptase polymerase chain reaction (RT-PCR), reverse transcription-quantitative PCR (qRT-PCR) and in situ hybridization in different tissues and different developmental stages of flowers in both species. The spatial expression patterns of PiMAW and PaMAW were similar in P. inflata and P. axillaris. Nevertheless, PaMAW expression level in P. axillaris was higher during the late bud development stage as compared to PiMAW in P. inflata. This work represents an expansion of petunia developmental research to wild accessions.

[Development of spatial orientation during pilot training].

PubMed

Ivanov, V V; Vorob'ev, O A; Snipkov, Iu Iu

1988-01-01

The problem of spatial orientation of pilots flying high-altitude aircraft is in the focus of present-day aviation medicine because of a growing number of accidents in the air. One of the productive lines of research is to study spatial orientation in terms of active formation and maintenance of its imagery in a complex environment. However investigators usually emphasize the role of visual (instrumental) information in the image construction, almost ignoring the sensorimotor component of spatial orientation. The theoretical analysis of the process of spatial orientation has facilitated the development of the concept assuming that the pattern of space perception changes with growing professional experience. The concept is based on an active approach to the essence, emergence, formation and variation in the pattern of sensory perception of space in man's consciousness. This concept asserts that as pilot's professional expertise increases, the pattern of spatial orientation becomes geocentric because a new system of spatial perception evolves which is a result of the development of a new (instrumental) type of motor activity in space. This finds expression in the fact that perception of spatial position inflight occurs when man has to resolve a new motor task--movement along a complex trajectory in the three-dimensional space onboard a flying vehicle. The meaningful structure of this problem which is to be implemented through controlling movements of the pilot acts as a factor that forms this new system of perception. All this underlies the arrangement of meaningful collection of instrumental data and detection of noninstrumental signals in the comprehensive perception of changes in the spatial position of a flying vehicle.

EXPRESSION PATTERNS OF ESTROGEN RECEPTORS IN THE CENTRAL AUDITORY SYSTEM CHANGE IN PREPUBERTAL AND AGED MICE

PubMed Central

Charitidi, K.; Frisina, R. D.; Vasilyeva, O. N.; Zhu, X.; Canlon, B.

2011-01-01

Estrogens are important in the development, maintenance and physiology of the CNS. Several studies have shown their effects on the processing of hearing in both males and females, and these effects, in part, are thought to result from regulation of the transcription of genes via their classical estrogen receptor (ER) pathway. In order to understand the spatiotemporal changes that occur with age, we have studied the expression of ERs in the central auditory pathway in prepubertal and aged CBA mice with immunohistochemistry. In prepubertal mice a clear dichotomy was noted between the expression of ERα and ERβ. ERβ-positive neurons were found in the metencephalon whereas the majority of ERα was found in mesencephalon, diencephalon or the telencephalon. In the aged animals a different pattern of ER expression was found in terms of location and overall intensity. These age-induced changes in the expression pattern were generally not uniform, suggesting that region-specific mechanisms regulate the ERs’ age-related expression. Neither the prepubertal nor the aged animals showed sex differences in any auditory structure. Our results demonstrate different age-dependent spatial and temporal changes in the pattern of expression of ERα and ERβ, suggesting that each ER type may be involved in distinct roles across the central auditory pathway in different periods of maturation. PMID:20736049

Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity.

PubMed

Jackson, Daniel J; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M; Fleck, Claudia

2017-11-01

Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent "GS" domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Overlapping but distinct topology for zebrafish V2R-like olfactory receptors reminiscent of odorant receptor spatial expression zones.

PubMed

Ahuja, Gaurav; Reichel, Vera; Kowatschew, Daniel; Syed, Adnan S; Kotagiri, Aswani Kumar; Oka, Yuichiro; Weth, Franco; Korsching, Sigrun I

2018-05-23

The sense of smell is unrivaled in terms of molecular complexity of its input channels. Even zebrafish, a model vertebrate system in many research fields including olfaction, possesses several hundred different olfactory receptor genes, organized in four different gene families. For one of these families, the initially discovered odorant receptors proper, segregation of expression into distinct spatial subdomains within a common sensory surface has been observed both in teleost fish and in mammals. However, for the remaining three families, little to nothing was known about their spatial coding logic. Here we wished to investigate, whether the principle of spatial segregation observed for odorant receptors extends to another olfactory receptor family, the V2R-related OlfC genes. Furthermore we thought to examine, how expression of OlfC genes is integrated into expression zones of odorant receptor genes, which in fish share a single sensory surface with OlfC genes. To select representative genes, we performed a comprehensive phylogenetic study of the zebrafish OlfC family, which identified a novel OlfC gene, reduced the number of pseudogenes to 1, and brought the total family size to 60 intact OlfC receptors. We analyzed the spatial pattern of OlfC-expressing cells for seven representative receptors in three dimensions (height within the epithelial layer, horizontal distance from the center of the olfactory organ, and height within the olfactory organ). We report non-random distributions of labeled neurons for all OlfC genes analysed. Distributions for sparsely expressed OlfC genes are significantly different from each other in nearly all cases, broad overlap notwithstanding. For two of the three coordinates analyzed, OlfC expression zones are intercalated with those of odorant receptor zones, whereas in the third dimension some segregation is observed. Our results show that V2R-related OlfC genes follow the same spatial logic of expression as odorant receptors and their expression zones intermingle with those of odorant receptor genes. Thus, distinctly different expression zones for individual receptor genes constitute a general feature shared by teleost and tetrapod V2R/OlfC and odorant receptor families alike.

Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves

PubMed Central

Ay, Ahmet; Holland, Jack; Sperlea, Adriana; Devakanmalai, Gnanapackiam Sheela; Knierer, Stephan; Sangervasi, Sebastian; Stevenson, Angel; Özbudak, Ertuğrul M.

2014-01-01

The vertebrate segmentation clock is a gene expression oscillator controlling rhythmic segmentation of the vertebral column during embryonic development. The period of oscillations becomes longer as cells are displaced along the posterior to anterior axis, which results in traveling waves of clock gene expression sweeping in the unsegmented tissue. Although various hypotheses necessitating the inclusion of additional regulatory genes into the core clock network at different spatial locations have been proposed, the mechanism underlying traveling waves has remained elusive. Here, we combined molecular-level computational modeling and quantitative experimentation to solve this puzzle. Our model predicts the existence of an increasing gradient of gene expression time delays along the posterior to anterior direction to recapitulate spatiotemporal profiles of the traveling segmentation clock waves in different genetic backgrounds in zebrafish. We validated this prediction by measuring an increased time delay of oscillatory Her1 protein production along the unsegmented tissue. Our results refuted the need for spatial expansion of the core feedback loop to explain the occurrence of traveling waves. Spatial regulation of gene expression time delays is a novel way of creating dynamic patterns; this is the first report demonstrating such a control mechanism in any tissue and future investigations will explore the presence of analogous examples in other biological systems. PMID:25336742

Expression pattern of the pre-prothaumatin II gene under the control of the CaMV 35S promoter in transgenic cucumber (Cucumis sativus L.) flower buds and fruits.

PubMed

Szwacka, M; Siedlecka, E; Zawirska-Wojtasiak, R; Wiśniewski, Ł; Malepszy, S

2009-01-01

Thaumatin II is an extremely sweet-tasting protein produced by fruits of the West African shrub Thaumatococcus daniellii Benth, so it can be used in biotechnology to improve the tastes of various plant products. This study is concerned with the spatial and temporal aspects of expression of the 35S-pre-prothaumatin II chimeric gene in flower buds and fruits of transgenic cucumber (Cucumis sativus L.) line 225. The activity of the 35S promoter in organs of line 225 was compared with its activity in 2 other transgenic lines. The accumulation of recombinant thaumatin varied spatially in flower bud tissues of transgenic lines. We found that these differences in the spatial accumulation of transgenic protein concerned the ovary of female buds and the perianth of male buds. In contrast to flower parts, recombinant thaumatin was found in nearly all parts of the young fruit from the transgenic plants. The pre-prothaumatin II gene expression was detected at a very early developmental stage in male buds, and its pattern was rather conserved as the buds aged. The expression of the transgene was also detected in vascular tissues of examined organs but was undetectable in pollen grains, in agreement with the generally held view that the CaMV 35S promoter is virtually silent in pollen. Immunocytochemical analyses of sections of control organs revealed endogenous homolog(s) of thaumatin when using polyclonal antisera, but not when using monoclonal antibodies for recombinant thaumatin detection in transgenic cucumber.

Emergent Archetype Hydrological-Biogeochemical Response Patterns in Heterogeneous Catchments

NASA Astrophysics Data System (ADS)

Jawitz, J. W.; Gall, H. E.; Rao, P.

2013-12-01

What can spatiotemporally integrated patterns observed in stream hydrologic and biogeochemical signals generated in response to transient hydro-climatic and anthropogenic forcing tell us about the interactions between spatially heterogeneous soil-mediated hydrological and biogeochemical processes? We seek to understand how the spatial structure of solute sources coupled with hydrologic responses affect observed concentration-discharge (C-Q) patterns. These patterns are expressions of the spatiotemporal structure of solute loads exported from managed catchments, and their likely ecological consequences manifested in receiving water bodies (e.g., wetlands, rivers, lakes, and coastal waters). We investigated the following broad questions: (1) How does the correlation between flow-generating areas and biogeochemical source areas across a catchment evolve under stochastic hydro-climatic forcing? (2) What are the feasible hydrologic and biogeochemical responses that lead to the emergence of the observed archetype C-Q patterns? and; (3) What implications do these coupled dynamics have for catchment monitoring and implementation of management practices? We categorize the observed temporal signals into three archetypical C-Q patterns: dilution; accretion, and constant concentration. We introduce a parsimonious stochastic model of heterogeneous catchments, which act as hydrologic and biogeochemical filters, to examine the relationship between spatial heterogeneity and temporal history of solute export signals. The core concept of the modeling framework is considering the types and degree of spatial correlation between solute source zones and flow generating zones, and activation of different portions of the catchments during rainfall events. Our overarching hypothesis is that each of the archetype C-Q patterns can be generated by explicitly linking landscape-scale hydrologic responses and spatial distributions of solute source properties within a catchment. The model simulations reproduce the three major C-Q patterns observed in published data, offering valuable insight into coupled catchment processes. The findings have important implications for effective catchment management for water quality improvement, and stream monitoring strategies.

Multivoxel Pattern Analysis Reveals 3D Place Information in the Human Hippocampus.

PubMed

Kim, Misun; Jeffery, Kate J; Maguire, Eleanor A

2017-04-19

The spatial world is three dimensional (3D) and humans and other animals move both horizontally and vertically within it. Extant neuroscientific studies have typically investigated spatial navigation on a horizontal 2D plane, leaving much unknown about how 3D spatial information is represented in the brain. Specifically, horizontal and vertical information may be encoded in the same or different neural structures with equal or unequal sensitivity. Here, we investigated these possibilities using fMRI while participants were passively moved within a 3D lattice structure as if riding a rollercoaster. Multivoxel pattern analysis was used to test for the existence of information relating to where and in which direction participants were heading in this virtual environment. Behaviorally, participants had similarly accurate memory for vertical and horizontal locations and the right anterior hippocampus (HC) expressed place information that was sensitive to changes along both horizontal and vertical axes. This is suggestive of isotropic 3D place encoding. In contrast, participants indicated their heading direction faster and more accurately when they were heading in a tilted-up or tilted-down direction. This direction information was expressed in the right retrosplenial cortex and posterior HC and was only sensitive to vertical pitch, which could reflect the importance of the vertical (gravity) axis as a reference frame. Overall, our findings extend previous knowledge of how we represent the spatial world and navigate within it by taking into account the important third dimension. SIGNIFICANCE STATEMENT The spatial world is 3D. We can move horizontally across surfaces, but also vertically, going up slopes or stairs. Little is known about how the brain supports representations of 3D space. A key question is whether horizontal and vertical information is equally well represented. Here, we measured fMRI response patterns while participants moved within a virtual 3D environment and found that the anterior hippocampus (HC) expressed location information that was sensitive to the vertical and horizontal axes. In contrast, information about heading direction, found in retrosplenial cortex and posterior HC, favored the vertical axis, perhaps due to gravity effects. These findings provide new insights into how we represent our spatial 3D world and navigate within it. Copyright © 2017 Kim et al.

Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians.

PubMed

Stückemann, Tom; Cleland, James Patrick; Werner, Steffen; Thi-Kim Vu, Hanh; Bayersdorf, Robert; Liu, Shang-Yun; Friedrich, Benjamin; Jülicher, Frank; Rink, Jochen Christian

2017-02-06

Planarian flatworms maintain their body plan in the face of constant internal turnover and can regenerate from arbitrary tissue fragments. Both phenomena require self-maintaining and self-organizing patterning mechanisms, the molecular mechanisms of which remain poorly understood. We show that a morphogenic gradient of canonical Wnt signaling patterns gene expression along the planarian anteroposterior (A/P) axis. Our results demonstrate that gradient formation likely occurs autonomously in the tail and that an autoregulatory module of Wnt-mediated Wnt expression both shapes the gradient at steady state and governs its re-establishment during regeneration. Functional antagonism between the tail Wnt gradient and an unknown head patterning system further determines the spatial proportions of the planarian A/P axis and mediates mutually exclusive molecular fate choices during regeneration. Overall, our results suggest that the planarian A/P axis is patterned by self-organizing patterning systems deployed from either end that are functionally coupled by mutual antagonism. Copyright © 2017 Elsevier Inc. All rights reserved.

Tissue-specific NETs alter genome organization and regulation even in a heterologous system.

PubMed

de Las Heras, Jose I; Zuleger, Nikolaj; Batrakou, Dzmitry G; Czapiewski, Rafal; Kerr, Alastair R W; Schirmer, Eric C

2017-01-02

Different cell types exhibit distinct patterns of 3D genome organization that correlate with changes in gene expression in tissue and differentiation systems. Several tissue-specific nuclear envelope transmembrane proteins (NETs) have been found to influence the spatial positioning of genes and chromosomes that normally occurs during tissue differentiation. Here we study 3 such NETs: NET29, NET39, and NET47, which are expressed preferentially in fat, muscle and liver, respectively. We found that even when exogenously expressed in a heterologous system they can specify particular genome organization patterns and alter gene expression. Each NET affected largely different subsets of genes. Notably, the liver-specific NET47 upregulated many genes in HT1080 fibroblast cells that are normally upregulated in hepatogenesis, showing that tissue-specific NETs can favor expression patterns associated with the tissue where the NET is normally expressed. Similarly, global profiling of peripheral chromatin after exogenous expression of these NETs using lamin B1 DamID revealed that each NET affected the nuclear positioning of distinct sets of genomic regions with a significant tissue-specific component. Thus NET influences on genome organization can contribute to gene expression changes associated with differentiation even in the absence of other factors and overt cellular differentiation changes.

Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).

PubMed

Xu, Yuantao; Wu, Guizhi; Hao, Baohai; Chen, Lingling; Deng, Xiuxin; Xu, Qiang

2015-11-23

With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions. Two set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcriptomes. With the two sets of genes, gene structure and gene expression pattern were investigated. On average, both the CSGs and orphan genes have fewer exons, shorter gene length and higher GC content when compared with those evolutionarily conserved genes (ECs). Expression profiling indicated that most of the LSGs expressed in various tissues of sweet orange and some of them exhibited distinct temporal and spatial expression patterns. Particularly, the orphan genes were preferentially expressed in callus, which is an important pluripotent tissue of citrus. Besides, part of the CSGs and orphan genes expressed responsive to abiotic stress, indicating their potential functions during interaction with environment. This study identified and characterized two sets of LSGs in citrus, dissected their sequence features and expression patterns, and provided valuable clues for future functional analysis of the LSGs in sweet orange.

The dorsoventral patterning of Musca domestica embryos: insights into BMP/Dpp evolution from the base of the lower cyclorraphan flies.

PubMed

Hodar, Christian; Cambiazo, Verónica

2018-01-01

In the last few years, accumulated information has indicated that the evolution of an extra-embryonic membrane in dipterans was accompanied by changes in the gene regulatory network controlled by the BMP/Dpp pathway, which is responsible for dorsal patterning in these insects. However, only comparative analysis of gene expression levels between distant species with two extra-embryonic membranes, like A. gambiae or C. albipunctata , and D. melanogaster, has been conducted. Analysis of gene expression in ancestral species, which evolved closer to the amnioserosa origin, could provide new insights into the evolution of dorsoventral patterning in dipterans. Here we describe the spatial expression of several key and downstream elements of the Dpp pathway and show the compared patterns of expression between Musca and Drosophila embryos, both dipterans with amnioserosa. Most of the analyzed gene showed a high degree of expression conservation, however, we found several differences in the gene expression pattern of M. domestica orthologs for sog and tolloid . Bioinformatics analysis of the promoter of both genes indicated that the variations could be related to the gain of several binding sites for the transcriptional factor Dorsal in the Md.tld promoter and Snail in the Md.sog enhancer . These altered expressions could explain the unclear formation of the pMad gradient in the M. domestica embryo, compared to the formation of the gradient in D. melanogaster. Gene expression changes during the dorsal-ventral patterning in insects contribute to the differentiation of extra-embryonic tissues as a consequence of changes in the gene regulatory network controlled by BMP/Dpp. In this work, in early M. domestica embryos, we identified the expression pattern of several genes members involved in the dorsoventral specification of the embryo. We believe that these data can contribute to understanding the evolution of the BMP/Dpp pathway, the regulation of BMP ligands, and the formation of a Dpp gradient in higher cyclorraphan flies.

The transcriptional diversity of 25 Drosophila cell lines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cherbas, Lucy; Willingham, Aarron; Zhang, Dayu

2010-12-22

Drosophila melanogaster cell lines are important resources for cell biologists. In this article, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signalingmore » pathways are well represented: most differentiation pathways are ‘‘off’’ and survival/growth pathways ‘‘on.’’ Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common ‘‘cell line‘‘ gene expression pattern. We report the transcriptional profiles of 25 Drosophila melanogaster cell lines, principally by whole-genome tiling microarray analysis of total RNA, carried out as part of the modENCODE project. The data produced in this study add to our knowledge of the cell lines and of the Drosophila transcriptome in several ways. We summarize the expression of previously annotated genes in each of the 25 lines with emphasis on what those patterns reveal about the origins of the lines and the stability of spatial expression patterns. In addition, we offer an initial analysis of previously unannotated transcripts in the cell lines.« less

Vegetation-induced spatial variability of soil redox properties in wetlands

NASA Astrophysics Data System (ADS)

Szalai, Zoltán; Jakab, Gergely; Kiss, Klaudia; Ringer, Marianna; Balázs, Réka; Zacháry, Dóra; Horváth Szabó, Kata; Perényi, Katalin

2016-04-01

Vegetation induced land patches may result spatial pattern of on soil Eh and pH. These spatial pattern are mainly emerged by differences of aeration and exudation of assimilates. Present paper focuses on vertical extent and temporal dynamics of these patterns in wetlands. Two study sites were selected: 1. a plain wetland on calcareous sandy parent material (Ceglédbercel, Danube-Tisza Interfluve, Hungary); 2. headwater wetland with calcareous loamy parent material (Bátaapáti, Hungary). Two vegetation patches were studied in site 1: sedgy (dominated by Carex riparia) and reedy (dominated by Phragmites australis). Three patches were studied in site2: sedgy1 (dominated by C vulpina), sedgy 2 (C. riparia); nettle-horsetail (Urtica dioica and Equisetum arvense). Boundaries between patches were studied separately. Soil redox, pH and temperature studied by automated remote controlled instruments. Three digital sensors (Ponsell) were installed in each locations: 20cm and 40cm sensors represent the solum and 100 cm sensor monitors the subsoil). Groundwater wells were installed near to triplets for soil water sampling. Soil Eh, pH and temperature values were recorded in each 10 minutes. Soil water sampling for iron and DOC were carried out during saturated periods. Spatial pattern of soil Eh is clearly caused by vegetation. We measured significant differences between Eh values of the studied patches in the solum. We did not find this kinds horizontal differences in the subsoil. Boundaries of the patches usually had more reductive soil environment than the core areas. We have found temporal dynamics of the spatial redox pattern. Differences were not so well expressed during wintertime. These spatial patterns had influence on the DOC and iron content of porewater, as well. Highest temporal dynamics of soil redox properties and porewater iron could be found in the boundaries. These observations refer to importance patchiness of vegetation on soil chemical properties in wetlands. Authors are grateful to Hungarian Scientific research Fund (K100180)

Modelling Delta-Notch perturbations during zebrafish somitogenesis.

PubMed

Murray, Philip J; Maini, Philip K; Baker, Ruth E

2013-01-15

The discovery over the last 15 years of molecular clocks and gradients in the pre-somitic mesoderm of numerous vertebrate species has added significant weight to Cooke and Zeeman's 'clock and wavefront' model of somitogenesis, in which a travelling wavefront determines the spatial position of somite formation and the somitogenesis clock controls periodicity (Cooke and Zeeman, 1976). However, recent high-throughput measurements of spatiotemporal patterns of gene expression in different zebrafish mutant backgrounds allow further quantitative evaluation of the clock and wavefront hypothesis. In this study we describe how our recently proposed model, in which oscillator coupling drives the propagation of an emergent wavefront, can be used to provide mechanistic and testable explanations for the following observed phenomena in zebrafish embryos: (a) the variation in somite measurements across a number of zebrafish mutants; (b) the delayed formation of somites and the formation of 'salt and pepper' patterns of gene expression upon disruption of oscillator coupling; and (c) spatial correlations in the 'salt and pepper' patterns in Delta-Notch mutants. In light of our results, we propose a number of plausible experiments that could be used to further test the model. Copyright © 2012 Elsevier Inc. All rights reserved.

Aberrant patterns of visual facial information usage in schizophrenia.

PubMed

Clark, Cameron M; Gosselin, Frédéric; Goghari, Vina M

2013-05-01

Deficits in facial emotion perception have been linked to poorer functional outcome in schizophrenia. However, the relationship between abnormal emotion perception and functional outcome remains poorly understood. To better understand the nature of facial emotion perception deficits in schizophrenia, we used the Bubbles Facial Emotion Perception Task to identify differences in usage of visual facial information in schizophrenia patients (n = 20) and controls (n = 20), when differentiating between angry and neutral facial expressions. As hypothesized, schizophrenia patients required more facial information than controls to accurately differentiate between angry and neutral facial expressions, and they relied on different facial features and spatial frequencies to differentiate these facial expressions. Specifically, schizophrenia patients underutilized the eye regions, overutilized the nose and mouth regions, and virtually ignored information presented at the lowest levels of spatial frequency. In addition, a post hoc one-tailed t test revealed a positive relationship of moderate strength between the degree of divergence from "normal" visual facial information usage in the eye region and lower overall social functioning. These findings provide direct support for aberrant patterns of visual facial information usage in schizophrenia in differentiating between socially salient emotional states. © 2013 American Psychological Association

The Caenorhabditis elegans vulva: A post-embryonic gene regulatory network controlling organogenesis

PubMed Central

Ririe, Ted O.; Fernandes, Jolene S.; Sternberg, Paul W.

2008-01-01

The Caenorhabditis elegans vulva is an elegant model for dissecting a gene regulatory network (GRN) that directs postembryonic organogenesis. The mature vulva comprises seven cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique pattern of spatial and temporal gene expression. The mechanisms that specify these cell types in a precise spatial pattern are not well understood. Using reverse genetic screens, we identified novel components of the vulval GRN, including nhr-113 in vulA. Several transcription factors (lin-11, lin-29, cog-1, egl-38, and nhr-67) interact with each other and act in concert to regulate target gene expression in the diverse vulval cell types. For example, egl-38 (Pax2/5/8) stabilizes the vulF fate by positively regulating vulF characteristics and by inhibiting characteristics associated with the neighboring vulE cells. nhr-67 and egl-38 regulate cog-1, helping restrict its expression to vulE. Computational approaches have been successfully used to identify functional cis-regulatory motifs in the zmp-1 (zinc metalloproteinase) promoter. These results provide an overview of the regulatory network architecture for each vulval cell type. PMID:19104047

A Bmp/Admp regulatory circuit controls maintenance and regeneration of dorsal-ventral polarity in planarians

PubMed Central

Gaviño, Michael A.; Reddien, Peter W.

2011-01-01

Animal embryos have diverse anatomy and vary greatly in size. It is therefore remarkable that a common signaling pathway – BMP signaling – controls development of the dorsoventral (DV) axis throughout the Bilateria [1-8]. In vertebrates, spatially opposed expression of the BMP-family signaling proteins Bmp4 and Admp (anti-dorsalizing morphogenetic protein) can promote restoration of DV pattern following tissue removal [9-11]. bmp4 orthologs have been identified in all three groups of the Bilateria (deuterostomes, ecdysozoans, and lophotrochozoans) [12]. By contrast, the absence of admp orthologs in ecdysozoans such as Drosophila and C. elegans has suggested that a DV regulatory circuit of oppositely expressed bmp4 and admp genes represents an innovation specific to deuterostomes. Here we describe the existence of spatially opposed bmp and admp expression in a protostome. An admp ortholog (Smed-admp) is expressed at the ventral pole and laterally in adult Schmidtea mediterranea planarians, spatially opposing the dorsal-pole domain of Smed-bmp4 expression. Smed-admp is required for planarian regeneration following parasagittal amputation. Furthermore, Smed-admp promotes Smed-bmp4 expression and Smed-bmp4 inhibits Smed-admp expression, generating a regulatory circuit that buffers against perturbations of Bmp signaling. These results suggest that a Bmp/Admp regulatory circuit is a central feature of the Bilateria, used broadly for the establishment, maintenance, and regeneration of the DV axis. PMID:21295483

Describing the brain in autism in five dimensions--magnetic resonance imaging-assisted diagnosis of autism spectrum disorder using a multiparameter classification approach.

PubMed

Ecker, Christine; Marquand, Andre; Mourão-Miranda, Janaina; Johnston, Patrick; Daly, Eileen M; Brammer, Michael J; Maltezos, Stefanos; Murphy, Clodagh M; Robertson, Dene; Williams, Steven C; Murphy, Declan G M

2010-08-11

Autism spectrum disorder (ASD) is a neurodevelopmental condition with multiple causes, comorbid conditions, and a wide range in the type and severity of symptoms expressed by different individuals. This makes the neuroanatomy of autism inherently difficult to describe. Here, we demonstrate how a multiparameter classification approach can be used to characterize the complex and subtle structural pattern of gray matter anatomy implicated in adults with ASD, and to reveal spatially distributed patterns of discriminating regions for a variety of parameters describing brain anatomy. A set of five morphological parameters including volumetric and geometric features at each spatial location on the cortical surface was used to discriminate between people with ASD and controls using a support vector machine (SVM) analytic approach, and to find a spatially distributed pattern of regions with maximal classification weights. On the basis of these patterns, SVM was able to identify individuals with ASD at a sensitivity and specificity of up to 90% and 80%, respectively. However, the ability of individual cortical features to discriminate between groups was highly variable, and the discriminating patterns of regions varied across parameters. The classification was specific to ASD rather than neurodevelopmental conditions in general (e.g., attention deficit hyperactivity disorder). Our results confirm the hypothesis that the neuroanatomy of autism is truly multidimensional, and affects multiple and most likely independent cortical features. The spatial patterns detected using SVM may help further exploration of the specific genetic and neuropathological underpinnings of ASD, and provide new insights into the most likely multifactorial etiology of the condition.

Patterning C. elegans: homeotic cluster genes, cell fates and cell migrations.

PubMed

Salser, S J; Kenyon, C

1994-05-01

Despite its simple body form, the nematode C. elegans expresses homeotic cluster genes similar to those of insects and vertebrates in the patterning of many cell types and tissues along the anteroposterior axis. In the ventral nerve cord, these genes program spatial patterns of cell death, fusion, division and neurotransmitter production; in migrating cells they regulate the direction and extent of movement. Nematode development permits an analysis at the cellular level of how homeotic cluster genes interact to specify cell fates, and how cell behavior can be regulated to assemble an organism.

Expression of forkhead box transcription factor genes Foxp1 and Foxp2 during jaw development.

PubMed

Cesario, Jeffry M; Almaidhan, Asma A; Jeong, Juhee

2016-03-01

Development of the face is regulated by a large number of genes that are expressed in temporally and spatially specific patterns. While significant progress has been made on characterizing the genes that operate in the oral region of the face, those regulating development of the aboral (lateral) region remain largely unknown. Recently, we discovered that transcription factors LIM homeobox (LHX) 6 and LHX8, which are key regulators of oral development, repressed the expression of the genes encoding forkhead box transcription factors, Foxp1 and Foxp2, in the oral region. To gain insights into the potential role of the Foxp genes in region-specific development of the face, we examined their expression patterns in the first pharyngeal arch (primordium for the jaw) of mouse embryos at a high spatial and temporal resolution. Foxp1 and Foxp2 were preferentially expressed in the aboral and posterior parts of the first pharyngeal arch, including the developing temporomandibular joint. Through double immunofluorescence and double fluorescent RNA in situ hybridization, we found that Foxp1 was expressed in the progenitor cells for the muscle, bone, and connective tissue. Foxp2 was expressed in subsets of bone and connective tissue progenitors but not in the myoblasts. Neither gene was expressed in the dental mesenchyme nor in the oral half of the palatal shelf undergoing extensive growth and morphogenesis. Together, we demonstrated for the first time that Foxp1 and Foxp2 are expressed during craniofacial development. Our data suggest that the Foxp genes may regulate development of the aboral and posterior regions of the jaw. Copyright © 2016 Elsevier B.V. All rights reserved.

A Recommendation for Naming Transcription Factor Proteins in the Grasses

USDA-ARS?s Scientific Manuscript database

Transcription factors are central for the exquisite temporal and spatial expression patterns of many genes. These proteins are characterized by their ability to be tethered to particular regulatory sequences in the genes that they control. While many other proteins participate in the regulation of g...

Fragmentation of forest, grassland, and shrubland

Treesearch

Kurt H. Riitters

2013-01-01

As humans introduce competing land uses into natural landscapes, the public concerns regarding landcover patterns are expressed through headline issues such as urban sprawl, forest fragmentation, water quality, and wilderness preservation. The spatial arrangement of an environment affects all human perceptions and ecological processes within that environment, but this...

Mapping spatial patterns of people's risk perception of landslides

NASA Astrophysics Data System (ADS)

Kofler, Christian; Pedoth, Lydia; Elzbieta Stawinoga, Agnieszka; Schneiderbauer, Stefan

2016-04-01

The resilience of communities against natural hazards is largely influenced by how the individuals perceive risk. A good understanding of people's risk perception, awareness and hazard knowledge is crucial for developing and improving risk management and communication strategies between authorities and the affected population. A lot of research has been done in investigating the social aspects of risks to natural hazards by means of interviews or questionnaires. However, there is still a lack of research in the investigation of the influence of the spatial distance to a hazard event on peoples risk perception. While the spatial dimension of a natural hazard event is always assessed in works with a natural science approach, it is often neglected in works on social aspects of natural hazards. In the present study, we aimed to overcome these gaps by combining methods from different disciplines and assessing and mapping the spatial pattern of risk perception through multivariate statistical approaches based on empirical data from questionnaires. We will present results from a case study carried out in Badia, located in the Province of South Tyrol- Italy, where in December 2012 a landslide destroyed four residential buildings and led to the evacuation of 36 people. By means of questionnaires distributed to all adults living in the case study area we assessed people's risk perception and asked respondents to allocate their place of residence on a map of the case study area subdivided in 7 zones. Based on the data of the questionnaire results we developed a risk perception factor in order to express various assessed aspects linked to risk perception with one metric. We analyzed and mapped this factor according to the different zones reflecting the spatial distance to the event. Furthermore, a cluster analysis identified various risk behavior profiles within the population. We also investigated the spatial patterns of these risk profiles. We revealed that the residential zone in the immediate proximity to the landslide event showed significantly different results than all other zones. Though we have been able to observe spatial patterns of our developed metrics that changed significantly with geographic distance, our results led to the assumption that risk perception cannot be expressed in units of length. The appropriate spatial unit rather seems to be "immediate proximity" to the event. The results of our study can support response forces and authorities in planning and adopting different communication and management strategies tailored to different groups of affected persons.

Differential expression of neuroligin genes in the nervous system of zebrafish.

PubMed

Davey, Crystal; Tallafuss, Alexandra; Washbourne, Philip

2010-02-01

The establishment and maturation of appropriate synaptic connections is crucial in the development of neuronal circuits. Cellular adhesion is believed to play a central role in this process. Neuroligins are neuronal cell adhesion molecules that are hypothesized to act in the initial formation and maturation of synaptic connections. In order to establish the zebrafish as a model to investigate the in vivo role of Neuroligin proteins in nervous system development, we identified the zebrafish orthologs of neuroligin family members and characterized their expression. Zebrafish possess seven neuroligin genes. Synteny analysis and sequence comparisons show that NLGN2, NLGN3, and NLGN4X are duplicated in zebrafish, but NLGN1 has a single zebrafish ortholog. All seven zebrafish neuroligins are expressed in complex patterns in the developing nervous system and in the adult brain. The spatial and temporal expression patterns of these genes suggest that they occupy a role in nervous system development and maintenance.

Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling.

PubMed

Hinchliffe, Doug J; Meredith, William R; Yeater, Kathleen M; Kim, Hee Jin; Woodward, Andrew W; Chen, Z Jeffrey; Triplett, Barbara A

2010-05-01

Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete block design, with three spatially distinct biological replications for each NIL at each time point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton fiber gene expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high-fiber quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.

Dampened regulates the activating potency of Bicoid and the embryonic patterning outcome in Drosophila

PubMed Central

Liu, Junbo; Ma, Jun

2014-01-01

The Drosophila morphogen gradient of Bicoid (Bcd) initiates anterior-posterior (AP) patterning, but it is poorly understood how its ability to activate a target gene may impact this process. Here we report an F-box protein, Dampened (Dmpd) as a nuclear co-factor of Bcd that can enhance its activating potency. We establish a quantitative platform to specifically investigate two parameters of a Bcd target gene response, expression amplitude and boundary position. We show that embryos lacking Dmpd have a reduced amplitude of Bcd-activated hunchback (hb) expression at a critical time of development. This is due to a reduced Bcd-dependent transcribing probability. This defect is faithfully propagated further downstream of the AP patterning network to alter the spatial characteristics of even-skipped (eve) stripes. Thus, unlike another Bcd-interacting F-box protein Fates-shifted (Fsd), which controls AP patterning through regulating the Bcd gradient profile, Dmpd achieves its patterning role through regulating the activating potency of Bcd. PMID:24336107

Insulin-like growth factors I and II in starry flounder (Platichthys stellatus): molecular cloning and differential expression during embryonic development.

PubMed

Xu, Yongjiang; Zang, Kun; Liu, Xuezhou; Shi, Bao; Li, Cunyu; Shi, Xueying

2015-02-01

In order to elucidate the possible roles of insulin-like growth factors I and II (IGF-I and IGF-II) in the embryonic development of Platichthys stellatus, their cDNAs were isolated and their spatial expression pattern in adult organs and temporal expression pattern throughout embryonic development were examined by quantitative real-time PCR assay. The IGF-I cDNA sequence was 1,268 bp in length and contained an open reading frame (ORF) of 558 bp, which encoded 185 amino acid residues. With respect to IGF-II, the full-length cDNA was 899 bp in length and contained a 648-bp ORF, which encoded 215 amino acid residues. The amino acid sequences of IGF-I and IGF-II exhibited high identities with their fish counterparts. The highest IGF-I mRNA level was found in the liver for both sexes, whereas the IGF-II gene was most abundantly expressed in female liver and male liver, gill, and brain. The sex-specific and spatial expression patterns of IGF-I and IGF-II mRNAs are thought to be related to the sexually dimorphic growth and development of starry flounder. Both IGF-I and IGF-II mRNAs were detected in unfertilized eggs, which indicated that IGF-I and IGF-II were parentally transmitted. Nineteen embryonic development stages were tested. IGF-I mRNA level remained high from unfertilized eggs to low blastula followed by a significant decrease at early gastrula and then maintained a lower level. In contrast, IGF-II mRNA level was low from unfertilized eggs to high blastula and peaked at low blastula followed by a gradual decrease. Moreover, higher levels of IGF-I mRNA than that of IGF-II were found from unfertilized eggs to high blastula, vice versa from low blastula to newly hatched larva, and the different expression pattern verified the differential roles of IGF-I and IGF-II in starry flounder embryonic development. These results could help in understanding the endocrine mechanism involved in the early development and growth of starry flounder.

Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns.

PubMed

Shang, Haihong; Li, Wei; Zou, Changsong; Yuan, Youlu

2013-07-01

NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor (NAC-TF) genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 (55%) were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on transcriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii. © 2013 Institute of Botany, Chinese Academy of Sciences.

MAEWEST Expression in Flower Development of Two Petunia Species

PubMed Central

Segatto, Ana Lúcia A.; Turchetto-Zolet, Andreia Carina; Aizza, Lilian Cristina B.; Monte-Bello, Carolina C.; Dornelas, Marcelo C.; Margis, Rogerio; Freitas, Loreta B.

2013-01-01

Changes in flower morphology may influence the frequency and specificity of animal visitors. In Petunia (Solanaceae), adaptation to different pollinators is one of the factors leading to species diversification within the genus. This study provides evidence that differential expression patterns of MAWEWEST (MAW) homologs in different Petunia species may be associated with adaptive changes in floral morphology. The Petunia × hybrida MAW gene belongs to the WOX (WUSCHEL-related homeobox) transcription factor family and has been identified as a controller of petal fusion during corolla formation. We analyzed the expression patterns of P. inflata and P. axillaris MAW orthologs (PiMAW and PaMAW, respectively) by reverse transcriptase polymerase chain reaction (RT-PCR), reverse transcription–quantitative PCR (qRT-PCR) and in situ hybridization in different tissues and different developmental stages of flowers in both species. The spatial expression patterns of PiMAW and PaMAW were similar in P. inflata and P. axillaris. Nevertheless, PaMAW expression level in P. axillaris was higher during the late bud development stage as compared to PiMAW in P. inflata. This work represents an expansion of petunia developmental research to wild accessions. PMID:23823801

Differential Gene Expression at Coral Settlement and Metamorphosis - A Subtractive Hybridization Study

PubMed Central

Hayward, David C.; Hetherington, Suzannah; Behm, Carolyn A.; Grasso, Lauretta C.; Forêt, Sylvain; Miller, David J.; Ball, Eldon E.

2011-01-01

Background A successful metamorphosis from a planktonic larva to a settled polyp, which under favorable conditions will establish a future colony, is critical for the survival of corals. However, in contrast to the situation in other animals, e.g., frogs and insects, little is known about the molecular basis of coral metamorphosis. We have begun to redress this situation with previous microarray studies, but there is still a great deal to learn. In the present paper we have utilized a different technology, subtractive hybridization, to characterize genes differentially expressed across this developmental transition and to compare the success of this method to microarray. Methodology/Principal Findings Suppressive subtractive hybridization (SSH) was used to identify two pools of transcripts from the coral, Acropora millepora. One is enriched for transcripts expressed at higher levels at the pre-settlement stage, and the other for transcripts expressed at higher levels at the post-settlement stage. Virtual northern blots were used to demonstrate the efficacy of the subtractive hybridization technique. Both pools contain transcripts coding for proteins in various functional classes but transcriptional regulatory proteins were represented more frequently in the post-settlement pool. Approximately 18% of the transcripts showed no significant similarity to any other sequence on the public databases. Transcripts of particular interest were further characterized by in situ hybridization, which showed that many are regulated spatially as well as temporally. Notably, many transcripts exhibit axially restricted expression patterns that correlate with the pool from which they were isolated. Several transcripts are expressed in patterns consistent with a role in calcification. Conclusions We have characterized over 200 transcripts that are differentially expressed between the planula larva and post-settlement polyp of the coral, Acropora millepora. Sequence, putative function, and in some cases temporal and spatial expression are reported. PMID:22065994

Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

PubMed Central

2012-01-01

Background During sexual development, filamentous ascomycetes form complex, three-dimensional fruiting bodies for the protection and dispersal of sexual spores. Fruiting bodies contain a number of cell types not found in vegetative mycelium, and these morphological differences are thought to be mediated by changes in gene expression. However, little is known about the spatial distribution of gene expression in fungal development. Here, we used laser microdissection (LM) and RNA-seq to determine gene expression patterns in young fruiting bodies (protoperithecia) and non-reproductive mycelia of the ascomycete Sordaria macrospora. Results Quantitative analysis showed major differences in the gene expression patterns between protoperithecia and total mycelium. Among the genes strongly up-regulated in protoperithecia were the pheromone precursor genes ppg1 and ppg2. The up-regulation was confirmed by fluorescence microscopy of egfp expression under the control of ppg1 regulatory sequences. RNA-seq analysis of protoperithecia from the sterile mutant pro1 showed that many genes that are differentially regulated in these structures are under the genetic control of transcription factor PRO1. Conclusions We have generated transcriptional profiles of young fungal sexual structures using a combination of LM and RNA-seq. This allowed a high spatial resolution and sensitivity, and yielded a detailed picture of gene expression during development. Our data revealed significant differences in gene expression between protoperithecia and non-reproductive mycelia, and showed that the transcription factor PRO1 is involved in the regulation of many genes expressed specifically in sexual structures. The LM/RNA-seq approach will also be relevant to other eukaryotic systems in which multicellular development is investigated. PMID:23016559

General theory for integrated analysis of growth, gene, and protein expression in biofilms.

PubMed

Zhang, Tianyu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S

2013-01-01

A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.

Faster embryonic segmentation through elevated Delta-Notch signalling

PubMed Central

Liao, Bo-Kai; Jörg, David J.; Oates, Andrew C.

2016-01-01

An important step in understanding biological rhythms is the control of period. A multicellular, rhythmic patterning system termed the segmentation clock is thought to govern the sequential production of the vertebrate embryo's body segments, the somites. Several genetic loss-of-function conditions, including the Delta-Notch intercellular signalling mutants, result in slower segmentation. Here, we generate DeltaD transgenic zebrafish lines with a range of copy numbers and correspondingly increased signalling levels, and observe faster segmentation. The highest-expressing line shows an altered oscillating gene expression wave pattern and shortened segmentation period, producing embryos with more, shorter body segments. Our results reveal surprising differences in how Notch signalling strength is quantitatively interpreted in different organ systems, and suggest a role for intercellular communication in regulating the output period of the segmentation clock by altering its spatial pattern. PMID:27302627

Patterns of expression of position-dependent integrated transgenes in mouse embryo.

PubMed Central

Bonnerot, C; Grimber, G; Briand, P; Nicolas, J F

1990-01-01

The abilities to introduce foreign DNA into the genome of mice and to visualize gene expression at the single-cell level underlie a method for defining individual elements of a genetic program. We describe the use of an Escherichia coli lacZ reporter gene fused to the promoter of the gene for hypoxanthine phosphoribosyl transferase that is expressed in all tissues. Most transgenic mice (six of seven) obtained with this construct express the lacZ gene from the hypoxanthine phosphoribosyltransferase promoter. Unexpectedly, however, the expression is temporally and spatially regulated. Each transgenic line is characterized by a specific, highly reproducible pattern of lacZ expression. These results show that, for expression, the integrated construct must be complemented by elements of the genome. These elements exert dominant developmental control on the hypoxanthine phosphoribosyltransferase promoter. The expression patterns in some transgenic mice conform to a typological marker and in others to a subtle combination of typology and topography. These observations define discrete heterogeneities of cell types and of certain structures, particularly in the nervous system and in the mesoderm. This system opens opportunities for developmental studies by providing cellular, molecular, and genetic markers of cell types, cell states, and cells from developmental compartments. Finally this method illustrates that genes transduced or transposed to a different position in the genome acquire different spatiotemporal specificities, a result that has implications for evolution. Images PMID:1696727

Plasticity of human spatial cognition: spatial language and cognition covary across cultures.

PubMed

Haun, Daniel B M; Rapold, Christian J; Janzen, Gabriele; Levinson, Stephen C

2011-04-01

The present paper explores cross-cultural variation in spatial cognition by comparing spatial reconstruction tasks by Dutch and Namibian elementary school children. These two communities differ in the way they predominantly express spatial relations in language. Four experiments investigate cognitive strategy preferences across different levels of task-complexity and instruction. Data show a correlation between dominant linguistic spatial frames of reference and performance patterns in non-linguistic spatial memory tasks. This correlation is shown to be stable across an increase of complexity in the spatial array. When instructed to use their respective non-habitual cognitive strategy, participants were not easily able to switch between strategies and their attempts to do so impaired their performance. These results indicate a difference not only in preference but also in competence and suggest that spatial language and non-linguistic preferences and competences in spatial cognition are systematically aligned across human populations. Copyright © 2011 Elsevier B.V. All rights reserved.

Non-Cell-Autonomous Regulation of Root Hair Patterning Genes by WRKY75 in Arabidopsis1[W

PubMed Central

Rishmawi, Louai; Pesch, Martina; Juengst, Christian; Schauss, Astrid C.; Schrader, Andrea; Hülskamp, Martin

2014-01-01

In Arabidopsis (Arabidopsis thaliana), root hairs are formed in cell files over the cleft of underlying cortex cells. This pattern is established by a well-known gene regulatory network of transcription factors. In this study, we show that WRKY75 suppresses root hair development in nonroot hair files and that it represses the expression of TRIPTYCHON and CAPRICE. The WRKY75 protein binds to the CAPRICE promoter in a yeast one-hybrid assay. Binding to the promoter fragment requires an intact WRKY protein-binding motif, the W box. A comparison of the spatial expression of WRKY75 and the localization of the WRKY75 protein revealed that WRKY75 is expressed in the pericycle and vascular tissue and that the WRKY75 RNA or protein moves into the epidermis. PMID:24676857

Transient expression of collagen type II at epitheliomesenchymal interfaces during morphogenesis of the cartilaginous neurocranium.

PubMed

Thorogood, P; Bee, J; von der Mark, K

1986-08-01

In the avian embryo a matrix-mediated tissue interaction between retinal pigmented epithelium and neural crest-derived periocular mesenchyme leads to the differentiation of (scleral) cartilage. The composition of the extracellular matrix at the interface between these two tissues has been examined immunohistochemically, both during and after the interaction has taken place. Of the matrix components studied (fibronectin, laminin, and collagen types I, II, IV, and V) only collagen type II displayed a dramatic change in distribution between the two stages. During the interaction, at stage 15, type II was present in the extracellular compartment basal to the epithelium. After completion of the interaction, collagen type II was no longer detectable at the interface even though it was readily detectable in the vitreous humor, cornea, and perinotochordal sheath, and subsequently will be expressed by the chondrogenic tissue itself as overt differentiation commences. These results suggest that collagen type II might be causally involved in this particular epitheliomesenchymal interaction. Examination of the spatial and temporal patterns of collagen type II expression elsewhere in the developing craniofacial complex revealed a hitherto unreported pattern of distribution. In addition to its predictable locations (i.e., cornea, vitreous, and perinotochordal sheath) it was found to be present at certain other sites, for example, at the basal surfaces of some neuroepithelia. These additional locations are all known to be sites of chondrogenesis-promoting tissue interactions which result in the formation of the elements of the cartilaginous neurocranium (e.g., otic vesicle). Furthermore this spatial distribution exhibits a changing temporal pattern in that it is detectable at the time that the interactions are known to be taking place, but subsequently is no longer detectable by the immunohistochemical means employed. This definable pattern of transient collagen type II expression, occurring at very early stages of craniofacial development, is interpreted as reflecting one level of morphogenetic specification of chondrocranial/skull form in the developing vertebrate head.

Multiple PAR and E4BP4 bZIP transcription factors in zebrafish: diverse spatial and temporal expression patterns.

PubMed

Ben-Moshe, Zohar; Vatine, Gad; Alon, Shahar; Tovin, Adi; Mracek, Philipp; Foulkes, Nicholas S; Gothilf, Yoav

2010-09-01

Circadian rhythms of physiology and behavior are generated by an autonomous circadian oscillator that is synchronized daily with the environment, mainly by light input. The PAR subfamily of transcriptional activators and the related E4BP4 repressor belonging to the basic leucine zipper (bZIP) family are clock-controlled genes that are suggested to mediate downstream circadian clock processes and to feedback onto the core oscillator. Here, the authors report the characterization of these genes in the zebrafish, an increasingly important model in the field of chronobiology. Five novel PAR and six novel e4bp4 zebrafish homolog genes were identified using bioinformatic tools and their coding sequences were cloned. Based on their evolutionary relationships, these genes were annotated as ztef2, zhlf1 and zhlf2, zdbp1 and zdbp2, and ze4bp4-1 to -6. The spatial and temporal mRNA expression pattern of each of these factors was characterized in zebrafish embryos in the context of a functional circadian clock and regulation by light. Nine of the factors exhibited augmented and rhythmic expression in the pineal gland, a central clock organ in zebrafish. Moreover, these genes were found to be regulated, to variable extents, by the circadian clock and/or by light. Differential expression patterns of multiple paralogs in zebrafish suggest multiple roles for these factors within the vertebrate circadian clock. This study, in the genetically accessible zebrafish model, lays the foundation for further research regarding the involvement and specific roles of PAR and E4BP4 transcription factors in the vertebrate circadian clock mechanism.

Self-organization of human embryonic stem cells on micropatterns

PubMed Central

Deglincerti, Alessia; Etoc, Fred; Guerra, M. Cecilia; Martyn, Iain; Metzger, Jakob; Ruzo, Albert; Simunovic, Mijo; Yoney, Anna; Brivanlou, Ali H.; Siggia, Eric; Warmflash, Aryeh

2018-01-01

Fate allocation in the gastrulating embryo is spatially organized as cells differentiate to specialized cell types depending on their positions with respect to the body axes. There is a need for in vitro protocols that allow the study of spatial organization associated with this developmental transition. While embryoid bodies and organoids can exhibit some spatial organization of differentiated cells, these methods do not yield consistent and fully reproducible results. Here, we describe a micropatterning approach where human embryonic stem cells are confined to disk-shaped, sub-millimeter colonies. After 42 hours of BMP4 stimulation, cells form self-organized differentiation patterns in concentric radial domains, which express specific markers associated with the embryonic germ layers, reminiscent of gastrulating embryos. Our protocol takes 3 days; it uses commercial microfabricated slides (CYTOO), human laminin-521 (LN-521) as extra-cellular matrix coating, and either conditioned or chemically-defined medium (mTeSR). Differentiation patterns within individual colonies can be determined by immunofluorescence and analyzed with cellular resolution. Both the size of the micropattern and the type of medium affect the patterning outcome. The protocol is appropriate for personnel with basic stem cell culture training. This protocol describes a robust platform for quantitative analysis of the mechanisms associated with pattern formation at the onset of gastrulation. PMID:27735934

Role of heat shock protein Hsp25 in the response of the orofacial nuclei motor system to physiological stress

NASA Technical Reports Server (NTRS)

Murashov, A. K.; Talebian, S.; Wolgemuth, D. J.

1998-01-01

Although expression of the small heat shock protein family member Hsp25 has been previously observed in the central nervous system (CNS), both constitutively and upon induction, its function in the CNS remains far from clear. In the present study we have characterized the spatial pattern of expression of Hsp25 in the normal adult mouse brain as well as the changes in expression patterns induced by subjecting mice to experimental hyperthermia or hypoxia. Immunohistochemical analysis revealed a surprisingly restricted pattern of constitutive expression of Hsp25 in the brain, limited to the facial, trigeminal, ambiguus, hypoglossal and vagal motor nuclei of the brainstem. After hyperthermia or hypoxia treatment, significant increases in the levels of Hsp25 were observed in these same areas and also in fibers of the facial and trigeminal nerve tracts. Immunoblot analysis of protein lysates from brainstem also showed the same pattern of induction of Hsp25. Surprisingly, no other area in the brain showed expression of Hsp25, in either control or stressed animals. The highly restricted expression of Hsp25 implies that this protein may have a specific physiological role in the orofacial motor nuclei, which govern precise coordination between muscles of mastication and the pharynx, larynx, and face. Its rapid induction after stress further suggests that Hsp25 may serve as a specific molecular chaperone in the lower cholinergic motor neurons and along their fibers under conditions of stress or injury. Copyright 1998 Elsevier Science B.V.

Regulatory role of AINTEGUMENTA in organ initiation and growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krizek, Beth Allyn; Lebioda, Lukasz

2005-03-01

Although several members of the plant-specific AP2/ERF family of transcription factors are important developmental regulators, many genes in this large protein family remain uncharacterized. Here, we present a phylogenetic analysis of the18 genes that make up the AP2 subgroup of this family. We report expression analyses of seven Arabidopsis genes most closely related to the floral development gene AINTEGUMENTA and show that all AINTEGUMENTA-like (AIL) genes are transcribed in multiple tissues during development. They are expressed primarily in young actively dividing tissues of a plant and not in mature leaves or stems. The spatial distribution of AIL5, AIL6, and AIL7more » mRNA in inflorescences was characterized by in situ hybridization. Each of these genes is expressed in a spatially and temporally distinct pattern within inflorescence meristems and flowers. Ectopic expression of AIL5 resulted in a larger floral organ phenotype, similar to that resulting from ectopic expression of ANT. Our results are consistent with AIL genes having roles in specification of meristematic or division-competent states.« less

The homeobox gene mirror links EGF signalling to embryonic dorso-ventral axis formation through notch activation.

PubMed

Jordan, K C; Clegg, N J; Blasi, J A; Morimoto, A M; Sen, J; Stein, D; McNeill, H; Deng, W M; Tworoger, M; Ruohola-Baker, H

2000-04-01

Recent studies in vertebrates and Drosophila melanogaster have revealed that Fringe-mediated activation of the Notch pathway has a role in patterning cell layers during organogenesis. In these processes, a homeobox-containing transcription factor is responsible for spatially regulating fringe (fng) expression and thus directing activation of the Notch pathway along the fng expression border. Here we show that this may be a general mechanism for patterning epithelial cell layers. At three stages in Drosophila oogenesis, mirror (mirr) and fng have complementary expression patterns in the follicle-cell epithelial layer, and at all three stages loss of mirr enlarges, and ectopic expression of mirr restricts, fng expression, with consequences for follicle-cell patterning. These morphological changes are similar to those caused by Notch mutations. Ectopic expression of mirr in the posterior follicle cells induces a stripe of rhomboid (rho) expression and represses pipe (pip), a gene with a role in the establishment of the dorsal-ventral axis, at a distance. Ectopic Notch activation has a similar long-range effect on pip. Our results suggest that Mirror and Notch induce secretion of diffusible morphogens and we have identified TGF-beta (encoded by dpp) as such a molecule in germarium. We also found that mirr expression in dorsal follicle cells is induced by the EGF-receptor (EGFR) pathway and that mirr then represses pip expression in all but the ventral follicle cells, connecting EGFR activation in the dorsal follicle cells to repression of pip in the dorsal and lateral follicle cells. Our results suggest that the differentiation of ventral follicle cells is not a direct consequence of germline signalling, but depends on long-range signals from dorsal follicle cells, and provide a link between early and late events in Drosophila embryonic dorsal-ventral axis formation.

A SoxC gene related to larval shell development and co-expression analysis of different shell formation genes in early larvae of oyster.

PubMed

Liu, Gang; Huan, Pin; Liu, Baozhong

2017-06-01

Among the potential larval shell formation genes in mollusks, most are expressed in cells surrounding the shell field during the early phase of shell formation. The only exception (cgi-tyr1) is expressed in the whole larval mantle and thus represents a novel type of expression pattern. This study reports another gene with such an expression pattern. The gene encoded a SoxC homolog of the Pacific oyster Crassostrea gigas and was named cgi-soxc. Whole-mount in situ hybridization revealed that the gene was highly expressed in the whole larval mantle of early larvae. Based on its spatiotemporal expression, cgi-soxc is hypothesized to be involved in periostracum biogenesis, biomineralization, and regulation of cell proliferation. Furthermore, we investigated the interrelationship between cgi-soxc expression and two additional potential shell formation genes, cgi-tyr1 and cgi-gata2/3. The results confirmed co-expression of the three genes in the larval mantle of early D-veliger. Nevertheless, cgi-gata2/3 was only expressed in the mantle edge, and the other two genes were expressed in all mantle cells. Based on the spatial expression patterns of the three genes, two cell groups were identified from the larval mantle (tyr1 + /soxc + /gata2/3 + cells and tyr1 + /soxc + /gata2/3 - cells) and are important to study the differentiation and function of this tissue. The results of this study enrich our knowledge on the structure and function of larval mantle and provide important information to understand the molecular mechanisms of larval shell formation.

Ectopic application of recombinant BMP-2 and BMP-4 can change patterning of developing chick facial primordia.

PubMed

Barlow, A J; Francis-West, P H

1997-01-01

The facial primordia initially consist of buds of undifferentiated mesenchyme, which give rise to a variety of tissues including cartilage, muscle and nerve. These must be arranged in a precise spatial order for correct function. The signals that control facial outgrowth and patterning are largely unknown. The bone morphogenetic proteins Bmp-2 and Bmp-4 are expressed in discrete regions at the distal tips of the early facial primordia suggesting possible roles for BMP-2 and BMP-4 during chick facial development. We show that expression of Bmp-4 and Bmp-2 is correlated with the expression of Msx-1 and Msx-2 and that ectopic application of BMP-2 and BMP-4 can activate Msx-1 and Msx-2 gene expression in the developing facial primordia. We correlate this activation of gene expression with changes in skeletal development. For example, activation of Msx-1 gene expression across the distal tip of the mandibular primordium is associated with an extension of Fgf-4 expression in the epithelium and bifurcation of Meckel's cartilage. In the maxillary primordium, extension of the normal domain of Msx-1 gene expression is correlated with extended epithelial expression of shh and bifurcation of the palatine bone. We also show that application of BMP-2 can increase cell proliferation of the mandibular primordia. Our data suggest that BMP-2 and BMP-4 are part of a signalling cascade that controls outgrowth and patterning of the facial primordia.

Contrasting visual working memory for verbal and non-verbal material with multivariate analysis of fMRI

PubMed Central

Habeck, Christian; Rakitin, Brian; Steffener, Jason; Stern, Yaakov

2012-01-01

We performed a delayed-item-recognition task to investigate the neural substrates of non-verbal visual working memory with event-related fMRI (‘Shape task’). 25 young subjects (mean age: 24.0 years; STD=3.8 years) were instructed to study a list of either 1,2 or 3 unnamable nonsense line drawings for 3 seconds (‘stimulus phase’ or STIM). Subsequently, the screen went blank for 7 seconds (‘retention phase’ or RET), and then displayed a probe stimulus for 3 seconds in which subject indicated with a differential button press whether the probe was contained in the studied shape-array or not (‘probe phase’ or PROBE). Ordinal Trend Canonical Variates Analysis (Habeck et al., 2005a) was performed to identify spatial covariance patterns that showed a monotonic increase in expression with memory load during all task phases. Reliable load-related patterns were identified in the stimulus and retention phase (p<0.01), while no significant pattern could be discerned during the probe phase. Spatial covariance patterns that were obtained from an earlier version of this task (Habeck et al., 2005b) using 1, 3, or 6 letters (‘Letter task’) were also prospectively applied to their corresponding task phases in the current non-verbal task version. Interestingly, subject expression of covariance patterns from both verbal and non-verbal retention phases correlated positively in the non-verbal task for all memory loads (p<0.0001). Both patterns also involved similar frontoparietal brain regions that were increasing in activity with memory load, and mediofrontal and temporal regions that were decreasing. Mean subject expression of both patterns across memory load during retention also correlated positively with recognition accuracy (dL) in the Shape task (p<0.005). These findings point to similarities in the neural substrates of verbal and non-verbal rehearsal processes. Encoding processes, on the other hand, are critically dependent on the to-be-remembered material, and seem to necessitate material-specific neural substrates. PMID:22652306

A computational statistics approach for estimating the spatial range of morphogen gradients

PubMed Central

Kanodia, Jitendra S.; Kim, Yoosik; Tomer, Raju; Khan, Zia; Chung, Kwanghun; Storey, John D.; Lu, Hang; Keller, Philipp J.; Shvartsman, Stanislav Y.

2011-01-01

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo. PMID:22007136

Divergence in Patterns of Leaf Growth Polarity Is Associated with the Expression Divergence of miR396

PubMed Central

2015-01-01

Lateral appendages often show allometric growth with a specific growth polarity along the proximo-distal axis. Studies on leaf growth in model plants have identified a basipetal growth direction with the highest growth rate at the proximal end and progressively lower rates toward the distal end. Although the molecular mechanisms governing such a growth pattern have been studied recently, variation in leaf growth polarity and, therefore, its evolutionary origin remain unknown. By surveying 75 eudicot species, here we report that leaf growth polarity is divergent. Leaf growth in the proximo-distal axis is polar, with more growth arising from either the proximal or the distal end; dispersed with no apparent polarity; or bidirectional, with more growth contributed by the central region and less growth at either end. We further demonstrate that the expression gradient of the miR396-GROWTH-REGULATING FACTOR module strongly correlates with the polarity of leaf growth. Altering the endogenous pattern of miR396 expression in transgenic Arabidopsis thaliana leaves only partially modified the spatial pattern of cell expansion, suggesting that the diverse growth polarities might have evolved via concerted changes in multiple gene regulatory networks. PMID:26410303

Diffusion and scaling during early embryonic pattern formation.

PubMed

Gregor, Thomas; Bialek, William; de Ruyter van Steveninck, Rob R; Tank, David W; Wieschaus, Eric F

2005-12-20

Development of spatial patterns in multicellular organisms depends on gradients in the concentration of signaling molecules that control gene expression. In the Drosophila embryo, Bicoid (Bcd) morphogen controls cell fate along 70% of the anteroposterior axis but is translated from mRNA localized at the anterior pole. Gradients of Bcd and other morphogens are thought to arise through diffusion, but this basic assumption has never been rigorously tested in living embryos. Furthermore, because diffusion sets a relationship between length and time scales, it is hard to see how patterns of gene expression established by diffusion would scale proportionately as egg size changes during evolution. Here, we show that the motion of inert molecules through the embryo is well described by the diffusion equation on the relevant length and time scales, and that effective diffusion constants are essentially the same in closely related dipteran species with embryos of very different size. Nonetheless, patterns of gene expression in these different species scale with egg length. We show that this scaling can be traced back to scaling of the Bcd gradient itself. Our results, together with constraints imposed by the time scales of development, suggest that the mechanism for scaling is a species-specific adaptation of the Bcd lifetime.

A MS-lesion pattern discrimination plot based on geostatistics.

PubMed

Marschallinger, Robert; Schmidt, Paul; Hofmann, Peter; Zimmer, Claus; Atkinson, Peter M; Sellner, Johann; Trinka, Eugen; Mühlau, Mark

2016-03-01

A geostatistical approach to characterize MS-lesion patterns based on their geometrical properties is presented. A dataset of 259 binary MS-lesion masks in MNI space was subjected to directional variography. A model function was fit to express the observed spatial variability in x, y, z directions by the geostatistical parameters Range and Sill. Parameters Range and Sill correlate with MS-lesion pattern surface complexity and total lesion volume. A scatter plot of ln(Range) versus ln(Sill), classified by pattern anisotropy, enables a consistent and clearly arranged presentation of MS-lesion patterns based on geometry: the so-called MS-Lesion Pattern Discrimination Plot. The geostatistical approach and the graphical representation of results are considered efficient exploratory data analysis tools for cross-sectional, follow-up, and medication impact analysis.

Spatial cell firing during virtual navigation of open arenas by head-restrained mice.

PubMed

Chen, Guifen; King, John Andrew; Lu, Yi; Cacucci, Francesca; Burgess, Neil

2018-06-18

We present a mouse virtual reality (VR) system which restrains head-movements to horizontal rotations, compatible with multi-photon imaging. This system allows expression of the spatial navigation and neuronal firing patterns characteristic of real open arenas (R). Comparing VR to R: place and grid, but not head-direction, cell firing had broader spatial tuning; place, but not grid, cell firing was more directional; theta frequency increased less with running speed; whereas increases in firing rates with running speed and place and grid cells' theta phase precession were similar. These results suggest that the omni-directional place cell firing in R may require local-cues unavailable in VR, and that the scale of grid and place cell firing patterns, and theta frequency, reflect translational motion inferred from both virtual (visual and proprioceptive) and real (vestibular translation and extra-maze) cues. By contrast, firing rates and theta phase precession appear to reflect visual and proprioceptive cues alone. © 2018, Chen et al.

Regularized Filters for L1-Norm-Based Common Spatial Patterns.

PubMed

Wang, Haixian; Li, Xiaomeng

2016-02-01

The l1 -norm-based common spatial patterns (CSP-L1) approach is a recently developed technique for optimizing spatial filters in the field of electroencephalogram (EEG)-based brain computer interfaces. The l1 -norm-based expression of dispersion in CSP-L1 alleviates the negative impact of outliers. In this paper, we further improve the robustness of CSP-L1 by taking into account noise which does not necessarily have as large a deviation as with outliers. The noise modelling is formulated by using the waveform length of the EEG time course. With the noise modelling, we then regularize the objective function of CSP-L1, in which the l1-norm is used in two folds: one is the dispersion and the other is the waveform length. An iterative algorithm is designed to resolve the optimization problem of the regularized objective function. A toy illustration and the experiments of classification on real EEG data sets show the effectiveness of the proposed method.

METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters.

PubMed

Geffers, Lars; Tetzlaff, Benjamin; Cui, Xiao; Yan, Jun; Eichele, Gregor

2013-01-01

METscout (http://metscout.mpg.de) brings together metabolism and gene expression landscapes. It is a MySQL relational database linking biochemical pathway information with 3D patterns of gene expression determined by robotic in situ hybridization in the E14.5 mouse embryo. The sites of expression of ∼1500 metabolic enzymes and of ∼350 solute carriers (SLCs) were included and are accessible as single cell resolution images and in the form of semi-quantitative image abstractions. METscout provides several graphical web-interfaces allowing navigation through complex anatomical and metabolic information. Specifically, the database shows where in the organism each of the many metabolic reactions take place and where SLCs transport metabolites. To link enzymatic reactions and transport, the KEGG metabolic reaction network was extended to include metabolite transport. This network in conjunction with spatial expression pattern of the network genes allows for a tracing of metabolic reactions and transport processes across the entire body of the embryo.

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

PubMed

Knowles, David W; Biggin, Mark D

2013-01-01

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

High temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

PubMed Central

Kuang, Zheng; Cai, Ling; Zhang, Xuekui; Ji, Hongkai; Tu, Benjamin P.; Boeke, Jef D.

2014-01-01

Under continuous, glucose-limited conditions, budding yeast exhibit robust metabolic cycles associated with major oscillations of gene expression. How such fluctuations are linked to changes in chromatin status is not well understood. Here we examine the correlated genome-wide transcription and chromatin states across the yeast metabolic cycle at unprecedented temporal resolution, revealing a “just-in-time supply chain” by which components from specific cellular processes such as ribosome biogenesis become available in a highly coordinated manner. We identify distinct chromatin and splicing patterns associated with different gene categories and determine the relative timing of chromatin modifications to maximal transcription. There is unexpected variation in the chromatin modification and expression relationship, with histone acetylation peaks occurring with varying timing and “sharpness” relative to RNA expression both within and between cycle phases. Chromatin modifier occupancy reveals subtly distinct spatial and temporal patterns compared to the modifications themselves. PMID:25173176

A segmental pattern of alkaline phosphatase activity within the notochord coincides with the initial formation of the vertebral bodies.

PubMed

Grotmol, Sindre; Nordvik, Kari; Kryvi, Harald; Totland, Geir K

2005-05-01

This study shows that segmental expression of alkaline phosphatase (ALP) activity by the notochord of the Atlantic salmon (Salmo salar L.) coincides with the initial mineralization of the vertebral body (chordacentrum), and precedes ALP expression by presumed somite-derived cells external to the notochordal sheath. The early expression of ALP indicates that the notochord plays an instructive role in the segmental patterning of the vertebral column. The chordacentra form segmentally as mineralized rings within the notochordal sheath, and ALP activity spreads within the chordoblast layer from ventral to dorsal, displaying the same progression and spatial distribution as the mineralization process. No ALP activity was observed in sclerotomal mesenchyme surrounding the notochordal sheath during initial formation of the chordacentra. Our results support previous findings indicating that the chordoblasts initiate a segmental differentiation of the notochordal sheath into chordacentra and intervertebral regions.

Diurnal lighting patterns and habitat alter opsin expression and colour preferences in a killifish

PubMed Central

Johnson, Ashley M.; Stanis, Shannon; Fuller, Rebecca C.

2013-01-01

Spatial variation in lighting environments frequently leads to population variation in colour patterns, colour preferences and visual systems. Yet lighting conditions also vary diurnally, and many aspects of visual systems and behaviour vary over this time scale. Here, we use the bluefin killifish (Lucania goodei) to compare how diurnal variation and habitat variation (clear versus tannin-stained water) affect opsin expression and the preference to peck at different-coloured objects. Opsin expression was generally lowest at midnight and dawn, and highest at midday and dusk, and this diurnal variation was many times greater than variation between habitats. Pecking preference was affected by both diurnal and habitat variation but did not correlate with opsin expression. Rather, pecking preference matched lighting conditions, with higher preferences for blue at noon and for red at dawn/dusk, when these wavelengths are comparatively scarce. Similarly, blue pecking preference was higher in tannin-stained water where blue wavelengths are reduced. In conclusion, L. goodei exhibits strong diurnal cycles of opsin expression, but these are not tightly correlated with light intensity or colour. Temporally variable pecking preferences probably result from lighting environment rather than from opsin production. These results may have implications for the colour pattern diversity observed in these fish. PMID:23698009

Hox genes and the parasitic flatworms: new opportunities, challenges and lessons from the free-living.

PubMed

Olson, P D

2008-03-01

Research into the roles played by Hox and related homeotic gene families in the diverse and complex developmental programmes exhibited by parasitic flatworms (Platyhelminthes) can hardly be said to have begun, and thus presents considerable opportunity for new research. Although featured in some of the earliest screens for homeotic genes outside Drosophila and mice, surveys in parasitic flatworms are few in number and almost nothing is yet known of where or when the genes are expressed during ontogeny. This contrasts sharply with a significant body of literature concerning Hox genes in free-living flatworms which have long served as models for the study of regeneration and the maintenance of omnipotent cell lines. Nevertheless, available information suggests that the complement of Hox genes and other classes of homeobox-containing genes in parasitic flatworms is typical of their free-living cousins and of other members of the Lophotrochozoa. Recent work on Schistosoma combined with information on Hox gene expression in planarians indicates that at least some disruption of the clustered genomic arrangement of the genes, as well as of the strict spatial and temporal colinear patterns of expression typical in other groups, may be characteristic of flatworms. However, available data on the genomic arrangement and expression of flatworm Hox genes is so limited at present that such generalities are highly tenuous. Moreover, a basic underlying pattern of colinearity is still observed in their spatial expression patterns making them suitable as cell or region-specific markers. I discuss a number of fundamental developmental questions and some of the challenges to addressing them in relation to each of the major parasitic lineages. In addition, I present newly characterized Hox genes from the model tapeworm Hymenolepis and analyze these by Bayesian inference together with >100 Hox and ParaHox homeodomains of flatworms and select lophotrochozoan taxa, providing a phylogenetic scaffold for their identification.

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

PubMed Central

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J.

2015-01-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes. PMID:25950438

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans.

PubMed

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J

2015-05-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3' UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes.

Pattern Formation and Strong Nonlinear Interactions in Exciton-Polariton Condensates

NASA Astrophysics Data System (ADS)

Ge, Li; Nersisyan, Ani; Oztop, Baris; Tureci, Hakan

2014-03-01

Exciton-polaritons generated by light-induced potentials can spontaneously condense into macroscopic quantum states that display nontrivial spatial and temporal density modulation. While these patterns and their dynamics can be reproduced through the solution of the generalized Gross-Pitaevskii equation, a predictive theory of their thresholds, oscillation frequencies, and multi-pattern interactions has so far been lacking. Here we represent such an approach based on current-carrying quasi-modes of the non-Hermitian potential induced by the pump. The presented theory allows us to capture the patterns formed in the steady-state directly and account for nonlinearities exactly. We find a simple but powerful expression for thresholds of condensation and the associated frequencies of oscillations, quantifying the contribution of particle formation, leakage, and interactions. We also show that the evolution of the condensate with increasing pump strength is strongly geometry dependent and can display contrasting features such as enhancement or reduction of the spatial localization of the condensate. We acknowledge support by DARPA under Grant No. N66001-11-1-4162 and NSF under CAREER Grant No. DMR-1151810.

Integrated circuit-based electrochemical sensor for spatially resolved detection of redox-active metabolites in biofilms.

PubMed

Bellin, Daniel L; Sakhtah, Hassan; Rosenstein, Jacob K; Levine, Peter M; Thimot, Jordan; Emmett, Kevin; Dietrich, Lars E P; Shepard, Kenneth L

2014-01-01

Despite advances in monitoring spatiotemporal expression patterns of genes and proteins with fluorescent probes, direct detection of metabolites and small molecules remains challenging. A technique for spatially resolved detection of small molecules would benefit the study of redox-active metabolites that are produced by microbial biofilms and can affect their development. Here we present an integrated circuit-based electrochemical sensing platform featuring an array of working electrodes and parallel potentiostat channels. 'Images' over a 3.25 × 0.9 mm(2) area can be captured with a diffusion-limited spatial resolution of 750 μm. We demonstrate that square wave voltammetry can be used to detect, identify and quantify (for concentrations as low as 2.6 μM) four distinct redox-active metabolites called phenazines. We characterize phenazine production in both wild-type and mutant Pseudomonas aeruginosa PA14 colony biofilms, and find correlations with fluorescent reporter imaging of phenazine biosynthetic gene expression.

Integrated circuit-based electrochemical sensor for spatially resolved detection of redox-active metabolites in biofilms

PubMed Central

Bellin, Daniel L.; Sakhtah, Hassan; Rosenstein, Jacob K.; Levine, Peter M.; Thimot, Jordan; Emmett, Kevin; Dietrich, Lars E. P.; Shepard, Kenneth L.

2014-01-01

Despite advances in monitoring spatiotemporal expression patterns of genes and proteins with fluorescent probes, direct detection of metabolites and small molecules remains challenging. A technique for spatially resolved detection of small molecules would benefit the study of redox-active metabolites produced by microbial biofilms, which can drastically affect colony development. Here we present an integrated circuit-based electrochemical sensing platform featuring an array of working electrodes and parallel potentiostat channels. “Images” over a 3.25 × 0.9 mm area can be captured with a diffusion-limited spatial resolution of 750 μm. We demonstrate that square wave voltammetry can be used to detect, identify, and quantify (for concentrations as low as 2.6 μM) four distinct redox-active metabolites called phenazines. We characterize phenazine production in both wild-type and mutant Pseudomonas aeruginosa PA14 colony biofilms, and find correlations with fluorescent reporter imaging of phenazine biosynthetic gene expression. PMID:24510163

Development of the Neurochemical Architecture of the Central Complex

PubMed Central

Boyan, George S.; Liu, Yu

2016-01-01

The central complex represents one of the most conspicuous neuroarchitectures to be found in the insect brain and regulates a wide repertoire of behaviors including locomotion, stridulation, spatial orientation and spatial memory. In this review article, we show that in the grasshopper, a model insect system, the intricate wiring of the fan-shaped body (FB) begins early in embryogenesis when axons from the first progeny of four protocerebral stem cells (called W, X, Y, Z, respectively) in each brain hemisphere establish a set of tracts to the primary commissural system. Decussation of subsets of commissural neurons at stereotypic locations across the brain midline then establishes a columnar neuroarchitecture in the FB which is completed during embryogenesis. Examination of the expression patterns of various neurochemicals in the central complex including neuropeptides, a neurotransmitter and the gas nitric oxide (NO), show that these appear progressively and in a substance-specific manner during embryogenesis. Each neuroactive substance is expressed by neurons located at stereotypic locations in a given central complex lineage, confirming that the stem cells are biochemically multipotent. The organization of axons expressing the various neurochemicals within the central complex is topologically related to the location, and hence birthdate, of the neurons within the lineages. The neurochemical expression patterns within the FB are layered, and so reflect the temporal topology present in the lineages. This principle relates the neuroanatomical to the neurochemical architecture of the central complex and so may provide insights into the development of adaptive behaviors. PMID:27630548

Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci.

PubMed

Scemama, Jean-Luc; Hunter, Michael; McCallum, Jeff; Prince, Victoria; Stellwag, Edmund

2002-10-15

Hox gene expression is regulated by a complex array of cis-acting elements that control spatial and temporal gene expression in developing embryos. Here, we report the isolation of the striped bass Hoxb2a gene, comparison of its expression to the orthologous gene from zebrafish, and comparative genomic analysis of the upstream regulatory region to that of other vertebrates. Comparison of the Hoxb2a gene expression patterns from striped bass to zebrafish revealed similar expression patterns within rhombomeres 3, 4, and 5 of the hindbrain but a notable absence of expression in neural crest tissues of striped bass while neural crest expression is observed in zebrafish and common to other vertebrates. Comparative genomic analysis of the striped bass Hoxb2a-b3a intergenic region to those from zebrafish, pufferfish, human, and mouse demonstrated the presence of common Meis, Hox/Pbx, Krox-20, and Box 1 elements, which are necessary for rhombomere 3, 4, and 5 expression. Despite their common occurrence, the location and orientation of these transcription elements differed among the five species analyzed, such that Krox-20 and Box 1 elements are located 3' to the Meis, Hox/Pbx elements in striped bass, pufferfish, and human while they are located 5' of this r4 enhancer in zebrafish and mouse. Our results suggest that the plasticity exhibited in the organization of key regulatory elements responsible for rhombomere-specific Hoxb2a expression may reflect the effects of stabilizing selection in the evolution cis-acting elements. Copyright 2002 Wiley-Liss, Inc.

Genome-wide characterization of the Pectate Lyase-like (PLL) genes in Brassica rapa.

PubMed

Jiang, Jingjing; Yao, Lina; Miao, Ying; Cao, Jiashu

2013-11-01

Pectate lyases (PL) depolymerize demethylated pectin (pectate, EC 4.2.2.2) by catalyzing the eliminative cleavage of α-1,4-glycosidic linked galacturonan. Pectate Lyase-like (PLL) genes are one of the largest and most complex families in plants. However, studies on the phylogeny, gene structure, and expression of PLL genes are limited. To understand the potential functions of PLL genes in plants, we characterized their intron-exon structure, phylogenetic relationships, and protein structures, and measured their expression patterns in various tissues, specifically the reproductive tissues in Brassica rapa. Sequence alignments revealed two characteristic motifs in PLL genes. The chromosome location analysis indicated that 18 of the 46 PLL genes were located in the least fractionated sub-genome (LF) of B. rapa, while 16 were located in the medium fractionated sub-genome (MF1) and 12 in the more fractionated sub-genome (MF2). Quantitative RT-PCR analysis showed that BrPLL genes were expressed in various tissues, with most of them being expressed in flowers. Detailed qRT-PCR analysis identified 11 pollen specific PLL genes and several other genes with unique spatial expression patterns. In addition, some duplicated genes showed similar expression patterns. The phylogenetic analysis identified three PLL gene subfamilies in plants, among which subfamily II might have evolved from gene neofunctionalization or subfunctionalization. Therefore, this study opens the possibility for exploring the roles of PLL genes during plant development.

cis-Regulatory control of the initial neurogenic pattern of onecut gene expression in the sea urchin embryo.

PubMed

Barsi, Julius C; Davidson, Eric H

2016-01-01

Specification of the ciliated band (CB) of echinoid embryos executes three spatial functions essential for postgastrular organization. These are establishment of a band about 5 cells wide which delimits and bounds other embryonic territories; definition of a neurogenic domain within this band; and generation within it of arrays of ciliary cells that bear the special long cilia from which the structure derives its name. In Strongylocentrotus purpuratus the spatial coordinates of the future ciliated band are initially and exactly determined by the disposition of a ring of cells that transcriptionally activate the onecut homeodomain regulatory gene, beginning in blastula stage, long before the appearance of the CB per se. Thus the cis-regulatory apparatus that governs onecut expression in the blastula directly reveals the genomic sequence code by which these aspects of the spatial organization of the embryo are initially determined. We screened the entire onecut locus and its flanking region for transcriptionally active cis-regulatory elements, and by means of BAC recombineered deletions identified three separated and required cis-regulatory modules that execute different functions. The operating logic of the crucial spatial control module accounting for the spectacularly precise and beautiful early onecut expression domain depends on spatial repression. Previously predicted oral ectoderm and aboral ectoderm repressors were identified by cis-regulatory mutation as the products of goosecoid and irxa genes respectively, while the pan-ectodermal activator SoxB1 supplies a transcriptional driver function. Copyright © 2015. Published by Elsevier Inc.

Examination of the genetic basis for sexual dimorphism in the Aedes aegypti (dengue vector mosquito) pupal brain

PubMed Central

2014-01-01

Background Most animal species exhibit sexually dimorphic behaviors, many of which are linked to reproduction. A number of these behaviors, including blood feeding in female mosquitoes, contribute to the global spread of vector-borne illnesses. However, knowledge concerning the genetic basis of sexually dimorphic traits is limited in any organism, including mosquitoes, especially with respect to differences in the developing nervous system. Methods Custom microarrays were used to examine global differences in female vs. male gene expression in the developing pupal head of the dengue vector mosquito, Aedes aegypti. The spatial expression patterns of a subset of differentially expressed transcripts were examined in the developing female vs. male pupal brain through in situ hybridization experiments. Small interfering RNA (siRNA)-mediated knockdown studies were used to assess the putative role of Doublesex, a terminal component of the sex determination pathway, in the regulation of sex-specific gene expression observed in the developing pupal brain. Results Transcripts (2,527), many of which were linked to proteolysis, the proteasome, metabolism, catabolic, and biosynthetic processes, ion transport, cell growth, and proliferation, were found to be differentially expressed in A. aegypti female vs. male pupal heads. Analysis of the spatial expression patterns for a subset of dimorphically expressed genes in the pupal brain validated the data set and also facilitated the identification of brain regions with dimorphic gene expression. In many cases, dimorphic gene expression localized to the optic lobe. Sex-specific differences in gene expression were also detected in the antennal lobe and mushroom body. siRNA-mediated gene targeting experiments demonstrated that Doublesex, a transcription factor with consensus binding sites located adjacent to many dimorphically expressed transcripts that function in neural development, is required for regulation of sex-specific gene expression in the developing A. aegypti brain. Conclusions These studies revealed sex-specific gene expression profiles in the developing A. aegypti pupal head and identified Doublesex as a key regulator of sexually dimorphic gene expression during mosquito neural development. PMID:25729562

Differential expression of syndecan isoforms during mouse incisor amelogenesis.

PubMed

Muto, Taro; Miyoshi, Keiko; Munesue, Seiichi; Nakada, Hiroshi; Okayama, Minoru; Matsuo, Takashi; Noma, Takafumi

2007-08-01

Syndecans are transmembranous heparan sulfate proteoglycans (HSPGs) with covalently attached glycosaminoglycan side-chains located on the cell surface. The mammalian syndecan family is composed of four types of syndecans (syndecan-1 to -4). Syndecans interact with the intracellular cytoskeleton through the cytoplasmic domains of their core proteins and membrane proteins, extracellular enzymes, growth factors, and matrix components, through their heparan-sulfate chains, to regulate developmental processes.Here, as a first step to assess the possible roles of syndecan proteins in amelogenesis, we examined the expression patterns of all syndecan isoforms in continuously growing mouse incisors, in which we can overview major differentiation stages of amelogenesis at a glance. Understanding the expression domain of each syndecan isoform during specific developmental stages seems useful for investigating their physiological roles in amelogenesis. Immunohistochemical analysis of syndecan core proteins in the lower incisors from postnatal day 1 mice revealed spatially and temporally specific expression patterns, with syndecan-1 expressed in undifferentiated epithelial and mesenchymal cells, and syndecan-2, -3, and -4 in more differentiated cells. These findings suggest that each syndecan isoform functions distinctly during the amelogenesis of the incisors of mice.

Tree-based approach for exploring marine spatial patterns with raster datasets.

PubMed

Liao, Xiaohan; Xue, Cunjin; Su, Fenzhen

2017-01-01

From multiple raster datasets to spatial association patterns, the data-mining technique is divided into three subtasks, i.e., raster dataset pretreatment, mining algorithm design, and spatial pattern exploration from the mining results. Comparison with the former two subtasks reveals that the latter remains unresolved. Confronted with the interrelated marine environmental parameters, we propose a Tree-based Approach for eXploring Marine Spatial Patterns with multiple raster datasets called TAXMarSP, which includes two models. One is the Tree-based Cascading Organization Model (TCOM), and the other is the Spatial Neighborhood-based CAlculation Model (SNCAM). TCOM designs the "Spatial node→Pattern node" from top to bottom layers to store the table-formatted frequent patterns. Together with TCOM, SNCAM considers the spatial neighborhood contributions to calculate the pattern-matching degree between the specified marine parameters and the table-formatted frequent patterns and then explores the marine spatial patterns. Using the prevalent quantification Apriori algorithm and a real remote sensing dataset from January 1998 to December 2014, a successful application of TAXMarSP to marine spatial patterns in the Pacific Ocean is described, and the obtained marine spatial patterns present not only the well-known but also new patterns to Earth scientists.

Inter-dependent tissue growth and Turing patterning in a model for long bone development

NASA Astrophysics Data System (ADS)

Tanaka, Simon; Iber, Dagmar

2013-10-01

The development of long bones requires a sophisticated spatial organization of cellular signalling, proliferation, and differentiation programs. How such spatial organization emerges on the growing long bone domain is still unresolved. Based on the reported biochemical interactions we developed a regulatory model for the core signalling factors IHH, PTCH1, and PTHrP and included two cell types, proliferating/resting chondrocytes and (pre-)hypertrophic chondrocytes. We show that the reported IHH-PTCH1 interaction gives rise to a Schnakenberg-type Turing kinetics, and that inclusion of PTHrP is important to achieve robust patterning when coupling patterning and tissue dynamics. The model reproduces relevant spatiotemporal gene expression patterns, as well as a number of relevant mutant phenotypes. In summary, we propose that a ligand-receptor based Turing mechanism may control the emergence of patterns during long bone development, with PTHrP as an important mediator to confer patterning robustness when the sensitive Turing system is coupled to the dynamics of a growing and differentiating tissue. We have previously shown that ligand-receptor based Turing mechanisms can also result from BMP-receptor, SHH-receptor, and GDNF-receptor interactions, and that these reproduce the wildtype and mutant patterns during digit formation in limbs and branching morphogenesis in lung and kidneys. Receptor-ligand interactions may thus constitute a general mechanism to generate Turing patterns in nature.

Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method.

PubMed

Chen, Jiawen; Xie, Zhong-Ru; Wu, Yinghao

2016-07-01

The ligand-binding of membrane receptors on cell surfaces initiates the dynamic process of cross-membrane signal transduction. It is an indispensable part of the signaling network for cells to communicate with external environments. Recent experiments revealed that molecular components in signal transduction are not randomly mixed, but spatially organized into distinctive patterns. These patterns, such as receptor clustering and ligand oligomerization, lead to very different gene expression profiles. However, little is understood about the molecular mechanisms and functional impacts of this spatial-temporal regulation in cross-membrane signal transduction. In order to tackle this problem, we developed a hybrid computational method that decomposes a model of signaling network into two simulation modules. The physical process of binding between receptors and ligands on cell surfaces are simulated by a diffusion-reaction algorithm, while the downstream biochemical reactions are modeled by stochastic simulation of Gillespie algorithm. These two processes are coupled together by a synchronization framework. Using this method, we tested the dynamics of a simple signaling network in which the ligand binding of cell surface receptors triggers the phosphorylation of protein kinases, and in turn regulates the expression of target genes. We found that spatial aggregation of membrane receptors at cellular interfaces is able to either amplify or inhibit downstream signaling outputs, depending on the details of clustering mechanism. Moreover, by providing higher binding avidity, the co-localization of ligands into multi-valence complex modulates signaling in very different ways that are closely related to the binding affinity between ligand and receptor. We also found that the temporal oscillation of the signaling pathway that is derived from genetic feedback loops can be modified by the spatial clustering of membrane receptors. In summary, our method demonstrates the functional importance of spatial organization in cross-membrane signal transduction. The method can be applied to any specific signaling pathway in cells.

Comparative study of MSX-2, DLX-5, and DLX-7 gene expression during early human tooth development.

PubMed

Davideau, J L; Demri, P; Hotton, D; Gu, T T; MacDougall, M; Sharpe, P; Forest, N; Berdal, A

1999-12-01

Msx and Dlx family transcription factors are key elements of craniofacial development and act in specific combinations with growth factors to control the position and shape of various skeletal structures in mice. In humans, the mutations of MSX and DLX genes are associated with specific syndromes, such as tooth agenesis, craniosynostosis, and tricho-dento-osseous syndrome. To establish some relationships between those reported human syndromes, previous experimental data in mice, and the expression patterns of MSX and DLX homeogenes in the human dentition, we investigated MSX-2, DLX-5, and DLX-7 expression patterns and compared them in orofacial tissues of 7.5- to 9-wk-old human embryos by using in situ hybridization. Our data showed that MSX-2 was strongly expressed in the progenitor cells of human orofacial skeletal structures, including mandible and maxilla bones, Meckel's cartilage, and tooth germs, as shown for DLX-5. DLX-7 expression was restricted to the vestibular lamina and, later on, to the vestibular part of dental epithelium. The comparison of MSX-2, DLX-5, and DLX-7 expression patterns during the early stages of development of different human tooth types showed the existence of spatially ordered sequences of homeogene expression along the vestibular/lingual axis of dental epithelium. The expression of MSX-2 in enamel knot, as well as the coincident expression of MSX-2, DLX-5, and DLX-7 in a restricted vestibular area of dental epithelium, suggests the existence of various organizing centers involved in the control of human tooth morphogenesis.

Dynamic expression of chymotrypsin-like elastase 1 over the course of murine lung development

PubMed Central

Liu, Sheng; Young, Sarah Marie

2014-01-01

Postnatal lung development requires coordination of three processes (surface area expansion, microvascular growth, and matrix remodeling). Because normal elastin structure is important for lung morphogenesis, because physiological remodeling of lung elastin has never been defined, and because elastin remodeling is angiogenic, we sought to test the hypothesis that, during lung development, elastin is remodeled in a defined temporal-spatial pattern, that a novel protease is associated with this remodeling, and that angiogenesis is associated with elastin remodeling. By elastin in situ zymography, lung elastin remodeling increased 24-fold between embryonic day (E) 15.5 and postnatal day (PND) 14. Remodeling was restricted to major vessels and airways on PND1 with a sevenfold increase in alveolar wall elastin remodeling from PND1 to PND14. By inhibition assays and literature review, we identified chymotrypsin-like elastase 1 (CELA1) as a potential mediator of elastin remodeling. CELA1 mRNA levels increased 12-fold from E15.5 to PND9, and protein levels increased 3.4-fold from E18.5 to PND9. By costaining experiments, the temporal-spatial pattern of CELA1 expression matched that of elastin remodeling, and 58–85% of CELA1+ cells were <10 μm from an elastase signal. An association between elastin remodeling and angiogenesis was tested by similar methods. At PND7 and PND14, 60–95% of angiogenin+ cells were associated with elastin remodeling. Both elastase inhibition and CELA1 silencing impaired angiogenesis in vitro. Our data defines the temporal-spatial pattern of elastin remodeling during lung development, demonstrates an association of this remodeling with CELA1, and supports a role for elastin remodeling in regulating angiogenesis. PMID:24793170

Detailed analysis of the δ-crystallin mRNA-expressing region in early development of the chick pituitary gland.

PubMed

Inoue, Makiko; Shiina, Tomoya; Aizawa, Sayaka; Sakata, Ichiro; Takagi, Hiroyasu; Sakai, Takafumi

2012-06-01

Although δ-crystallin (δ-crys), also known as lens protein, is transiently expressed in Rathke's pouch (RP) of the chick embryo, detailed temporal and spatial expression patterns have been obscure. In this study, to understand the relationship between the δ-crys mRNA-expressing region and RP formation, we examined the embryonic expression pattern of δ-crys mRNA in the primordium of the adenohypophysis. δ-crys mRNA expression was initially found at stage 15 anterior to the foregut and posterior to the invaginated oral ectoderm. After RP formation, the δ-crys mRNA was expressed in the post-ventral region of RP and the anterior region of RP. δ-crys mRNA expression was then restricted to the cephalic lobe of the pituitary gland. From stage 20, the δ-crys and alpha-glycoprotein subunit (αGSU) mRNA-expressing regions were almost completely overlapping. The αGSU mRNA-expressing region is thought to be the primordium of the pars tuberalis, and these regions were overlapped with the Lhx3 mRNA-expressing region. The intensity of δ-crys mRNA expression gradually decreased with development and completely disappeared by stage 34. These results suggest that the embryonic chick pituitary gland consists of two different regions labeled with δ-crys and Lhx3.

Long-lasting spatial learning and memory impairments caused by chronic cerebral hypoperfusion associate with a dynamic change of HCN1/HCN2 expression in hippocampal CA1 region.

PubMed

Luo, Pan; Lu, Yun; Li, Changjun; Zhou, Mei; Chen, Cheng; Lu, Qing; Xu, Xulin; He, Zhi; Guo, Lianjun

2015-09-01

Chronic cerebral hypoperfusion (CCH) causes learning and memory impairments and increases the risk of Alzheimer disease (AD) and vascular dementia (VD) through several biologically plausible pathways, yet the mechanisms underlying the disease process remained unclear particularly in a temporal manner. We performed permanent bilateral occlusion of the common carotid arteries (two-vessel occlusion, 2VO) to induce CCH. To determine whether hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are altered at different stages of cognitive impairment caused by CCH, adult male SD rats were randomly distributed into sham-operated 4, 8 and 12weeks group, 2VO 4, 8 and 12weeks group. Learning and memory performance were evaluated with Morris water maze (MWM) and long-term potentiation (LTP) was used to address the underlying synaptic mechanisms. Expression of NeuN, HCN1 and HCN2 in hippocampal CA1, DG and CA3 areas was quantified by immunohistochemistry and western blotting. Our data showed that CCH induced a remarkable spatial learning and memory deficits in rats of 2VO 4, 8, and 12weeks group although neuronal loss only occurred after 4weeks of 2VO surgery in CA1. In addition, a significant reduction of HCN1 surface expression in CA1 was observed in the group that suffered 4weeks ischemia but neither 8 nor 12weeks. However, HCN2 surface expression in CA1 increased throughout the ischemia time-scales (4, 8 and 12w). Our findings indicate spatial learning and memory deficits in the CCH model are associated with disturbed HCN1 and HCN2 surface expression in hippocampal CA1. The altered patterns of both HCN1 and HCN2 surface expression may be implicated in the early stage (4w) of spatial learning and memory impairments; and the stable and long-lasting impairments of spatial learning and memory may partially attribute to the up-regulated HCN2 surface expression. Copyright © 2015 Elsevier Inc. All rights reserved.

Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development.

PubMed

Endale, Mehari; Ahlfeld, Shawn; Bao, Erik; Chen, Xiaoting; Green, Jenna; Bess, Zach; Weirauch, Matthew T; Xu, Yan; Perl, Anne Karina

2017-05-15

Many studies have investigated the source and role of epithelial progenitors during lung development; such information is limited for fibroblast populations and their complex role in the developing lung. In this study, we characterized the spatial location, mRNA expression and Immunophenotyping of PDGFRα + fibroblasts during sacculation and alveolarization. Confocal microscopy identified spatial association of PDGFRα expressing fibroblasts with proximal epithelial cells of the branching bronchioles and the dilating acinar tubules at E16.5; with distal terminal saccules at E18.5; and with alveolar epithelial cells at PN7 and PN28. Immunohistochemistry for alpha smooth muscle actin revealed that PDGFRα + fibroblasts contribute to proximal peribronchiolar smooth muscle at E16.5 and to transient distal alveolar myofibroblasts at PN7. Time series RNA-Seq analyses of PDGFRα + fibroblasts identified differentially expressed genes that, based on gene expression similarity were clustered into 7 major gene expression profile patterns. The presence of myofibroblast and smooth muscle precursors at E16.5 and PN7 was reflected by a two-peak gene expression profile on these days and gene ontology enrichment in muscle contraction. Additional molecular and functional differences between peribronchiolar smooth muscle cells at E16.5 and transient intraseptal myofibroblasts at PN7 were suggested by a single peak in gene expression at PN7 with functional enrichment in cell projection and muscle cell differentiation. Immunophenotyping of subsets of PDGFRα + fibroblasts by flow cytometry confirmed the predicted increase in proliferation at E16.5 and PN7, and identified subsets of CD29 + myofibroblasts and CD34 + lipofibroblasts. These data can be further mined to develop novel hypotheses and valuable understanding of the molecular and cellular basis of alveolarization. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development☆

PubMed Central

Endale, Mehari; Ahlfeld, Shawn; Bao, Erik; Chen, Xiaoting; Green, Jenna; Bess, Zach; Weirauch, Matthew T.; Xu, Yan; Perl, Anne Karina

2017-01-01

Many studies have investigated the source and role of epithelial progenitors during lung development; such information is limited for fibroblast populations and their complex role in the developing lung. In this study, we characterized the spatial location, mRNA expression and Immunophenotyping of PDGFRα+ fibroblasts during sacculation and alveolarization. Confocal microscopy identified spatial association of PDGFRα expressing fibroblasts with proximal epithelial cells of the branching bronchioles and the dilating acinar tubules at E16.5; with distal terminal saccules at E18.5; and with alveolar epithelial cells at PN7 and PN28. Immunohistochemistry for alpha smooth muscle actin revealed that PDGFRα+ fibroblasts contribute to proximal peribronchiolar smooth muscle at E16.5 and to transient distal alveolar myofibroblasts at PN7. Time series RNA-Seq analyses of PDGFRα+ fibroblasts identified differentially expressed genes that, based on gene expression similarity were clustered into 7 major gene expression profile patterns. The presence of myofibroblast and smooth muscle precursors at E16.5 and PN7 was reflected by a two-peak gene expression profile on these days and gene ontology enrichment in muscle contraction. Additional molecular and functional differences between peribronchiolar smooth muscle cells at E16.5 and transient intraseptal myofibroblasts at PN7 were suggested by a single peak in gene expression at PN7 with functional enrichment in cell projection and muscle cell differentiation. Immunophenotyping of subsets of PDGFRα+ fibroblasts by flow cytometry confirmed the predicted increase in proliferation at E16.5 and PN7, and identified subsets of CD29+ myofibroblasts and CD34+ lipofibroblasts. These data can be further mined to develop novel hypotheses and valuable understanding of the molecular and cellular basis of alveolarization. PMID:28408205

The isolation of spatial patterning modes in a mathematical model of juxtacrine cell signalling.

PubMed

O'Dea, R D; King, J R

2013-06-01

Juxtacrine signalling mechanisms are known to be crucial in tissue and organ development, leading to spatial patterns in gene expression. We investigate the patterning behaviour of a discrete model of juxtacrine cell signalling due to Owen & Sherratt (1998, Mathematical modelling of juxtacrine cell signalling. Math. Biosci., 153, 125-150) in which ligand molecules, unoccupied receptors and bound ligand-receptor complexes are modelled. Feedback between the ligand and receptor production and the level of bound receptors is incorporated. By isolating two parameters associated with the feedback strength and employing numerical simulation, linear stability and bifurcation analysis, the pattern-forming behaviour of the model is analysed under regimes corresponding to lateral inhibition and induction. Linear analysis of this model fails to capture the patterning behaviour exhibited in numerical simulations. Via bifurcation analysis, we show that since the majority of periodic patterns fold subcritically from the homogeneous steady state, a wide variety of stable patterns exists at a given parameter set, providing an explanation for this failure. The dominant pattern is isolated via numerical simulation. Additionally, by sampling patterns of non-integer wavelength on a discrete mesh, we highlight a disparity between the continuous and discrete representations of signalling mechanisms: in the continuous case, patterns of arbitrary wavelength are possible, while sampling such patterns on a discrete mesh leads to longer wavelength harmonics being selected where the wavelength is rational; in the irrational case, the resulting aperiodic patterns exhibit 'local periodicity', being constructed from distorted stable shorter wavelength patterns. This feature is consistent with experimentally observed patterns, which typically display approximate short-range periodicity with defects.

Analysis of AtGUS1 and AtGUS2 in Arabidopsis root apex by a highly sensitive TSA-MISH method.

PubMed

Bruno, Leonardo; Ronchini, Matteo; Gagliardi, Olimpia; Corinti, Tamara; Chiappetta, Adriana; Gerola, Paolo; Bitonti, Maria B

2015-01-01

A new highly sensitive whole-mount in situ hybridization method, based on tyramide signal amplification (TSA-MISH) was developed and a combined GFP detection and TSA-MISH procedure was applied for the first time in plants, to precisely define the spatial pattern of AtGUS1 and AtGUS2 expression in the root apex. β-glucuronidases (GUSs) belonging to the glycosyl hydrolases (GHs) 79 family, are widely distributed in plants, but their functional role has not yet been fully investigated. In the model system Arabidopsis Thaliana, three different AtGUS genes have been identified which encode proteins with putative different fates. Endogenous GUS expression has been detected in different organs and tissues, but the cyto-histological domains of gene expression remain unclear. The results here reported show co-expression of AtGUS1 and AtGUS2 in different functional zones of the root apex (the cap central zone, the root cap meristem, the staminal cell niche and the cortical cell layers of the proximal meristem), while AtGUS2 is exclusively expressed in the cap peripheral layer and in the epidermis in the elongation zone. Interestingly, both genes are not expressed in the stelar portion of the proximal meristem. A spatial (cortex vs. stele) and temporal (proximal meristem vs. transition zone) regulation of AtGUS1 and AtGUS2 expression is therefore active in the root apex. This expression pattern, although globally consistent with the involvement of GUS activity in both cell proliferation and elongation, clearly indicates that AtGUS1 and AtGUS2 could control distinct downstream process depending on the developmental context and the interaction with other players of root growth control. In the future, the newly developed approaches may well be very useful to dissect such interactions.

Reconstructing a spatially heterogeneous epidemic: Characterising the geographic spread of 2009 A/H1N1pdm infection in England

NASA Astrophysics Data System (ADS)

Birrell, Paul J.; Zhang, Xu-Sheng; Pebody, Richard G.; Gay, Nigel J.; de Angelis, Daniela

2016-07-01

Understanding how the geographic distribution of and movements within a population influence the spatial spread of infections is crucial for the design of interventions to curb transmission. Existing knowledge is typically based on results from simulation studies whereas analyses of real data remain sparse. The main difficulty in quantifying the spatial pattern of disease spread is the paucity of available data together with the challenge of incorporating optimally the limited information into models of disease transmission. To address this challenge the role of routine migration on the spatial pattern of infection during the epidemic of 2009 pandemic influenza in England is investigated here through two modelling approaches: parallel-region models, where epidemics in different regions are assumed to occur in isolation with shared characteristics; and meta-region models where inter-region transmission is expressed as a function of the commuter flux between regions. Results highlight that the significantly less computationally demanding parallel-region approach is sufficiently flexible to capture the underlying dynamics. This suggests that inter-region movement is either inaccurately characterized by the available commuting data or insignificant once its initial impact on transmission has subsided.

Distinct spatiotemporal activity in principal neurons of the mouse olfactory bulb in anesthetized and awake states

PubMed Central

Blauvelt, David G.; Sato, Tomokazu F.; Wienisch, Martin; Murthy, Venkatesh N.

2013-01-01

The acquisition of olfactory information and its early processing in mammals are modulated by brain states through sniffing behavior and neural feedback. We imaged the spatiotemporal pattern of odor-evoked activity in a population of output neurons (mitral/tufted cells, MTCs) in the olfactory bulb (OB) of head-restrained mice expressing a genetically-encoded calcium indicator. The temporal dynamics of MTC population activity were relatively simple in anesthetized animals, but were highly variable in awake animals. However, the apparently irregular activity in awake animals could be predicted well using sniff timing measured externally, or inferred through fluctuations in the global responses of MTC population even without explicit knowledge of sniff times. The overall spatial pattern of activity was conserved across states, but odor responses had a diffuse spatial component in anesthetized mice that was less prominent during wakefulness. Multi-photon microscopy indicated that MTC lateral dendrites were the likely source of spatially disperse responses in the anesthetized animal. Our data demonstrate that the temporal and spatial dynamics of MTCs can be significantly modulated by behavioral state, and that the ensemble activity of MTCs can provide information about sniff timing to downstream circuits to help decode odor responses. PMID:23543674

Slit/Robo Signaling Mediates Spatial Positioning of Spiral Ganglion Neurons during Development of Cochlear Innervation

PubMed Central

Wang, Sheng-zhi; Ibrahim, Leena A.; Kim, Young J.; Gibson, Daniel A.; Leung, Haiwen C.; Yuan, Wei; Zhang, Ke K.; Tao, Huizhong W.

2013-01-01

During the development of periphery auditory circuits, spiral ganglion neurons (SGNs) extend their neurites to innervate cochlear hair cells (HCs) with their soma aggregated into a cluster spatially segregated from the cochlear sensory epithelium. The molecular mechanisms underlying this spatial patterning remain unclear. In this study, in situ hybridization in the mouse cochlea suggests that Slit2 and its receptor, Robo1/2, exhibit apparently complementary expression patterns in the spiral ganglion and its nearby region, the spiral limbus. In Slit2 and Robo1/2 mutants, the spatial restriction of SGNs was disrupted. Mispositioned SGNs were found to scatter in the space between the cochlear epithelium and the main body of spiral ganglion, and the neurites of mispositioned SGNs were misrouted and failed to innervate HCs. Furthermore, in Robo1/2 mutants, SGNs were displaced toward the cochlear epithelium as an entirety. Examination of different embryonic stages in the mutants revealed that the mispositioning of SGNs was due to a progressive displacement to ectopic locations after their initial normal settlement at an earlier stage. Our results suggest that Slit/Robo signaling imposes a restriction force on SGNs to ensure their precise positioning for correct SGN-HC innervations. PMID:23884932

In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

PubMed Central

Zagrijchuk, Elizaveta A.; Sabirov, Marat A.; Holloway, David M.; Spirov, Alexander V.

2014-01-01

Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes. PMID:24712536

Developmental expression of Drosophila Wiskott-Aldrich Syndrome family proteins

PubMed Central

Rodriguez-Mesa, Evelyn; Abreu-Blanco, Maria Teresa; Rosales-Nieves, Alicia E.; Parkhurst, Susan M.

2012-01-01

Background Wiskott-Aldrich Syndrome (WASP) family proteins participate in many cellular processes involving rearrangements of the actin cytoskeleton. To the date, four WASP subfamily members have been described in Drosophila: Wash, WASp, SCAR, and Whamy. Wash, WASp, and SCAR are essential during early Drosophila development where they function in orchestrating cytoplasmic events including membrane-cytoskeleton interactions. A mutant for Whamy has not yet been reported. Results We generated monoclonal antibodies that are specific to Drosophila Wash, WASp, SCAR, and Whamy, and use these to describe their spatial and temporal localization patterns. Consistent with the importance of WASP family proteins in flies, we find that Wash, WASp, SCAR, and Whamy are dynamically expressed throughout oogenesis and embryogenesis. For example, we find that Wash accumulates at the oocyte cortex. WASp is highly expressed in the PNS, while SCAR is the most abundantly expressed in the CNS. Whamy exhibits an asymmetric subcellular localization that overlaps with mitochondria and is highly expressed in muscle. Conclusion All four WASP family members show specific expression patterns, some of which reflect their previously known roles and others revealing new potential functions. The monoclonal antibodies developed offer valuable new tools to investigate how WASP family proteins regulate actin cytoskeleton dynamics. PMID:22275148

Molecular identification of a pancreatic lipase-like gene involved in sex pheromone biosynthesis of Bombyx mori.

PubMed

Zhang, Song-Dou; Li, Xun; Bin, Zhu; Du, Meng-Fang; Yin, Xin-Ming; An, Shi-Heng

2014-08-01

Cytoplasmic lipid droplet (LD) lipolysis is regulated by pheromone biosynthesis activating neuropeptide (PBAN) in Bombyx mori. To elucidate the molecular mechanism of cytoplasm LD lipolysis, the pancreatic lipase-like gene in B. mori pheromone glands (PGs), designated as B. mori pancreatic lipase-like gene (BmPLLG), was identified in this study. Spatial expression analysis revealed that BmPLLG is a ubiquitous gene present in all studied tissues, such as PGs, brain, epidermis, egg, midgut, flight muscle and fat body. Temporal expression analysis showed that the BmPLLG transcript begins to express 96 h before eclosion (-96 h), continues to increase, peaks in newly emerged females and steadily decreases after eclosion. Translational expression analysis of BmPLLG using a prepared antiserum demonstrated that BmPLLG was expressed in an age-dependent pattern at different development stages in B. mori. This finding was similar to the transcript expression pattern. Further RNA interference-mediated knockdown of BmPLLG significantly inhibited bombykol production. Overall, these results demonstrated that BmPLLG is involved in PBAN-induced sex pheromone biosynthesis and release. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Sheep YAP1 temporal and spatial expression trend and its relation with MyHCs expression.

PubMed

Gao, W; Sun, W; Su, R; Lv, X Y; Wang, Q Z; Li, D; Musa, H H; Chen, L; Zhou, H; Xu, H S; Hua, W H

2016-04-04

RT-PCR was used to study the temporal and spatial pattern of Yes-associated protein 1 (YAP1) and myosin heavy chain (MyHC) expression in four different skeletal muscles (i.e., longissimus dorsi muscle, soleus muscle, gastrocnemius muscle, and extensor digitorum longus) and three growth stages (i.e., 2 days old, 2 and 6 months old) of Hu Sheep. The results showed that YAP1 was differentially expressed in skeletal muscles of sheep, that expression increased gradually with age, and that there were high levels of expression in the gastrocnemius muscle and lower levels in the longissimus dorsi muscle. MyHCI was expressed at high levels in the soleus muscle and at lower levels in the longissimus dorsi muscle. In contrast, MyHCIIA and MyHCIIX were expressed at high levels in the extensor digitorum longus and at lower levels in the soleus muscle. The expression of MyHCI and MyHCIIA decreased with increasing age while that of MyHCIIX increased. YAP1 expression was negatively correlated with MyHCII (P < 0.01) and positively correlated with MyHCIIX (P < 0.01) across all growth stages and skeletal muscle types studied. We speculate that after birth, the thicker muscle fiber diameter is associated with the high expression of MyHCIIX. Therefore, we conclude that YAP1 expression affects sheep muscle fiber development after birth and provides important genetic information for the selection candidate genes for sheep muscle growth.

Expression Patterns of CREBs in Oocyte Growth and Maturation of Fish

PubMed Central

Wang, De-Shou; Sudhakumari, Cheni-Chery; Kobayashi, Tohru; Nagahama, Yoshitaka

2015-01-01

In fish, oocyte meiotic maturation is regulated by 17α, 20β-dihydroxy-progesterone through cAMP. To study the role of cAMP response element binding protein (CREB) in meiotic maturation, we cloned and characterized the expression pattern of CREBs from two fish models, the Nile tilapia and catfish. In the Nile tilapia three different CREBs were identified where in CREB1 was found in many tissues including gonads with abundant expression in testis. CREB2, few amino acids shorter than CREB1, was expressed in several tissues with abundant expression in ovary. In addition, a 3’UTR variant form, CREB3 was exclusively found in ovary. During natural 14-day ovarian cycle of the Nile tilapia, CREB1 expression was stable throughout vitellogenesis with a sharp decrease on the day of spawning. In contrast, CREB2 remain unchanged throughout the ovarian cycle, however elevated in 11-day full-grown immature ovarian follicle and after hCG-induction. Interestingly, CREB3 expression was induced three folds on the day of spawning as well as during hCG-induced oocyte maturation. Based on the synergistic expression pattern, CREB1 is likely to control oocyte growth, whereas CREB 2 and 3 contribute to oocyte maturation in tilapia and the latter seems to be critical. In catfish, a single form of CREB showed a maximum expression during spawning phase and hCG-induced maturation both in vivo and in vitro augmented CREB expression. These results suggest that spatial and temporal expression of CREBs seems to be important for final oocyte maturation and may also regulate oocyte growth in fish. PMID:26700177

Hox gene expression during postlarval development of the polychaete Alitta virens.

PubMed

Bakalenko, Nadezhda I; Novikova, Elena L; Nesterenko, Alexander Y; Kulakova, Milana A

2013-05-01

Hox genes are the family of transcription factors that play a key role in the patterning of the anterior-posterior axis of all bilaterian animals. These genes display clustered organization and colinear expression. Expression boundaries of individual Hox genes usually correspond with morphological boundaries of the body. Previously, we studied Hox gene expression during larval development of the polychaete Alitta virens (formerly Nereis virens) and discovered that Hox genes are expressed in nereid larva according to the spatial colinearity principle. Adult Alitta virens consist of multiple morphologically similar segments, which are formed sequentially in the growth zone. Since the worm grows for most of its life, postlarval segments constantly change their position along the anterior-posterior axis. We studied the expression dynamics of the Hox cluster during postlarval development of the nereid Alitta virens and found that 8 out of 11 Hox genes are transcribed as wide gene-specific gradients in the ventral nerve cord, ectoderm, and mesoderm. The expression domains constantly shift in accordance with the changing proportions of the growing worm, so expression domains of most Hox genes do not have stable anterior or/and posterior boundaries.In the course of our study, we revealed long antisense RNA (asRNA) for some Hox genes. Expression patterns of two of these genes were analyzed using whole-mount in-situ hybridization. This is the first discovery of antisense RNA for Hox genes in Lophotrochozoa. Hox gene expression in juvenile A. virens differs significantly from Hox gene expression patterns both in A. virens larva and in other Bilateria.We suppose that the postlarval function of the Hox genes in this polychaete is to establish and maintain positional coordinates in a constantly growing body, as opposed to creating morphological difference between segments.

MK-801 Impairs Cognitive Coordination on a Rotating Arena (Carousel) and Contextual Specificity of Hippocampal Immediate-Early Gene Expression in a Rat Model of Psychosis

PubMed Central

Kubík, Štěpán; Buchtová, Helena; Valeš, Karel; Stuchlík, Aleš

2014-01-01

Flexible behavior in dynamic, real-world environments requires more than static spatial learning and memory. Discordant and unstable cues must be organized in coherent subsets to give rise to meaningful spatial representations. We model this form of cognitive coordination on a rotating arena – Carousel where arena- and room-bound spatial cues are dissociated. Hippocampal neuronal ensemble activity can repeatedly switch between multiple representations of such an environment. Injection of tetrodotoxin into one hippocampus prevents cognitive coordination during avoidance of a stationary room-defined place on the Carousel and increases coactivity of previously unrelated neurons in the uninjected hippocampus. Place avoidance on the Carousel is impaired after systemic administration of non-competitive NMDAr blockers (MK-801) used to model schizophrenia in animals and people. We tested if this effect is due to cognitive disorganization or other effect of NMDAr antagonism such as hyperlocomotion, spatial memory impairment, or general learning deficit. We also examined if the same dose of MK-801 alters patterns of immediate-early gene (IEG) expression in the hippocampus. IEG expression is triggered in neuronal nuclei in a context-specific manner after behavioral exploration and it is used to map activity in neuronal populations. IEG expression is critical for maintenance of synaptic plasticity and memory consolidation. We show that the same dose of MK-801 that impairs spatial coordination of rats on the Carousel also eliminates contextual specificity of IEG expression in hippocampal CA1 ensembles. This effect is due to increased similarity between ensembles activated in different environments, consistent with the idea that it is caused by increased coactivity between neurons, which did not previously fire together. Our data support the proposition of the Hypersynchrony theory that cognitive disorganization in psychosis is due to increased coactivity between unrelated neurons. PMID:24659959

Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies.

PubMed

Herberg, Maria; Zerjatke, Thomas; de Back, Walter; Glauche, Ingmar; Roeder, Ingo

2015-06-01

Pluripotent embryonic stem cells (ESCs) have the potential to differentiate into cells of all three germ layers. This unique property has been extensively studied on the intracellular, transcriptional level. However, ESCs typically form clusters of cells with distinct size and shape, and establish spatial structures that are vital for the maintenance of pluripotency. Even though it is recognized that the cells' arrangement and local interactions play a role in fate decision processes, the relations between transcriptional and spatial patterns have not yet been studied. We present a systems biology approach which combines live-cell imaging, quantitative image analysis, and multiscale, mathematical modeling of ESC growth. In particular, we develop quantitative measures of the morphology and of the spatial clustering of ESCs with different expression levels and apply them to images of both in vitro and in silico cultures. Using the same measures, we are able to compare model scenarios with different assumptions on cell-cell adhesions and intercellular feedback mechanisms directly with experimental data. Applying our methodology to microscopy images of cultured ESCs, we demonstrate that the emerging colonies are highly variable regarding both morphological and spatial fluorescence patterns. Moreover, we can show that most ESC colonies contain only one cluster of cells with high self-renewing capacity. These cells are preferentially located in the interior of a colony structure. The integrated approach combining image analysis with mathematical modeling allows us to reveal potential transcription factor related cellular and intercellular mechanisms behind the emergence of observed patterns that cannot be derived from images directly. © 2015 International Society for Advancement of Cytometry.

Zebrafish: an exciting model for investigating the spatio-temporal pattern of enteric nervous system development.

PubMed

Doodnath, Reshma; Dervan, Adrian; Wride, Michael A; Puri, Prem

2010-12-01

Recently, the zebrafish (Danio rerio) has been shown to be an excellent model for human paediatric research. Advantages over other models include its small size, externally visually accessible development and ease of experimental manipulation. The enteric nervous system (ENS) consists of neurons and enteric glia. Glial cells permit cell bodies and processes of neurons to be arranged and maintained in a proper spatial arrangement, and are essential in the maintenance of basic physiological functions of neurons. Glial fibrillary acidic protein (GFAP) is expressed in astrocytes, but also expressed outside of the central nervous system. The aim of this study was to investigate the spatio-temporal pattern of GFAP expression in developing zebrafish ENS from 24 h post-fertilization (hpf), using transgenic fish that express green fluorescent protein (GFP). Zebrafish embryos were collected from transgenic GFP Tg(GFAP:GFP)(mi2001) adult zebrafish from 24 to 120 hpf, fixed and processed for whole mount immunohistochemistry. Antibodies to Phox2b were used to identify enteric neurons. Specimens were mounted on slides and imaging was performed using a fluorescent laser confocal microscope. GFAP:GFP labelling outside the spinal cord was identified in embryos from 48 hpf. The patterning was intracellular and consisted of elongated profiles that appeared to migrate away from the spinal cord into the periphery. At 72 and 96 hpf, GFAP:GFP was expressed dorsally and ventrally to the intestinal tract. At 120 hpf, GFAP:GFP was expressed throughout the intestinal wall, and clusters of enteric neurons were identified using Phox2b immunofluorescence along the pathway of GFAP:GFP positive processes, indicative of a migratory pathway of ENS precursors from the spinal cord into the intestine. The pattern of migration of GFAP:GFP expressing cells outside the spinal cord suggests an organized, early developing migratory pathway to the ENS. This shows for the first time that Tg(GFAP:GFP)(mi2001) zebrafish model is an ideal one to study spatio-temporal patterning of early ENS development.

It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms.

PubMed

Costa, Angela M; Mergulhão, Filipe J; Briandet, Romain; Azevedo, Nuno F

2017-09-01

Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.

Divergence in Patterns of Leaf Growth Polarity Is Associated with the Expression Divergence of miR396.

PubMed

Das Gupta, Mainak; Nath, Utpal

2015-10-01

Lateral appendages often show allometric growth with a specific growth polarity along the proximo-distal axis. Studies on leaf growth in model plants have identified a basipetal growth direction with the highest growth rate at the proximal end and progressively lower rates toward the distal end. Although the molecular mechanisms governing such a growth pattern have been studied recently, variation in leaf growth polarity and, therefore, its evolutionary origin remain unknown. By surveying 75 eudicot species, here we report that leaf growth polarity is divergent. Leaf growth in the proximo-distal axis is polar, with more growth arising from either the proximal or the distal end; dispersed with no apparent polarity; or bidirectional, with more growth contributed by the central region and less growth at either end. We further demonstrate that the expression gradient of the miR396-GROWTH-REGULATING FACTOR module strongly correlates with the polarity of leaf growth. Altering the endogenous pattern of miR396 expression in transgenic Arabidopsis thaliana leaves only partially modified the spatial pattern of cell expansion, suggesting that the diverse growth polarities might have evolved via concerted changes in multiple gene regulatory networks. © 2015 American Society of Plant Biologists. All rights reserved.

Diffusion and scaling during early embryonic pattern formation

PubMed Central

Gregor, Thomas; Bialek, William; van Steveninck, Rob R. de Ruyter; Tank, David W.; Wieschaus, Eric F.

2005-01-01

Development of spatial patterns in multicellular organisms depends on gradients in the concentration of signaling molecules that control gene expression. In the Drosophila embryo, Bicoid (Bcd) morphogen controls cell fate along 70% of the anteroposterior axis but is translated from mRNA localized at the anterior pole. Gradients of Bcd and other morphogens are thought to arise through diffusion, but this basic assumption has never been rigorously tested in living embryos. Furthermore, because diffusion sets a relationship between length and time scales, it is hard to see how patterns of gene expression established by diffusion would scale proportionately as egg size changes during evolution. Here, we show that the motion of inert molecules through the embryo is well described by the diffusion equation on the relevant length and time scales, and that effective diffusion constants are essentially the same in closely related dipteran species with embryos of very different size. Nonetheless, patterns of gene expression in these different species scale with egg length. We show that this scaling can be traced back to scaling of the Bcd gradient itself. Our results, together with constraints imposed by the time scales of development, suggest that the mechanism for scaling is a species-specific adaptation of the Bcd lifetime. PMID:16352710

A Modified ABCDE Model of Flowering in Orchids Based on Gene Expression Profiling Studies of the Moth Orchid Phalaenopsis aphrodite

PubMed Central

Lee, Ann-Ying; Chen, Chun-Yi; Chang, Yao-Chien Alex; Chao, Ya-Ting; Shih, Ming-Che

2013-01-01

Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns. PMID:24265826

Ectopic KNOX Expression Affects Plant Development by Altering Tissue Cell Polarity and Identity[OPEN

PubMed Central

Rebocho, Alexandra B.

2016-01-01

Plant development involves two polarity types: tissue cell (asymmetries within cells are coordinated across tissues) and regional (identities vary spatially across tissues) polarity. Both appear altered in the barley (Hordeum vulgare) Hooded mutant, in which ectopic expression of the KNOTTED1-like Homeobox (KNOX) gene, BKn3, causes inverted polarity of differentiated hairs and ectopic flowers, in addition to wing-shaped outgrowths. These lemma-specific effects allow the spatiotemporal analysis of events following ectopic BKn3 expression, determining the relationship between KNOXs, polarity, and shape. We show that tissue cell polarity, based on localization of the auxin transporter SISTER OF PINFORMED1 (SoPIN1), dynamically reorients as ectopic BKn3 expression increases. Concurrently, ectopic expression of the auxin importer LIKE AUX1 and boundary gene NO APICAL MERISTEM is activated. The polarity of hairs reflects SoPIN1 patterns, suggesting that tissue cell polarity underpins oriented cell differentiation. Wing cell files reveal an anisotropic growth pattern, and computational modeling shows how polarity guiding growth can account for this pattern and wing emergence. The inverted ectopic flower orientation does not correlate with SoPIN1, suggesting that this form of regional polarity is not controlled by tissue cell polarity. Overall, the results suggest that KNOXs trigger different morphogenetic effects through interplay between tissue cell polarity, identity, and growth. PMID:27553356

Combining satellite data and appropriate objective functions for improved spatial pattern performance of a distributed hydrologic model

NASA Astrophysics Data System (ADS)

Demirel, Mehmet C.; Mai, Juliane; Mendiguren, Gorka; Koch, Julian; Samaniego, Luis; Stisen, Simon

2018-02-01

Satellite-based earth observations offer great opportunities to improve spatial model predictions by means of spatial-pattern-oriented model evaluations. In this study, observed spatial patterns of actual evapotranspiration (AET) are utilised for spatial model calibration tailored to target the pattern performance of the model. The proposed calibration framework combines temporally aggregated observed spatial patterns with a new spatial performance metric and a flexible spatial parameterisation scheme. The mesoscale hydrologic model (mHM) is used to simulate streamflow and AET and has been selected due to its soil parameter distribution approach based on pedo-transfer functions and the build in multi-scale parameter regionalisation. In addition two new spatial parameter distribution options have been incorporated in the model in order to increase the flexibility of root fraction coefficient and potential evapotranspiration correction parameterisations, based on soil type and vegetation density. These parameterisations are utilised as they are most relevant for simulated AET patterns from the hydrologic model. Due to the fundamental challenges encountered when evaluating spatial pattern performance using standard metrics, we developed a simple but highly discriminative spatial metric, i.e. one comprised of three easily interpretable components measuring co-location, variation and distribution of the spatial data. The study shows that with flexible spatial model parameterisation used in combination with the appropriate objective functions, the simulated spatial patterns of actual evapotranspiration become substantially more similar to the satellite-based estimates. Overall 26 parameters are identified for calibration through a sequential screening approach based on a combination of streamflow and spatial pattern metrics. The robustness of the calibrations is tested using an ensemble of nine calibrations based on different seed numbers using the shuffled complex evolution optimiser. The calibration results reveal a limited trade-off between streamflow dynamics and spatial patterns illustrating the benefit of combining separate observation types and objective functions. At the same time, the simulated spatial patterns of AET significantly improved when an objective function based on observed AET patterns and a novel spatial performance metric compared to traditional streamflow-only calibration were included. Since the overall water balance is usually a crucial goal in hydrologic modelling, spatial-pattern-oriented optimisation should always be accompanied by traditional discharge measurements. In such a multi-objective framework, the current study promotes the use of a novel bias-insensitive spatial pattern metric, which exploits the key information contained in the observed patterns while allowing the water balance to be informed by discharge observations.

SCARLESS SKIN WOUND HEALING IN FOXN1 DEFICIENT (NUDE) MICE IS ASSOCIATED WITH DISTINCTIVE MATRIX METALLOPROTEINASE EXPRESSION

PubMed Central

Gawronska-Kozak, Barbara

2011-01-01

Similar to mammalian fetuses FOXN1 deficient (nude) mice are able to restore the structure and integrity of injured skin in a scarless healing process by mechanisms independent of the genetic background. Matrix metalloproteinases (MMPs) are required for regular skin wound healing and the distinctive pattern of their expression has been implicated to promote scarless healing. In this study, we analyzed the temporal and spatial expression patterns of these molecules during the incisional skin wounds in adult nude mice. Macroscopic and histological analyses of skin wounds revealed an accelerated wound healing process, minimal granulation tissue formation and markedly diminished scarring in nude mice. Quantitative RT-PCR (Mmp-2,-3,-8,-9,-10,-12,-13,-14 and Timp-1, -2, -3), Western blots (MMP-13) and gelatin zymography (MMP-9) revealed that MMP-9 and MMP-13 showed a unique, bimodal pattern of up-regulation during the early and late phases of wound healing in nude mice. Immunohistochemically MMP-9 and MMP-13 were generally detected in epidermis during the early phase and in dermis during the late (remodeling) phase. Consistent with these in vivo observations, dermal fibroblasts cultured from nude mice expressed higher levels of type I and III collagen, MMP-9 and MMP-13 mRNA levels and higher MMP enzyme activity than wild type controls. Collectively, these finding suggest that the bimodal pattern of MMP-9 and MMP-13 expression during skin repair process in nude mice could be a major component of their ability for scarless healing. PMID:21539913

Spatial information is preferentially processed by the distal part of CA3: implication for memory retrieval.

PubMed

Flasbeck, Vera; Atucha, Erika; Nakamura, Nozomu H; Yoshida, Motoharu; Sauvage, Magdalena M

2018-07-16

For the past decades, CA3 was considered as a single functional entity. However, strong differences between the proximal (close to the dentate gyrus) and the distal (close to CA2) parts of CA3 in terms of connectivity patterns, gene expression and electrophysiological properties suggest that it is not the case. We recently showed that proximal CA3 (together with distal CA1) preferentially deals with non-spatial information [1]. In contrast to proximal CA3, distal CA3 mainly receives and predominantly projects to spatially tuned areas. Here, we tested if distal CA3 preferentially processes spatial information, which would suggest a segregation of the spatial information along the proximodistal axis of CA3. We used a high-resolution imaging technique based on the detection of the expression of the immediate-early gene Arc, commonly used to map activity in the medial temporal lobe. We showed that distal CA3 is strongly recruited in a newly designed delayed nonmatching-to-location task with high memory demands in rats, while proximal CA3 is not. These results indicate a functional segregation of CA3 that mirrors the one reported in CA1, and suggest the existence of a distal CA3- proximal CA1 spatial subnetwork. These findings bring further evidence for the existence of 'specialized' spatial and non-spatial subnetworks segregated along the proximodistal axis of the hippocampus and put forward the 'segregated' view of information processing in the hippocampus as a reasonable alternative to the well-accepted 'integrated' view, according to which spatial and non-spatial information are systematically integrated in the hippocampus to form episodic memory. Copyright © 2018. Published by Elsevier B.V.

Notch activates Wnt-4 signalling to control medio-lateral patterning of the pronephros.

PubMed

Naylor, Richard W; Jones, Elizabeth A

2009-11-01

Previous studies have highlighted a role for the Notch signalling pathway during pronephrogenesis in the amphibian Xenopus laevis, and in nephron development in the mammalian metanephros, yet a mechanism for this function remains elusive. Here, we further the understanding of how Notch signalling patterns the early X. laevis pronephros anlagen, a function that might be conserved in mammalian nephron segmentation. Our results indicate that early phase pronephric Notch signalling patterns the medio-lateral axis of the dorso-anterior pronephros anlagen, permitting the glomus and tubules to develop in isolation. We show that this novel function acts through the Notch effector gene hrt1 by upregulating expression of wnt4. Wnt-4 then patterns the proximal pronephric anlagen to establish the specific compartments that span the medio-lateral axis. We also identified pronephric expression of lunatic fringe and radical fringe that is temporally and spatially appropriate for a role in regulating Notch signalling in the dorso-anterior region of the pronephros anlagen. On the basis of these results, along with data from previous publications, we propose a mechanism by which the Notch signalling pathway regulates a Wnt-4 function that patterns the proximal pronephric anlagen.

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

PubMed Central

Verd, Berta; Crombach, Anton

2017-01-01

Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. We use a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, we simulate the system in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. We use a newly developed method for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, our study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory processes in development. PMID:28158178

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression.

PubMed

Verd, Berta; Crombach, Anton; Jaeger, Johannes

2017-02-01

Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. We use a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, we simulate the system in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. We use a newly developed method for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, our study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory processes in development.

Identification and expression pattern analysis of BoMYB51 involved in indolic glucosinolate biosynthesis from broccoli (Brassica oleracea var. italica).

PubMed

Yu, Qingyue; Hao, Guodong; Zhou, Jianxin; Wang, Jingying; Evivie, Ejiroghene Ruona; Li, Jing

2018-06-22

Glucosinolates are a class of amino acid-derived specialized metabolites characteristic of the Brassicales order. Trp derived indolic glucosinolates are essential for the effective plant defense responses to a wide range of pathogens and herbivores. In Arabidopsis, MYB51 is the key transcription factor positively regulates indolic glucosinolate production by activating certain biosynthetic genes. In this study, we report the isolation and identification of a MYB51 from broccoli designated as BoMYB51. Overexpression of BoMYB51 in Arabidopsis increased indolic glucosinolate production by upregulating biosynthetic genes and resulted in enhanced flagellin22 (Flg22) induced callose deposition. The spatial expression pattern and responsive expression of BoMYB51 to several hormones and stress treatments were investigated by expressing the β-glucuronidase (GUS) reporter gene driven by BoMYB51 promotor in Arabidopsis and quantitative real-time PCR analysis in broccoli. Our study provides information on molecular characteristics of BoMYB51 and possible physiological process BoMYB51 may involve. Copyright © 2018 Elsevier Inc. All rights reserved.

Generalized reproduction numbers and the prediction of patterns in waterborne disease

PubMed Central

Gatto, Marino; Mari, Lorenzo; Bertuzzo, Enrico; Casagrandi, Renato; Righetto, Lorenzo; Rodriguez-Iturbe, Ignacio; Rinaldo, Andrea

2012-01-01

Understanding, predicting, and controlling outbreaks of waterborne diseases are crucial goals of public health policies, but pose challenging problems because infection patterns are influenced by spatial structure and temporal asynchrony. Although explicit spatial modeling is made possible by widespread data mapping of hydrology, transportation infrastructure, population distribution, and sanitation, the precise condition under which a waterborne disease epidemic can start in a spatially explicit setting is still lacking. Here we show that the requirement that all the local reproduction numbers be larger than unity is neither necessary nor sufficient for outbreaks to occur when local settlements are connected by networks of primary and secondary infection mechanisms. To determine onset conditions, we derive general analytical expressions for a reproduction matrix , explicitly accounting for spatial distributions of human settlements and pathogen transmission via hydrological and human mobility networks. At disease onset, a generalized reproduction number (the dominant eigenvalue of ) must be larger than unity. We also show that geographical outbreak patterns in complex environments are linked to the dominant eigenvector and to spectral properties of . Tests against data and computations for the 2010 Haiti and 2000 KwaZulu-Natal cholera outbreaks, as well as against computations for metapopulation networks, demonstrate that eigenvectors of provide a synthetic and effective tool for predicting the disease course in space and time. Networked connectivity models, describing the interplay between hydrology, epidemiology, and social behavior sustaining human mobility, thus prove to be key tools for emergency management of waterborne infections. PMID:23150538

Spatial fluctuations in expression of the heterocyst differentiation regulatory gene hetR in Anabaena filaments.

PubMed

Corrales-Guerrero, Laura; Tal, Asaf; Arbel-Goren, Rinat; Mariscal, Vicente; Flores, Enrique; Herrero, Antonia; Stavans, Joel

2015-04-01

Under nitrogen deprivation, filaments of the cyanobacterium Anabaena undergo a process of development, resulting in a one-dimensional pattern of nitrogen-fixing heterocysts separated by about ten photosynthetic vegetative cells. Many aspects of gene expression before nitrogen deprivation and during the developmental process remain to be elucidated. Furthermore, the coupling of gene expression fluctuations between cells along a multicellular filament is unknown. We studied the statistics of fluctuations of gene expression of HetR, a transcription factor essential for heterocyst differentiation, both under steady-state growth in nitrogen-rich conditions and at different times following nitrogen deprivation, using a chromosomally-encoded translational hetR-gfp fusion. Statistical analysis of fluorescence at the individual cell level in wild-type and mutant filaments demonstrates that expression fluctuations of hetR in nearby cells are coupled, with a characteristic spatial range of circa two to three cells, setting the scale for cellular interactions along a filament. Correlations between cells predominantly arise from intercellular molecular transfer and less from cell division. Fluctuations after nitrogen step-down can build up on those under nitrogen-replete conditions. We found that under nitrogen-rich conditions, basal, steady-state expression of the HetR inhibitor PatS, cell-cell communication influenced by the septal protein SepJ and positive HetR auto-regulation are essential determinants of fluctuations in hetR expression and its distribution along filaments. A comparison between the expression of hetR-gfp under nitrogen-rich and nitrogen-poor conditions highlights the differences between the two HetR inhibitors PatS and HetN, as well as the differences in specificity between the septal proteins SepJ and FraC/FraD. Activation, inhibition and cell-cell communication lie at the heart of developmental processes. Our results show that proteins involved in these basic ingredients combine together in the presence of inevitable stochasticity in gene expression, to control the coupled fluctuations of gene expression that give rise to a one-dimensional developmental pattern in this organism.

Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas.

PubMed

Herlitze, Ines; Marie, Benjamin; Marin, Frédéric; Jackson, Daniel J

2018-06-01

Conchiferan molluscs construct a biocalcified shell that likely supported much of their evolutionary success. However, beyond broad proteomic and transcriptomic surveys of molluscan shells and the shell-forming mantle tissue, little is known of the spatial and ontogenetic regulation of shell fabrication. In addition, most efforts have been focused on species that deposit nacre, which is at odds with the majority of conchiferan species that fabricate shells using a crossed-lamellar microstructure, sensu lato. By combining proteomic and transcriptomic sequencing with in situ hybridization we have identified a suite of gene products associated with the production of the crossed-lamellar shell in Lymnaea stagnalis. With this spatial expression data we are able to generate novel hypotheses of how the adult mantle tissue coordinates the deposition of the calcified shell. These hypotheses include functional roles for unusual and otherwise difficult-to-study proteins such as those containing repetitive low-complexity domains. The spatial expression readouts of shell-forming genes also reveal cryptic patterns of asymmetry and modularity in the shell-forming cells of larvae and adult mantle tissue. This molecular modularity of the shell-forming mantle tissue hints at intimate associations between structure, function, and evolvability and may provide an elegant explanation for the evolutionary success of the second largest phylum among the Metazoa.

The Toll pathway is required in the epidermis for muscle development in the Drosophila embryo

NASA Technical Reports Server (NTRS)

Halfon, M. S.; Keshishian, H.

1998-01-01

The Toll signaling pathway functions in several Drosophila processes, including dorsal-ventral pattern formation and the immune response. Here, we demonstrate that this pathway is required in the epidermis for proper muscle development. Previously, we showed that the zygotic Toll protein is necessary for normal muscle development; in the absence of zygotic Toll, close to 50% of hemisegments have muscle patterning defects consisting of missing, duplicated and misinserted muscle fibers (Halfon, M.S., Hashimoto, C., and Keshishian, H., Dev. Biol. 169, 151-167, 1995). We have now also analyzed the requirements for easter, spatzle, tube, and pelle, all of which function in the Toll-mediated dorsal-ventral patterning pathway. We find that spatzle, tube, and pelle, but not easter, are necessary for muscle development. Mutations in these genes give a phenotype identical to that seen in Toll mutants, suggesting that elements of the same pathway used for Toll signaling in dorsal-ventral development are used during muscle development. By expressing the Toll cDNA under the control of distinct Toll enhancer elements in Toll mutant flies, we have examined the spatial requirements for Toll expression during muscle development. Expression of Toll in a subset of epidermal cells that includes the epidermal muscle attachment cells, but not Toll expression in the musculature, is necessary for proper muscle development. Our results suggest that signals received by the epidermis early during muscle development are an important part of the muscle patterning process.

Dynamic texture recognition using local binary patterns with an application to facial expressions.

PubMed

Zhao, Guoying; Pietikäinen, Matti

2007-06-01

Dynamic texture (DT) is an extension of texture to the temporal domain. Description and recognition of DTs have attracted growing attention. In this paper, a novel approach for recognizing DTs is proposed and its simplifications and extensions to facial image analysis are also considered. First, the textures are modeled with volume local binary patterns (VLBP), which are an extension of the LBP operator widely used in ordinary texture analysis, combining motion and appearance. To make the approach computationally simple and easy to extend, only the co-occurrences of the local binary patterns on three orthogonal planes (LBP-TOP) are then considered. A block-based method is also proposed to deal with specific dynamic events such as facial expressions in which local information and its spatial locations should also be taken into account. In experiments with two DT databases, DynTex and Massachusetts Institute of Technology (MIT), both the VLBP and LBP-TOP clearly outperformed the earlier approaches. The proposed block-based method was evaluated with the Cohn-Kanade facial expression database with excellent results. The advantages of our approach include local processing, robustness to monotonic gray-scale changes, and simple computation.

Tissue specific characterisation of Lim-kinase 1 expression during mouse embryogenesis

PubMed Central

Lindström, Nils O.; Neves, Carlos; McIntosh, Rebecca; Miedzybrodzka, Zosia; Vargesson, Neil; Collinson, J. Martin

2012-01-01

The Lim-kinase (LIMK) proteins are important for the regulation of the actin cytoskeleton, in particular the control of actin nucleation and depolymerisation via regulation of cofilin, and hence may control a large number of processes during development, including cell tensegrity, migration, cell cycling, and axon guidance. LIMK1/LIMK2 knockouts disrupt spinal cord morphogenesis and synapse formation but other tissues and developmental processes that require LIMK are yet to be fully determined. To identify tissues and cell-types that may require LIMK, we characterised the pattern of LIMK1 protein during mouse embryogenesis. We showed that LIMK1 displays an expression pattern that is temporally dynamic and tissue-specific. In several tissues LIMK1 is detected in cell-types that also express Wilms’ tumour protein 1 and that undergo transitions between epithelial and mesenchymal states, including the pleura, epicardium, kidney nephrons, and gonads. LIMK1 was also found in a subset of cells in the dorsal retina, and in mesenchymal cells surrounding the peripheral nerves. This detailed study of the spatial and temporal expression of LIMK1 shows that LIMK1 expression is more dynamic than previously reported, in particular at sites of tissue–tissue interactions guiding multiple developmental processes. PMID:21167960

Spatial Models for Prediction and Early Warning of Aedes aegypti Proliferation from Data on Climate Change and Variability in Cuba.

PubMed

Ortiz, Paulo L; Rivero, Alina; Linares, Yzenia; Pérez, Alina; Vázquez, Juan R

2015-04-01

Climate variability, the primary expression of climate change, is one of the most important environmental problems affecting human health, particularly vector-borne diseases. Despite research efforts worldwide, there are few studies addressing the use of information on climate variability for prevention and early warning of vector-borne infectious diseases. Show the utility of climate information for vector surveillance by developing spatial models using an entomological indicator and information on predicted climate variability in Cuba to provide early warning of danger of increased risk of dengue transmission. An ecological study was carried out using retrospective and prospective analyses of time series combined with spatial statistics. Several entomological and climatic indicators were considered using complex Bultó indices -1 and -2. Moran's I spatial autocorrelation coefficient specified for a matrix of neighbors with a radius of 20 km, was used to identify the spatial structure. Spatial structure simulation was based on simultaneous autoregressive and conditional autoregressive models; agreement between predicted and observed values for number of Aedes aegypti foci was determined by the concordance index Di and skill factor Bi. Spatial and temporal distributions of populations of Aedes aegypti were obtained. Models for describing, simulating and predicting spatial patterns of Aedes aegypti populations associated with climate variability patterns were put forward. The ranges of climate variability affecting Aedes aegypti populations were identified. Forecast maps were generated for the municipal level. Using the Bultó indices of climate variability, it is possible to construct spatial models for predicting increased Aedes aegypti populations in Cuba. At 20 x 20 km resolution, the models are able to provide warning of potential changes in vector populations in rainy and dry seasons and by month, thus demonstrating the usefulness of climate information for epidemiological surveillance.

Expression pattern of cdkl5 during zebrafish early development: implications for use as model for atypical Rett syndrome.

PubMed

Vitorino, Marta; Cunha, Nídia; Conceição, Natércia; Cancela, M Leonor

2018-05-11

Atypical Rett syndrome is a child neurodevelopmental disorder induced by mutations in CDKL5 gene and characterized by a progressive regression in development with loss of purposeful use of the hands, slowed brain and head growth, problems with walking, seizures, and intellectual disability. At the moment, there is no cure for this pathology and little information is available concerning animal models capable of mimicking its phenotypes, thus the development of additional animal models should be of interest to gain more knowledge about the disease. Zebrafish has been used successfully as model organism for many human genetic diseases; however, no information is available concerning the spatial and temporal expression of cdkl5 orthologous in this organism. In the present study, we identified the developmental expression patterns of cdkl5 in zebrafish by quantitative PCR and whole-mount in situ hybridization. cdkl5 is expressed maternally at low levels during the first 24 h of development. After that the expression of the gene increases significantly and it starts to be expressed mainly in the nervous system and in several brain structures, such as telencephalon, mesencephalon and diencephalon. The expression patterns of cdkl5 in zebrafish is in accordance with the tissues known to be affected in humans and associated to symptoms and deficits observed in Rett syndrome patients thus providing the first evidence that zebrafish could be an alternative model to study the molecular pathways of this disease as well as to test possible therapeutic approaches capable of rescuing the phenotype.

A Bmp/Admp regulatory circuit controls maintenance and regeneration of dorsal-ventral polarity in planarians.

PubMed

Gaviño, Michael A; Reddien, Peter W

2011-02-22

Animal embryos have diverse anatomy and vary greatly in size. It is therefore remarkable that a common signaling pathway, BMP signaling, controls development of the dorsoventral (DV) axis throughout the Bilateria. In vertebrates, spatially opposed expression of the BMP family proteins Bmp4 and Admp (antidorsalizing morphogenetic protein) can promote restoration of DV pattern following tissue removal. bmp4 orthologs have been identified in all three groups of the Bilateria (deuterostomes, ecdysozoans, and lophotrochozoans). By contrast, the absence of admp orthologs in ecdysozoans such as Drosophila and C. elegans has suggested that a regulatory circuit of oppositely expressed bmp4 and admp genes represents a deuterostome-specific innovation. Here we describe the existence of spatially opposed bmp and admp expression in a protostome. An admp ortholog (Smed-admp) is expressed ventrally and laterally in adult Schmidtea mediterranea planarians, opposing the dorsal-pole expression of Smed-bmp4. Smed-admp is required for regeneration following parasagittal amputation. Furthermore, Smed-admp promotes Smed-bmp4 expression and Smed-bmp4 inhibits Smed-admp expression, generating a regulatory circuit that buffers against perturbations of Bmp signaling. These results suggest that a Bmp/Admp regulatory circuit is a central feature of the Bilateria, used broadly for the establishment, maintenance, and regeneration of the DV axis. Copyright © 2011 Elsevier Ltd. All rights reserved.

COMPARISON OF SPATIAL PATTERNS OF POLLUTANT DISTRIBUTION WITH CMAQ PREDICTIONS

EPA Science Inventory

One indication of model performance is the comparison of spatial patterns of pollutants, either as concentration or deposition, predicted by the model with spatial patterns derived from measurements. If the spatial patterns produced by the model are similar to the observations i...

Temporal Differences in MicroRNA Expression Patterns in Astrocytes and Neurons after Ischemic Injury

PubMed Central

Ziu, Mateo; Fletcher, Lauren; Rana, Shushan; Jimenez, David F.; Digicaylioglu, Murat

2011-01-01

MicroRNAs (miRNAs) are small, non-protein-coding RNA molecules that modulate gene translation. Their expression is altered in many central nervous system (CNS) injuries suggesting a role in the cellular response to stress. Current studies in brain tissue have not yet described the cell-specific temporal miRNA expression patterns following ischemic injury. In this study, we analyzed the expression alterations of a set of miRNAs in neurons and astrocytes subjected to 60 minutes of ischemia and collected at different time-points following this injury. To mimic ischemic conditions and reperfusion in vitro, cortical primary neuronal and astrocytic cultures prepared from fetal rats were first placed in oxygen and glucose deprived (OGD) medium for 60 minutes, followed by their transfer into normoxic pre-conditioned medium. Total RNA was extracted at different time-points after the termination of the ischemic insult and the expression levels of miRNAs were measured. In neurons exposed to OGD, expression of miR-29b was upregulated 2-fold within 6 h and up to 4-fold at 24 h post-OGD, whereas induction of miR-21 was upregulated 2-fold after 24 h when compared to expression in neurons under normoxic conditions. In contrast, in astrocytes, miR-29b and miR-21 were upregulated only after 12 h. MiR-30b, 107, and 137 showed expression alteration in astrocytes, but not in neurons. Furthermore, we show that expression of miR-29b was significantly decreased in neurons exposed to Insulin-Like Growth Factor I (IGF-I), a well documented neuroprotectant in ischemic models. Our study indicates that miRNAs expression is altered in neurons and astrocytes after ischemic injury. Furthermore, we found that following OGD, specific miRNAs have unique cell-specific temporal expression patterns in CNS. Therefore the specific role of each miRNA in different intracellular processes in ischemic brain and the relevance of their temporal and spatial expression patterns warrant further investigation that may lead to novel strategies for therapeutic interventions. PMID:21373187

Mining Co-Location Patterns with Clustering Items from Spatial Data Sets

NASA Astrophysics Data System (ADS)

Zhou, G.; Li, Q.; Deng, G.; Yue, T.; Zhou, X.

2018-05-01

The explosive growth of spatial data and widespread use of spatial databases emphasize the need for the spatial data mining. Co-location patterns discovery is an important branch in spatial data mining. Spatial co-locations represent the subsets of features which are frequently located together in geographic space. However, the appearance of a spatial feature C is often not determined by a single spatial feature A or B but by the two spatial features A and B, that is to say where A and B appear together, C often appears. We note that this co-location pattern is different from the traditional co-location pattern. Thus, this paper presents a new concept called clustering terms, and this co-location pattern is called co-location patterns with clustering items. And the traditional algorithm cannot mine this co-location pattern, so we introduce the related concept in detail and propose a novel algorithm. This algorithm is extended by join-based approach proposed by Huang. Finally, we evaluate the performance of this algorithm.

CLOCK expression identifies developing circadian oscillator neurons in the brains of Drosophila embryos.

PubMed

Houl, Jerry H; Ng, Fanny; Taylor, Pete; Hardin, Paul E

2008-12-18

The Drosophila circadian oscillator is composed of transcriptional feedback loops in which CLOCK-CYCLE (CLK-CYC) heterodimers activate their feedback regulators period (per) and timeless (tim) via E-box mediated transcription. These feedback loop oscillators are present in distinct clusters of dorsal and lateral neurons in the adult brain, but how this pattern of expression is established during development is not known. Since CLK is required to initiate feedback loop function, defining the pattern of CLK expression in embryos and larvae will shed light on oscillator neuron development. A novel CLK antiserum is used to show that CLK expression in the larval CNS and adult brain is limited to circadian oscillator cells. CLK is initially expressed in presumptive small ventral lateral neurons (s-LNvs), dorsal neurons 2 s (DN2s), and dorsal neuron 1 s (DN1s) at embryonic stage (ES) 16, and this CLK expression pattern persists through larval development. PER then accumulates in all CLK-expressing cells except presumptive DN2s during late ES 16 and ES 17, consistent with the delayed accumulation of PER in adult oscillator neurons and antiphase cycling of PER in larval DN2s. PER is also expressed in non-CLK-expressing cells in the embryonic CNS starting at ES 12. Although PER expression in CLK-negative cells continues in ClkJrk embryos, PER expression in cells that co-express PER and CLK is eliminated. These data demonstrate that brain oscillator neurons begin development during embryogenesis, that PER expression in non-oscillator cells is CLK-independent, and that oscillator phase is an intrinsic characteristic of brain oscillator neurons. These results define the temporal and spatial coordinates of factors that initiate Clk expression, imply that circadian photoreceptors are not activated until the end of embryogenesis, and suggest that PER functions in a different capacity before oscillator cell development is initiated.

Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures

PubMed Central

Liu, Juan; Franks, Robert G.; Feng, Chun-Miao; Liu, Xiang; Fu, Cheng-Xin;  (Jenny) Xiang, Qiu-Yun

2013-01-01

Background and Aims LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus. Methods Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT–PCR and RNA in situ hybridization. Phylogenetic analyses were conducted using the maximum likelihood methods implemented in RAxML-HPC v7.2.8. Key Results cDNA clones of LFY homologues (designated CorLFY) were isolated from six Cornus species bearing different types of inflorescence. CorLFY cDNAs were predicted to encode proteins of approximately 375 amino acids. The detection of CorLFY expression patterns using in situ RNA hybridization demonstrated the expression of CorLFY within the inflorescence meristems, inflorescence branch meristems, floral meristems and developing floral organ primordia. PCR analyses for cDNA libraries derived from reverse transcription of total RNAs showed that CorLFY was also expressed during the late-stage development of flowers and inflorescences, as well as in bracts and developing leaves. Consistent differences in the CorLFY expression patterns were not detected among the distinct inflorescence types. Conclusions The results suggest a role for CorLFY genes during floral and inflorescence development in dogwoods. However, the failure to detect expression differences between the inflorescence types in the Cornus species analysed suggests that the evolutionary shift between major inflorescence types in the genus is not controlled by dramatic alterations in the levels of CorLFY gene transcript accumulation. However, due to spatial, temporal and quantitative limitations of the expression data, it cannot be ruled out that subtle differences in the level or location of CorLFY transcripts may underlie the different inflorescence architectures that are observed across these species. Alternatively, differences in CorLFY protein function or the expression or function of other regulators (e.g. TFL1 and UFO homologues) may support the divergent developmental trajectories. PMID:24052556

Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures.

PubMed

Liu, Juan; Franks, Robert G; Feng, Chun-Miao; Liu, Xiang; Fu, Cheng-Xin; Jenny Xiang, Qiu-Yun

2013-11-01

LFY homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus. Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT-PCR and RNA in situ hybridization. Phylogenetic analyses were conducted using the maximum likelihood methods implemented in RAxML-HPC v7.2.8. cDNA clones of LFY homologues (designated CorLFY) were isolated from six Cornus species bearing different types of inflorescence. CorLFY cDNAs were predicted to encode proteins of approximately 375 amino acids. The detection of CorLFY expression patterns using in situ RNA hybridization demonstrated the expression of CorLFY within the inflorescence meristems, inflorescence branch meristems, floral meristems and developing floral organ primordia. PCR analyses for cDNA libraries derived from reverse transcription of total RNAs showed that CorLFY was also expressed during the late-stage development of flowers and inflorescences, as well as in bracts and developing leaves. Consistent differences in the CorLFY expression patterns were not detected among the distinct inflorescence types. The results suggest a role for CorLFY genes during floral and inflorescence development in dogwoods. However, the failure to detect expression differences between the inflorescence types in the Cornus species analysed suggests that the evolutionary shift between major inflorescence types in the genus is not controlled by dramatic alterations in the levels of CorLFY gene transcript accumulation. However, due to spatial, temporal and quantitative limitations of the expression data, it cannot be ruled out that subtle differences in the level or location of CorLFY transcripts may underlie the different inflorescence architectures that are observed across these species. Alternatively, differences in CorLFY protein function or the expression or function of other regulators (e.g. TFL1 and UFO homologues) may support the divergent developmental trajectories.

Baculovirus-mediated gene transfer in butterfly wings in vivo: an efficient expression system with an anti-gp64 antibody.

PubMed

Dhungel, Bidur; Ohno, Yoshikazu; Matayoshi, Rie; Otaki, Joji M

2013-03-25

Candidate genes for color pattern formation in butterfly wings have been known based on gene expression patterns since the 1990s, but their functions remain elusive due to a lack of a functional assay. Several methods of transferring and expressing a foreign gene in butterfly wings have been reported, but they have suffered from low success rates or low expression levels. Here, we developed a simple, practical method to efficiently deliver and express a foreign gene using baculovirus-mediated gene transfer in butterfly wings in vivo. A recombinant baculovirus containing a gene for green fluorescent protein (GFP) was injected into pupae of the blue pansy butterfly Junonia orithya (Nymphalidae). GFP fluorescence was detected in the pupal wings and other body parts of the injected individuals three to five days post-injection at various degrees of fluorescence. We obtained a high GFP expression rate at relatively high virus titers, but it was associated with pupal death before color pattern formation in wings. To reduce the high mortality rate caused by the baculovirus treatment, we administered an anti-gp64 antibody, which was raised against baculovirus coat protein gp64, to infected pupae after the baculovirus injection. This treatment greatly reduced the mortality rate of the infected pupae. GFP fluorescence was observed in pupal and adult wings and other body parts of the antibody-treated individuals at various degrees of fluorescence. Importantly, we obtained completely developed wings with a normal color pattern, in which fluorescent signals originated directly from scales or the basal membrane after the removal of scales. GFP fluorescence in wing tissues spatially coincided with anti-GFP antibody staining, confirming that the fluorescent signals originated from the expressed GFP molecules. Our baculovirus-mediated gene transfer system with an anti-gp64 antibody is reasonably efficient, and it can be an invaluable tool to transfer, express, and functionally examine foreign genes in butterfly wings and also in other non-model insect systems.

The impact of spatial and temporal patterns on multi-cellular behavior

NASA Astrophysics Data System (ADS)

Nikolic, Djordje L.

What makes a fruit fly a fruit fly? Essentially this question stems from one of the most fascinating problems in biology: how a single cell (fertilized egg) can give rise to a fully grown animal. To be able to answer this question, the importance to how spatial and temporal patterns of gene and protein expression influence the development of an organism must be understood. After all, fruit fly larvae are segmented, while fertilized eggs are not. Pattern formation is fundamental to establishing this organization of the developing embryo with the ultimate goal being the precise arrangements of specialized cells and tissues within each organ in an adult organism. The research presented here showcases the examples of studies that assess the impact spatial and temporal protein patterns have on the behavior of a collection of cells. By introducing new experimental, non-traditional techniques we developed model systems that allowed us to examine the dependence of the strength of adhesion of cells on the protein organization on sub-cellular, micron length scales, and to investigate how epithelial cell sheets coordinate their migration incorporating individual cell locomotion, molecular signal propagation and different boundary conditions. The first part of this dissertation presents a photolithography-based silanization patterning technique that allowed us to homogeneously pattern large areas with high precision. This method is then applied to organizing cell adhesion-promoting proteins on surfaces for the purposes of studying and manipulating cell behavior. We show how the strength of adhesion is dependent on high local density of an adhesive extracellular matrix protein fibronectin. The varied appeal of this technique is exhibited by showing its applicability to pattern stretched DNA, too. The second part of this dissertation focuses on the impact of spatial and temporal propagation of a molecular signal (ERK 1/2 MAPK) in migrating epithelial sheets during wound healing. By tracking the motion of individual cells within the sheet under the three constructed conditions, we show how the dynamics of the individual cells' motion is responsible for the coordinated migration of the sheet in accordance with the activation of ERK 1/2 MAPK.

Macroscale patterns of synchrony identify complex relationships among spatial and temporal ecosystem drivers

USGS Publications Warehouse

Lottig, Noah R.; Tan, Pang-Ning; Wagner, Tyler; Cheruvelil, Kendra Spence; Soranno, Patricia A.; Stanley, Emily H.; Scott, Caren E.; Stow, Craig A.; Yuan, Shuai

2017-01-01

Ecology has a rich history of studying ecosystem dynamics across time and space that has been motivated by both practical management needs and the need to develop basic ideas about pattern and process in nature. In situations in which both spatial and temporal observations are available, similarities in temporal behavior among sites (i.e., synchrony) provide a means of understanding underlying processes that create patterns over space and time. We used pattern analysis algorithms and data spanning 22–25 yr from 601 lakes to ask three questions: What are the temporal patterns of lake water clarity at sub‐continental scales? What are the spatial patterns (i.e., geography) of synchrony for lake water clarity? And, what are the drivers of spatial and temporal patterns in lake water clarity? We found that the synchrony of water clarity among lakes is not spatially structured at sub‐continental scales. Our results also provide strong evidence that the drivers related to spatial patterns in water clarity are not related to the temporal patterns of water clarity. This analysis of long‐term patterns of water clarity and possible drivers contributes to understanding of broad‐scale spatial patterns in the geography of synchrony and complex relationships between spatial and temporal patterns across ecosystems.

Spatial and Temporal Patterns of Impervious Cover Relative to Watershed Stream Location

EPA Science Inventory

The influence of spatial pattern on ecological processes is a guiding principle of landscape ecology. The guiding principle of spatial pattern was used for a U.S. nationwide assessment of impervious cover (IC). Spatial pattern was measured by comparing IC concentration near strea...

Regulation of NF-κB oscillation by spatial parameters in true intracellular space (TiCS)

NASA Astrophysics Data System (ADS)

Ohshima, Daisuke; Sagara, Hiroshi; Ichikawa, Kazuhisa

2013-10-01

Transcription factor NF-κB is activated by cytokine stimulation, viral infection, or hypoxic environment leading to its translocation to the nucleus. The nuclear NF-κB is exported from the nucleus to the cytoplasm again, and by repetitive import and export, NF-κB shows damped oscillation with the period of 1.5-2.0 h. Oscillation pattern of NF-κB is thought to determine the gene expression profile. We published a report on a computational simulation for the oscillation of nuclear NF-κB in a 3D spherical cell, and showed the importance of spatial parameters such as diffusion coefficient and locus of translation for determining the oscillation pattern. Although the value of diffusion coefficient is inherent to protein species, its effective value can be modified by organelle crowding in intracellular space. Here we tested this possibility by computer simulation. The results indicate that the effective value of diffusion coefficient is significantly changed by the organelle crowding, and this alters the oscillation pattern of nuclear NF-κB.

Reactivation of Rate Remapping in CA3.

PubMed

Schwindel, C Daniela; Navratilova, Zaneta; Ali, Karim; Tatsuno, Masami; McNaughton, Bruce L

2016-09-07

The hippocampus is thought to contribute to episodic memory by creating, storing, and reactivating patterns that are unique to each experience, including different experiences that happen at the same location. Hippocampus can combine spatial and contextual/episodic information using a dual coding scheme known as "global" and "rate" remapping. Global remapping selects which set of neurons can activate at a given location. Rate remapping readjusts the firing rates of this set depending on current experience, thus expressing experience-unique patterns at each location. But can the experience-unique component be retrieved spontaneously? Whereas reactivation of recent, spatially selective patterns in hippocampus is well established, it is never perfect, raising the issue of whether the experiential component might be absent. This question is key to the hypothesis that hippocampus can assist memory consolidation by reactivating and broadcasting experience-specific "index codes" to neocortex. In CA3, global remapping exhibits attractor-like dynamics, whereas rate remapping apparently does not, leading to the hypothesis that only the former can be retrieved associatively and casting doubt on the general consolidation hypothesis. Therefore, we studied whether the rate component is reactivated spontaneously during sleep. We conducted neural ensemble recordings from CA3 while rats ran on a circular track in different directions (in different sessions) and while they slept. It was shown previously that the two directions of running result in strong rate remapping. During sleep, the most recent rate distribution was reactivated preferentially. Therefore, CA3 can retrieve patterns spontaneously that are unique to both the location and the content of recent experience. The hippocampus is required for memory of events and their spatial contexts. The primary correlate of hippocampal activity is location in space, but multiple memories can occur in the same location. To be useful for distinguishing these memories, the hippocampus must be able, not only to express, but also to retrieve both spatial and nonspatial information about events. Whether it can retrieve nonspatial information has been challenged recently. We exposed rats to two different experiences (running in different directions) in the same locations and showed that even the nonspatial components of hippocampal cell firing are reactivated spontaneously during sleep, supporting the conclusion that both types of information about a recent experience can be retrieved. Copyright © 2016 the authors 0270-6474/16/369342-09$15.00/0.

Probabilistic cluster labeling of imagery data

NASA Technical Reports Server (NTRS)

Chittineni, C. B. (Principal Investigator)

1980-01-01

The problem of obtaining the probabilities of class labels for the clusters using spectral and spatial information from a given set of labeled patterns and their neighbors is considered. A relationship is developed between class and clusters conditional densities in terms of probabilities of class labels for the clusters. Expressions are presented for updating the a posteriori probabilities of the classes of a pixel using information from its local neighborhood. Fixed-point iteration schemes are developed for obtaining the optimal probabilities of class labels for the clusters. These schemes utilize spatial information and also the probabilities of label imperfections. Experimental results from the processing of remotely sensed multispectral scanner imagery data are presented.

Spatial regulation of bone morphogenetic proteins (BMPs) in postnatal articular and growth plate cartilage

PubMed Central

Garrison, Presley; Yue, Shanna; Hanson, Jeffrey; Baron, Jeffrey; Lui, Julian C.

2017-01-01

Articular and growth plate cartilage both arise from condensations of mesenchymal cells, but ultimately develop important histological and functional differences. Each is composed of three layers—the superficial, mid and deep zones of articular cartilage and the resting, proliferative and hypertrophic zones of growth plate cartilage. The bone morphogenetic protein (BMP) system plays an important role in cartilage development. A gradient in expression of BMP-related genes has been observed across growth plate cartilage, likely playing a role in zonal differentiation. To investigate the presence of a similar expression gradient in articular cartilage, we used laser capture microdissection (LCM) to separate murine growth plate and articular cartilage from the proximal tibia into their six constituent zones, and used a solution hybridization assay with color-coded probes (nCounter) to quantify mRNAs for 30 different BMP-related genes in each zone. In situ hybridization and immunohistochemistry were then used to confirm spatial expression patterns. Expression gradients for Bmp2 and 6 were observed across growth plate cartilage with highest expression in hypertrophic zone. However, intracellular BMP signaling, assessed by phospho-Smad1/5/8 immunohistochemical staining, appeared to be higher in the proliferative zone and prehypertrophic area than in hypertrophic zone, possibly due to high expression of Smad7, an inhibitory Smad, in the hypertrophic zone. We also found BMP expression gradients across the articular cartilage with BMP agonists primarily expressed in the superficial zone and BMP functional antagonists primarily expressed in the deep zone. Phospho-Smad1/5/8 immunohistochemical staining showed a similar gradient. In combination with previous evidence that BMPs regulate chondrocyte proliferation and differentiation, the current findings suggest that BMP signaling gradients exist across both growth plate and articular cartilage and that these gradients may contribute to the spatial differentiation of chondrocytes in the postnatal endochondral skeleton. PMID:28467498

Diurnal oscillation of SBE expression in sorghum endosperm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Chuanxin; Mutisya, J.; Rosenquist, S.

2009-01-15

Spatial and temporal expression patterns of the sorghum SBEI, SBEIIA and SBEIIB genes, encoding, respectively, starch branching enzyme (SBE) I, IIA and IIB, in the developing endosperm of sorghum (Sorghum bicolor) were studied. Full-length genomic and cDNA clones for sorghum was cloned and the SBEIIA cDNA was used together with gene-specific probes for sorghum SBEIIB and SBEI. In contrast to sorghum SBEIIB, which was expressed primarily in endosperm and embryo, SBEIIA was expressed also in vegetative tissues. All three genes shared a similar temporal expression profile during endosperm development, with a maximum activity at 15-24 days after pollination. This ismore » different from barley and maize where SBEI gene activity showed a significantly later onset compared to that of SBEIIA and SBEIIB. Expression of the three SBE genes in the sorghum endosperm exhibited a diurnal rhythm during a 24-h cycle.« less

Cis-regulatory underpinnings of human GLI3 expression in embryonic craniofacial structures and internal organs.

PubMed

Abbasi, Amir A; Minhas, Rashid; Schmidt, Ansgar; Koch, Sabine; Grzeschik, Karl-Heinz

2013-10-01

The zinc finger transcription factor Gli3 is an important mediator of Sonic hedgehog (Shh) signaling. During early embryonic development Gli3 participates in patterning and growth of the central nervous system, face, skeleton, limb, tooth and gut. Precise regulation of the temporal and spatial expression of Gli3 is crucial for the proper specification of these structures in mammals and other vertebrates. Previously we reported a set of human intronic cis-regulators controlling almost the entire known repertoire of endogenous Gli3 expression in mouse neural tube and limbs. However, the genetic underpinning of GLI3 expression in other embryonic domains such as craniofacial structures and internal organs remain elusive. Here we demonstrate in a transgenic mice assay the potential of a subset of human/fish conserved non-coding sequences (CNEs) residing within GLI3 intronic intervals to induce reporter gene expression at known regions of endogenous Gli3 transcription in embryonic domains other than central nervous system (CNS) and limbs. Highly specific reporter expression was observed in craniofacial structures, eye, gut, and genitourinary system. Moreover, the comparison of expression patterns directed by these intronic cis-acting regulatory elements in mouse and zebrafish embryos suggests that in accordance with sequence conservation, the target site specificity of a subset of these elements remains preserved among these two lineages. Taken together with our recent investigations, it is proposed here that during vertebrate evolution the Gli3 expression control acquired multiple, independently acting, intronic enhancers for spatiotemporal patterning of CNS, limbs, craniofacial structures and internal organs. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Spatial Noise in Coupling Strength and Natural Frequency within a Pacemaker Network; Consequences for Development of Intestinal Motor Patterns According to a Weakly Coupled Phase Oscillator Model

PubMed Central

Parsons, Sean P.; Huizinga, Jan D.

2016-01-01

Pacemaker activities generated by networks of interstitial cells of Cajal (ICC), in conjunction with the enteric nervous system, orchestrate most motor patterns in the gastrointestinal tract. It was our objective to understand the role of network features of ICC associated with the myenteric plexus (ICC-MP) in the shaping of motor patterns of the small intestine. To that end, a model of weakly coupled oscillators (oscillators influence each other's phase but not amplitude) was created with most parameters derived from experimental data. The ICC network is a uniform two dimensional network coupled by gap junctions. All ICC generate pacemaker (slow wave) activity with a frequency gradient in mice from 50/min at the proximal end of the intestine to 40/min at the distal end. Key features of motor patterns, directly related to the underlying pacemaker activity, are frequency steps and dislocations. These were accurately mimicked by reduction of coupling strength at a point in the chain of oscillators. When coupling strength was expressed as a product of gap junction density and conductance, and gap junction density was varied randomly along the chain (i.e., spatial noise) with a long-tailed distribution, plateau steps occurred at pointsof low density. As gap junction conductance was decreased, the number of plateaus increased, mimicking the effect of the gap junction inhibitor carbenoxolone. When spatial noise was added to the natural interval gradient, as gap junction conductance decreased, the number of plateaus increased as before but in addition the phase waves frequently changed direction of apparent propagation, again mimicking the effect of carbenoxolone. In summary, key features of the motor patterns that are governed by pacemaker activity may be a direct consequence of biological noise, specifically spatial noise in gap junction coupling and pacemaker frequency. PMID:26869875

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains.

PubMed

Onken, Arno; Liu, Jian K; Karunasekara, P P Chamanthi R; Delis, Ioannis; Gollisch, Tim; Panzeri, Stefano

2016-11-01

Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding.

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains

PubMed Central

Onken, Arno; Liu, Jian K.; Karunasekara, P. P. Chamanthi R.; Delis, Ioannis; Gollisch, Tim; Panzeri, Stefano

2016-01-01

Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding. PMID:27814363

The generation and diversification of butterfly eyespot color patterns.

PubMed

Brunetti, C R; Selegue, J E; Monteiro, A; French, V; Brakefield, P M; Carroll, S B

2001-10-16

A fundamental challenge of evolutionary and developmental biology is understanding how new characters arise and change. The recently derived eyespots on butterfly wings vary extensively in number and pattern between species and play important roles in predator avoidance. Eyespots form through the activity of inductive organizers (foci) at the center of developing eyespot fields. Foci are the proposed source of a morphogen, the levels of which determine the color of surrounding wing scale cells. However, it is unknown how reception of the focal signal translates into rings of different-colored scales, nor how different color schemes arise in different species. We have identified several transcription factors, including butterfly homologs of the Drosophila Engrailed/Invected and Spalt proteins, that are deployed in concentric territories corresponding to the future rings of pigmented scales that compose the adult eyespot. We have isolated a new Bicyclus anynana wing pattern mutant, Goldeneye, in which the scales of one inner color ring become the color of a different ring. These changes correlate with shifts in transcription factor expression, suggesting that Goldeneye affects an early regulatory step in eyespot color patterning. In different butterfly species, the same transcription factors are expressed in eyespot fields, but in different relative spatial domains that correlate with divergent eyespot color schemes. Our results suggest that signaling from the focus induces nested rings of regulatory gene expression that subsequently control the final color pattern. Furthermore, the remarkably plastic regulatory interactions downstream of focal signaling have facilitated the evolution of eyespot diversity.

The Stimulus-Dependent Gradient of Cyp26B1+ Olfactory Sensory Neurons Is Necessary for the Functional Integrity of the Olfactory Sensory Map.

PubMed

Login, Hande; Håglin, Sofia; Berghard, Anna; Bohm, Staffan

2015-10-07

Stimulus-dependent expression of the retinoic acid-inactivating enzyme Cyp26B1 in olfactory sensory neurons (OSNs) forms a dorsomedial (DM)-ventrolateral (VL) gradient in the mouse olfactory epithelium. The gradient correlates spatially with different rates of OSN turnover, as well as the functional organization of the olfactory sensory map, into overlapping zones of OSNs that express different odorant receptors (ORs). Here, we analyze transgenic mice that, instead of a stimulus-dependent Cyp26B1 gradient, have constitutive Cyp26B1 levels in all OSNs. Starting postnatally, OSN differentiation is decreased and progenitor proliferation is increased. Initially, these effects are selective to the VL-most zone and correlate with reduced ATF5 expression and accumulation of OSNs that do not express ORs. Transcription factor ATF5 is known to stabilize OR gene choice via onset of the stimulus-transducing enzyme adenylyl cyclase type 3. During further postnatal development of Cyp26B1 mice, an anomalous DM(high)-VL(low) expression gradient of adenylyl cyclase type 3 appears, which coincides with altered OR frequencies and OR zones. All OR zones expand ventrolaterally except for the VL-most zone, which contracts. The expansion results in an increased zonal overlap that is also evident in the innervation pattern of OSN axon terminals in olfactory bulbs. These findings together identify a mechanism by which postnatal sensory-stimulated vitamin A metabolism modifies the generation of spatially specified neurons and their precise topographic connectivity. The distributed patterns of vitamin A-metabolizing enzymes in the nervous system suggest the possibility that the mechanism may also regulate neuroplasticity in circuits other than the olfactory sensory map. The mouse olfactory sensory map is functionally wired according to precise axonal projections of spatially organized classes of olfactory sensory neurons in the nose. The genetically controlled mechanisms that regulate the development of the olfactory sensory map are beginning to be elucidated. Little is known about mechanisms by which sensory stimuli shape the organization of the map after birth. We show that a stimulus-dependent gradient of a retinoic acid-inactivating enzyme Cyp26B1 modifies the composition, localization, and axonal projections of olfactory sensory neuron classes. The mechanism is novel and suggests the interesting possibility that local vitamin A metabolism could also be a mediator of stimulus-dependent modifications of precise spatial connectivity in other parts of the nervous system. Copyright © 2015 the authors 0270-6474/15/3513807-12$15.00/0.

Robust patterning of gene expression based on internal coordinate system of cells.

PubMed

Ogawa, Ken-ichiro; Miyake, Yoshihiro

2015-06-01

Cell-to-cell communication in multicellular organisms is established through the transmission of various kinds of chemical substances such as proteins. It is well known that gene expression triggered by a chemical substance in individuals has stable spatial patterns despite the individual differences in concentration patterns of the chemical substance. This fact reveals an important property of multicellular organisms called "robustness", which allows the organisms to generate their forms while maintaining proportion. Robustness has been conventionally accounted for by the stability of solutions of dynamical equations that represent a specific interaction network of chemical substances. However, any biological system is composed of autonomous elements. In general, an autonomous element does not merely accept information on the chemical substance from the environment; instead, it accepts the information based on its own criteria for reaction. Therefore, this phenomenon needs to be considered from the viewpoint of cells. Such a viewpoint is expected to allow the consideration of the autonomy of cells in multicellular organisms. This study aims to explain theoretically the robust patterning of gene expression from the viewpoint of cells. For this purpose, we introduced a new operator for transforming a state variable of a chemical substance from an external coordinate system to an internal coordinate system of each cell, which describes the observation of the chemical substance by cells. We then applied this operator to the simplest reaction-diffusion model of the chemical substance to investigate observation effects by cells. Our mathematical analysis of this extended model indicates that the robust patterning of gene expression against individual differences in concentration pattern of the chemical substance can be explained from the viewpoint of cells if there is a regulation field that compensates for the difference between cells seen in the observation results. This result provides a new insight into the investigation of the mechanism of robust patterning in biological systems composed of individual elements. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Spatial and temporal drivers of wildfire occurrence in the context of rural development in northern Wisconsin, USA

Treesearch

Brian R Miranda; Brian R Sturtevant; Susan I Stewart; Roger B. Hammer

2012-01-01

Most drivers underlying wildfire are dynamic, but at different spatial and temporal scales. We quantified temporal and spatial trends in wildfire patterns over two spatial extents in northern Wisconsin to identify drivers and their change through time. We used spatial point pattern analysis to quantify the spatial pattern of wildfire occurrences, and linear regression...

Expression of Wnt pathway genes in polyps and medusa-like structures of Ectopleura larynx (Cnidaria: Hydrozoa).

PubMed

Nawrocki, Annalise M; Cartwright, Paulyn

2013-01-01

The canonical Wnt signaling pathway is conserved in its role in axial patterning throughout Metazoa. In some hydrozoans (Phylum Cnidaria), Wnt signaling is implicated in oral-aboral patterning of the different life cycle stages-the planula, polyp and medusa. Unlike most hydrozoans, members of Aplanulata lack a planula larva and the polyp instead develops directly from a brooded or encysted embryo. The Aplanulata species Ectopleura larynx broods such embryos within gonophores. These gonophores are truncated medusae that remain attached to the polyps from which they bud, and retain evolutionary remnants of medusa structures. In E. larynx, gonophores differ between males and females in their degree of medusa truncation, making them an ideal system for examining truncated medusa development. Using next-generation sequencing, we isolated genes from Wnt signaling pathways and examined their expression in E. larynx. Our data are consistent with the Wnt pathway being involved in axial patterning of the polyp and truncated medusa. Changes in the spatial expression of Wnt pathway genes are correlated with the development of different oral structures in male and female gonophores. The absence of expression of components of the Wnt pathway and presence of a Wnt pathway antagonist SFRP in the developing anterior end of the gonophore suggest that downregulation of the Wnt pathway could play a role in medusa reduction in E. larynx. © 2013 Wiley Periodicals, Inc.

A two-step patterning process increases the robustness of periodic patterning in the fly eye.

PubMed

Gavish, Avishai; Barkai, Naama

2016-06-01

Complex periodic patterns can self-organize through dynamic interactions between diffusible activators and inhibitors. In the biological context, self-organized patterning is challenged by spatial heterogeneities ('noise') inherent to biological systems. How spatial variability impacts the periodic patterning mechanism and how it can be buffered to ensure precise patterning is not well understood. We examine the effect of spatial heterogeneity on the periodic patterning of the fruit fly eye, an organ composed of ∼800 miniature eye units (ommatidia) whose periodic arrangement along a hexagonal lattice self-organizes during early stages of fly development. The patterning follows a two-step process, with an initial formation of evenly spaced clusters of ∼10 cells followed by a subsequent refinement of each cluster into a single selected cell. Using a probabilistic approach, we calculate the rate of patterning errors resulting from spatial heterogeneities in cell size, position and biosynthetic capacity. Notably, error rates were largely independent of the desired cluster size but followed the distributions of signaling speeds. Pre-formation of large clusters therefore greatly increases the reproducibility of the overall periodic arrangement, suggesting that the two-stage patterning process functions to guard the pattern against errors caused by spatial heterogeneities. Our results emphasize the constraints imposed on self-organized patterning mechanisms by the need to buffer stochastic effects. Author summary Complex periodic patterns are common in nature and are observed in physical, chemical and biological systems. Understanding how these patterns are generated in a precise manner is a key challenge. Biological patterns are especially intriguing, as they are generated in a noisy environment; cell position and cell size, for example, are subject to stochastic variations, as are the strengths of the chemical signals mediating cell-to-cell communication. The need to generate a precise and robust pattern in this 'noisy' environment restricts the space of patterning mechanisms that can function in the biological setting. Mathematical modeling is useful in comparing the sensitivity of different mechanisms to such variations, thereby highlighting key aspects of their design.We use mathematical modeling to study the periodic patterning of the fruit fly eye. In this system, a highly ordered lattice of differentiated cells is generated in a two-dimensional cell epithelium. The pattern is first observed by the appearance of evenly spaced clusters of ∼10 cells that express specific genes. Each cluster is subsequently refined into a single cell, which initiates the formation and differentiation of a miniature eye unit, the ommatidium. We formulate a mathematical model based on the known molecular properties of the patterning mechanism, and use a probabilistic approach to calculate the errors in cluster formation and refinement resulting from stochastic cell-to-cell variations ('noise') in different quantitative parameters. This enables us to define the parameters most influencing noise sensitivity. Notably, we find that this error is roughly independent of the desired cluster size, suggesting that large clusters are beneficial for ensuring the overall reproducibility of the periodic cluster arrangement. For the stage of cluster refinement, we find that rapid communication between cells is critical for reducing error. Our work provides new insights into the constraints imposed on mechanisms generating periodic patterning in a realistic, noisy environment, and in particular, discusses the different considerations in achieving optimal design of the patterning network.

Evolution of Sex-Specific Traits through Changes in HOX-Dependent doublesex Expression

PubMed Central

Tanaka, Kohtaro; Barmina, Olga; Sanders, Laura E.; Arbeitman, Michelle N.; Kopp, Artyom

2011-01-01

Almost every animal lineage is characterized by unique sex-specific traits, implying that such traits are gained and lost frequently in evolution. However, the genetic mechanisms responsible for these changes are not understood. In Drosophila, the activity of the sex determination pathway is restricted to sexually dimorphic tissues, suggesting that spatial regulation of this pathway may contribute to the evolution of sex-specific traits. We examine the regulation and function of doublesex (dsx), the main transcriptional effector of the sex determination pathway, in the development and evolution of Drosophila sex combs. Sex combs are a recent evolutionary innovation and show dramatic diversity in the relatively few Drosophila species that have them. We show that dsx expression in the presumptive sex comb region is activated by the HOX gene Sex combs reduced (Scr), and that the male isoform of dsx up-regulates Scr so that both genes become expressed at high levels in this region in males but not in females. Precise spatial regulation of dsx is essential for defining sex comb position and morphology. Comparative analysis of Scr and dsx expression reveals a tight correlation between sex comb morphology and the expression patterns of both genes. In species that primitively lack sex combs, no dsx expression is observed in the homologous region, suggesting that the origin and diversification of this structure were linked to the gain of a new dsx expression domain. Two other, distantly related fly lineages that independently evolved novel male-specific structures show evolutionary gains of dsx expression in the corresponding tissues, where dsx may also be controlled by Scr. These findings suggest that changes in the spatial regulation of sex-determining genes are a key mechanism that enables the evolution of new sex-specific traits, contributing to some of the most dramatic examples of phenotypic diversification in nature. PMID:21886483

The fundamentals of average local variance--Part II: Sampling simple regular patterns with optical imagery.

PubMed

Bøcher, Peder Klith; McCloy, Keith R

2006-02-01

In this investigation, the characteristics of the average local variance (ALV) function is investigated through the acquisition of images at different spatial resolutions of constructed scenes of regular patterns of black and white squares. It is shown that the ALV plot consistently peaks at a spatial resolution in which the pixels has a size corresponding to half the distance between scene objects, and that, under very specific conditions, it also peaks at a spatial resolution in which the pixel size corresponds to the whole distance between scene objects. It is argued that the peak at object distance when present is an expression of the Nyquist sample rate. The presence of this peak is, hence, shown to be a function of the matching between the phase of the scene pattern and the phase of the sample grid, i.e., the image. When these phases match, a clear and distinct peak is produced on the ALV plot. The fact that the peak at half the distance consistently occurs in the ALV plot is linked to the circumstance that the sampling interval (distance between pixels) and the extent of the sampling unit (size of pixels) are equal. Hence, at twice the Nyquist sampling rate, each fundamental period of the pattern is covered by four pixels; therefore, at least one pixel is always completely embedded within one pattern element, regardless of sample scene phase. If the objects in the scene are scattered with a distance larger than their extent, the peak will be related to the size by a factor larger than 1/2. This is suggested to be the explanation to the results presented by others that the ALV plot is related to scene-object size by a factor of 1/2-3/4.

The Ontogeny and Brain Distribution Dynamics of the Appetite Regulators NPY, CART and pOX in Larval Atlantic Cod (Gadus morhua L.)

PubMed Central

Le, Hoang T. M. D.; Angotzi, Anna Rita; Ebbesson, Lars O. E.; Karlsen, Ørjan

2016-01-01

Similar to many marine teleost species, Atlantic cod undergo remarkable physiological changes during the early life stages with concurrent and profound changes in feeding biology and ecology. In contrast to the digestive system, very little is known about the ontogeny and the localization of the centers that control appetite and feed ingestion in the developing brain of fish. We examined the expression patterns of three appetite regulating factors (orexigenic: neuropeptide Y, NPY; prepro-orexin, pOX and anorexigenic: cocaine- and amphetamine-regulated transcript, CART) in discrete brain regions of developing Atlantic cod using chromogenic and double fluorescent in situ hybridization. Differential temporal and spatial expression patterns for each appetite regulator were found from first feeding (4 days post hatch; dph) to juvenile stage (76 dph). Neurons expressing NPY mRNA were detected in the telencephalon (highest expression), diencephalon, and optic tectum from 4 dph onward. CART mRNA expression had a wider distribution along the anterior-posterior brain axis, including both telencephalon and diencephalon from 4 dph. From 46 dph, CART transcripts were also detected in the olfactory bulb, region of the nucleus of medial longitudinal fascicle, optic tectum and midbrain tegmentum. At 4 and 20 dph, pOX mRNA expression was exclusively found in the preoptic region, but extended to the hypothalamus at 46 and 76 dph. Co-expression of both CART and pOX genes were also observed in several hypothalamic neurons throughout larval development. Our results show that both orexigenic and anorexigenic factors are present in the telencephalon, diencephalon and mesencephalon in cod larvae. The telencephalon mostly contains key factors of hunger control (NPY), while the diencephalon, and particularly the hypothalamus may have a more complex role in modulating the multifunctional control of appetite in this species. As the larvae develop, the overall progression in temporal and spatial complexity of NPY, CART and pOX mRNAs expression might be correlated to the maturation of appetite control regulation. These observations suggest that teleost larvae continue to develop the regulatory networks underlying appetite control after onset of exogenous feeding. PMID:27100086

The Ontogeny and Brain Distribution Dynamics of the Appetite Regulators NPY, CART and pOX in Larval Atlantic Cod (Gadus morhua L.).

PubMed

Le, Hoang T M D; Angotzi, Anna Rita; Ebbesson, Lars O E; Karlsen, Ørjan; Rønnestad, Ivar

2016-01-01

Similar to many marine teleost species, Atlantic cod undergo remarkable physiological changes during the early life stages with concurrent and profound changes in feeding biology and ecology. In contrast to the digestive system, very little is known about the ontogeny and the localization of the centers that control appetite and feed ingestion in the developing brain of fish. We examined the expression patterns of three appetite regulating factors (orexigenic: neuropeptide Y, NPY; prepro-orexin, pOX and anorexigenic: cocaine- and amphetamine-regulated transcript, CART) in discrete brain regions of developing Atlantic cod using chromogenic and double fluorescent in situ hybridization. Differential temporal and spatial expression patterns for each appetite regulator were found from first feeding (4 days post hatch; dph) to juvenile stage (76 dph). Neurons expressing NPY mRNA were detected in the telencephalon (highest expression), diencephalon, and optic tectum from 4 dph onward. CART mRNA expression had a wider distribution along the anterior-posterior brain axis, including both telencephalon and diencephalon from 4 dph. From 46 dph, CART transcripts were also detected in the olfactory bulb, region of the nucleus of medial longitudinal fascicle, optic tectum and midbrain tegmentum. At 4 and 20 dph, pOX mRNA expression was exclusively found in the preoptic region, but extended to the hypothalamus at 46 and 76 dph. Co-expression of both CART and pOX genes were also observed in several hypothalamic neurons throughout larval development. Our results show that both orexigenic and anorexigenic factors are present in the telencephalon, diencephalon and mesencephalon in cod larvae. The telencephalon mostly contains key factors of hunger control (NPY), while the diencephalon, and particularly the hypothalamus may have a more complex role in modulating the multifunctional control of appetite in this species. As the larvae develop, the overall progression in temporal and spatial complexity of NPY, CART and pOX mRNAs expression might be correlated to the maturation of appetite control regulation. These observations suggest that teleost larvae continue to develop the regulatory networks underlying appetite control after onset of exogenous feeding.

Generalized reproduction numbers and the prediction of patterns in waterborne disease.

PubMed

Gatto, Marino; Mari, Lorenzo; Bertuzzo, Enrico; Casagrandi, Renato; Righetto, Lorenzo; Rodriguez-Iturbe, Ignacio; Rinaldo, Andrea

2012-11-27

Understanding, predicting, and controlling outbreaks of waterborne diseases are crucial goals of public health policies, but pose challenging problems because infection patterns are influenced by spatial structure and temporal asynchrony. Although explicit spatial modeling is made possible by widespread data mapping of hydrology, transportation infrastructure, population distribution, and sanitation, the precise condition under which a waterborne disease epidemic can start in a spatially explicit setting is still lacking. Here we show that the requirement that all the local reproduction numbers R0 be larger than unity is neither necessary nor sufficient for outbreaks to occur when local settlements are connected by networks of primary and secondary infection mechanisms. To determine onset conditions, we derive general analytical expressions for a reproduction matrix G0, explicitly accounting for spatial distributions of human settlements and pathogen transmission via hydrological and human mobility networks. At disease onset, a generalized reproduction number Λ0 (the dominant eigenvalue of G0) must be larger than unity. We also show that geographical outbreak patterns in complex environments are linked to the dominant eigenvector and to spectral properties of G0. Tests against data and computations for the 2010 Haiti and 2000 KwaZulu-Natal cholera outbreaks, as well as against computations for metapopulation networks, demonstrate that eigenvectors of G0 provide a synthetic and effective tool for predicting the disease course in space and time. Networked connectivity models, describing the interplay between hydrology, epidemiology, and social behavior sustaining human mobility, thus prove to be key tools for emergency management of waterborne infections.

Regional patterns of earthquake-triggered landslides and their relation to ground motion

NASA Astrophysics Data System (ADS)

Meunier, Patrick; Hovius, Niels; Haines, A. John

2007-10-01

We have documented patterns of landsliding associated with large earthquakes on three thrust faults: the Northridge earthquake in California, Chi-Chi earthquake in Taiwan, and two earthquakes on the Ramu-Markham fault bounding the Finisterre Mountains of Papua New Guinea. In each case, landslide densities are shown to be greatest in the area of strongest ground acceleration and to decay with distance from the epicenter. In California and Taiwan, the density of co-seismic landslides is linearly and highly correlated with both the vertical and horizontal components of measured peak ground acceleration. Based on this observation, we derive an expression for the spatial variation of landslide density analogous with regional seismic attenuation laws. In its general form, this expression applies to our three examples, and we determine best fit values for individual cases. Our findings open a window on the construction of shake maps from geomorphic observations for earthquakes in non-instrumented regions.

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Pattern Water Use Efficiency perspective on degradation and recovery of shrublands across Mediterranean to Arid transition zones

NASA Astrophysics Data System (ADS)

Shoshany, Maxim

2017-04-01

Shrublands cover a total of 12.7 million km2 , a considerable part of them along semi-arid to arid transition zones. Varying patterns of shrubs, grasses and barren land along such climatic gradients express the spatial dimension of climate change and human disturbance which attracted limited attention in the eco-geomorphic literature. Questions concerning relationships between rainfall, shrublands biomass and their patterns are fundamental for the understanding of these ecosystems response to the expected changes in water availability due to global warming and the increase in human disturbance to natural ecosystems following World population growth. While processes leading to the formation of patterns had attracted considerable attention, the spatial dimension of Water Use Efficiency (WUE) which is a parameter measuring ecosystems productivity in relation to water availability is severely missing. Relative shrub cover is a primary estimator of the fraction of water utilized for shrubs growth. Edge effects must be considered as well in fragmented ecosystems in general and in hot regions in particular since soil temperature in hot regions which frequently exceed 50oC during summer months decreases photosynthesis and productivity in plants bordering bare soil. This edge effect is decreasing with the increase in shrubs' height. Pattern Water Use Efficiency describes the combined effect of shrub cover, shrub height and shrub patches edge zone proportion on water use efficiency. In my presentation I will first present mapping od PWUEs across Mediterranean to arid transition zones in the Eastern Mediterranean. Then I will present several mathematical models describing PWUE for simulated patterns, searching for the spatial parameterization providing the highest sensitivity to patterns responses to changes in habitat conditions. Such simulations would allow us to discuss several PWUE strategies for shrublands recovery under the current scenarios of climate change and human driven degradation.

Expression pattern of zebrafish rxfp2 homologue genes during embryonic development.

PubMed

Donizetti, Aldo; Fiengo, Marcella; Del Gaudio, Rosanna; Iazzetti, Giovanni; Pariante, Paolo; Minucci, Sergio; Aniello, Francesco

2015-11-01

RXFP2 is one of the 4 receptors for relaxin insulin-like peptides, in particular it binds with high affinity the INSL3 peptide. INSL3/RXFP2 pair is essential for testicular descent during placental mammalian development. The evolutionary history of this ligand/receptor pair has received much attention, since its function in vertebrate species lacking testicular descent, such as the fishes, remains elusive. Herein, we analyzed the expression pattern of three rxfp2 homologue genes in zebrafish embryonic development. For all the three rxfp2 genes (rxfp2a, rxfp2b, and rxfp2-like) we showed the presence of maternally derived transcripts. Later in the development, rxfp2a is only expressed at larval stage, whereas rxfp2b is expressed in all the analyzed stage with highest level in the larvae. The rxfp2-like gene is expressed in all the analyzed stage with a transcript level that increased starting at early pharyngula stage. The spatial localization analysis of rxfp2-like gene showed that it is expressed in many cell clusters in the developing brain. In addition, other rxfp2-like-expressing cells were identified in the retina and oral epithelium. This analysis provides new insights to elucidate the evolution of rxfp2 genes in vertebrate lineage and lays the foundations to study their role in vertebrate embryonic development. © 2015 Wiley Periodicals, Inc.

BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeted expression to secondary cell-wall-forming cells of grasses

DOE PAGES

Petrik, Deborah L.; Cass, Cynthia L.; Padmakshan, Dharshana; ...

2016-02-04

Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels inmore » stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven expression was strongest in leaf veins, leaf margins, and trichomes; relatively weaker and patchy expression was observed in the epidermis. BdPMT promoter-driven expression was similar to the BdCESA promoters expression patterns, including strong expression in trichomes. The intensity and extent of GUS staining varied considerably between transgenic lines, suggesting that positional effects influenced promoter activity. Introducing the BdPMT and BdCESA8 Open Reading Frames into BdPMT and BdCESA8 utility promoter binary vectors, respectively, and transforming those constructs into Brachypodium pmt and cesa8 loss-of-function mutants resulted in rescue of the corresponding mutant phenotypes. This work therefore validates the functionality of these utility promoter binary vectors for use in Brachypodium and likely other grass species. Lastly, the identification, in Bdcesa8-1 T-DNA mutant stems, of an 80% reduction in crystalline cellulose levels confirms that the BdCESA8 gene is a secondary-cell-wall-forming cellulose synthase.« less

BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeted expression to secondary cell-wall-forming cells of grasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Deborah L.; Cass, Cynthia L.; Padmakshan, Dharshana

Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels inmore » stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven expression was strongest in leaf veins, leaf margins, and trichomes; relatively weaker and patchy expression was observed in the epidermis. BdPMT promoter-driven expression was similar to the BdCESA promoters expression patterns, including strong expression in trichomes. The intensity and extent of GUS staining varied considerably between transgenic lines, suggesting that positional effects influenced promoter activity. Introducing the BdPMT and BdCESA8 Open Reading Frames into BdPMT and BdCESA8 utility promoter binary vectors, respectively, and transforming those constructs into Brachypodium pmt and cesa8 loss-of-function mutants resulted in rescue of the corresponding mutant phenotypes. This work therefore validates the functionality of these utility promoter binary vectors for use in Brachypodium and likely other grass species. Lastly, the identification, in Bdcesa8-1 T-DNA mutant stems, of an 80% reduction in crystalline cellulose levels confirms that the BdCESA8 gene is a secondary-cell-wall-forming cellulose synthase.« less

PKMζ Differentially Utilized between Sexes for Remote Long-Term Spatial Memory

PubMed Central

Sebastian, Veronica; Vergel, Tatyana; Baig, Raheela; Schrott, Lisa M.; Serrano, Peter A.

2013-01-01

It is well established that male rats have an advantage in acquiring place-learning strategies, allowing them to learn spatial tasks more readily than female rats. However many of these differences have been examined solely during acquisition or in 24h memory retention. Here, we investigated whether sex differences exist in remote long-term memory, lasting 30d after training, and whether there are differences in the expression pattern of molecular markers associated with long-term memory maintenance. Specifically, we analyzed the expression of protein kinase M zeta (PKMζ) and the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit GluA2. To adequately evaluate memory retention, we used a robust training protocol to attenuate sex differences in acquisition and found differential effects in memory retention 1d and 30d after training. Female cohorts tested for memory retention 1d after 60 training trials outperformed males by making significantly fewer reference memory errors at test. In contrast, male cohorts tested 30d after 60 training trials outperformed females of the same condition, making fewer reference memory errors and achieving significantly higher retention test scores. Furthermore, given 60 training trials, females tested 30d later showed significantly worse memory compared to females tested 1d later, while males tested 30d later did not differ from males tested 1d later. Together these data suggest that with robust training males do no retain spatial information as well as females do 24h post-training but maintain this spatial information for longer. Males also showed a significant increase in synaptic PKMζ expression and a positive correlation with retention test scores, while females did not. Interestingly, both sexes showed a positive correlation between retention test scores and synaptic GluA2 expression. Furthermore, the increased expression of synaptic PKMζ, associated with male memory but not with female memory, identifies another potential sex-mediated difference in memory processing. PMID:24244733

Medium-range Performance of the Global NWP Model

NASA Astrophysics Data System (ADS)

Kim, J.; Jang, T.; Kim, J.; Kim, Y.

2017-12-01

The medium-range performance of the global numerical weather prediction (NWP) model in the Korea Meteorological Administration (KMA) is investigated. The performance is based on the prediction of the extratropical circulation. The mean square error is expressed by sum of spatial variance of discrepancy between forecasts and observations and the square of the mean error (ME). Thus, it is important to investigate the ME effect in order to understand the model performance. The ME is expressed by the subtraction of an anomaly from forecast difference against the real climatology. It is found that the global model suffers from a severe systematic ME in medium-range forecasts. The systematic ME is dominant in the entire troposphere in all months. Such ME can explain at most 25% of root mean square error. We also compare the extratropical ME distribution with that from other NWP centers. NWP models exhibit similar spatial ME structure each other. It is found that the spatial ME pattern is highly correlated to that of an anomaly, implying that the ME varies with seasons. For example, the correlation coefficient between ME and anomaly ranges from -0.51 to -0.85 by months. The pattern of the extratropical circulation also has a high correlation to an anomaly. The global model has trouble in faithfully simulating extratropical cyclones and blockings in the medium-range forecast. In particular, the model has a hard to simulate an anomalous event in medium-range forecasts. If we choose an anomalous period for a test-bed experiment, we will suffer from a large error due to an anomaly.

A vesicular glutamate transporter in lampreys: cDNA cloning and early expression in the nervous system.

PubMed

Villar-Cerviño, Verona; Rocancourt, Claire; Menuet, Arnaud; Da Silva, Corinne; Wincker, Patrick; Anadón, Ramón; Mazan, Sylvie; Rodicio, Maria Celina

2010-09-01

Vesicular glutamate transporters (VGLUTs) accumulate glutamate into synaptic vesicles of glutamatergic neurons, and thus are considered to define the phenotype of these neurons. Glutamate also appears to play a role in the development of the nervous system of vertebrates. Here we report the characterization of a vesicular glutamate transporter of lamprey (lVGluT), a novel member of the VGluT gene family. Phylogenetic analysis indicates that lVGLUT cannot be assigned to any of the three VGLUT isoforms characterized in teleosts and mammals, suggesting that these classes may have been fixed after the splitting between cyclostomes and gnathostomes. Expression pattern analysis during lamprey embryogenesis and prolarval stages shows that lVGluT expression is restricted to the nervous system. The first structure to express lVGluT was the olfactory epithelium of late embryos. In the brain of early prolarvae, lVGluT was expressed in most of the neuronal populations that generate the early axonal scaffold. lVGluT expression was also observed in neuronal populations of the rhombencephalon and spinal cord and in ganglia of the branchiomeric, octaval and posterior lateral line nerves. In the rhombencephalon, lVGluT expression appears to be spatially restricted in dorsal and ventral longitudinal domains. Comparison of the early expression of VGluT genes between the lamprey and some anamniotan gnathostomes (frog, zebrafish) reveals a conserved expression pattern, likely to reflect ancestral vertebrate characteristics. 2010 Elsevier B.V. All rights reserved.

Spatial pattern of Baccharis platypoda shrub as determined by sex and life stages

NASA Astrophysics Data System (ADS)

Fonseca, Darliana da Costa; de Oliveira, Marcio Leles Romarco; Pereira, Israel Marinho; Gonzaga, Anne Priscila Dias; de Moura, Cristiane Coelho; Machado, Evandro Luiz Mendonça

2017-11-01

Spatial patterns of dioecious species can be determined by their nutritional requirements and intraspecific competition, apart from being a response to environmental heterogeneity. The aim of the study was to evaluate the spatial pattern of populations of a dioecious shrub reporting to sex and reproductive stage patterns of individuals. Sampling was carried out in three areas located in the meridional portion of Serra do Espinhaço, where in individuals of the studied species were mapped. The spatial pattern was determined through O-ring analysis and Ripley's K-function and the distribution of individuals' frequencies was verified through x2 test. Populations in two areas showed an aggregate spatial pattern tending towards random or uniform according to the observed scale. Male and female adults presented an aggregate pattern at smaller scales, while random and uniform patterns were verified above 20 m for individuals of both sexes of the areas A2 and A3. Young individuals presented an aggregate pattern in all areas and spatial independence in relation to adult individuals, especially female plants. The interactions between individuals of both genders presented spatial independence with respect to spatial distribution. Baccharis platypoda showed characteristics in accordance with the spatial distribution of savannic and dioecious species, whereas the population was aggregated tending towards random at greater spatial scales. Young individuals showed an aggregated pattern at different scales compared to adults, without positive association between them. Female and male adult individuals presented similar characteristics, confirming that adult individuals at greater scales are randomly distributed despite their distinct preferences for environments with moisture variation.

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

PubMed Central

Bennett, James E. M.; Bair, Wyeth

2015-01-01

Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity.

PubMed

Bennett, James E M; Bair, Wyeth

2015-08-01

Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli.

Analysis of Spatial Point Patterns in Nuclear Biology

PubMed Central

Weston, David J.; Adams, Niall M.; Russell, Richard A.; Stephens, David A.; Freemont, Paul S.

2012-01-01

There is considerable interest in cell biology in determining whether, and to what extent, the spatial arrangement of nuclear objects affects nuclear function. A common approach to address this issue involves analyzing a collection of images produced using some form of fluorescence microscopy. We assume that these images have been successfully pre-processed and a spatial point pattern representation of the objects of interest within the nuclear boundary is available. Typically in these scenarios, the number of objects per nucleus is low, which has consequences on the ability of standard analysis procedures to demonstrate the existence of spatial preference in the pattern. There are broadly two common approaches to look for structure in these spatial point patterns. First a spatial point pattern for each image is analyzed individually, or second a simple normalization is performed and the patterns are aggregated. In this paper we demonstrate using synthetic spatial point patterns drawn from predefined point processes how difficult it is to distinguish a pattern from complete spatial randomness using these techniques and hence how easy it is to miss interesting spatial preferences in the arrangement of nuclear objects. The impact of this problem is also illustrated on data related to the configuration of PML nuclear bodies in mammalian fibroblast cells. PMID:22615822

Tree invasion of a montane meadow complex: temporal trends, spatial patterns, and biotic interactions

Treesearch

Charles B. Halpern; Joseph A. Antos; Janine M. Rice; Ryan D. Haugo; Nicole L. Lang

2010-01-01

We combined spatial point pattern analysis, population age structures, and a time-series of stem maps to quantify spatial and temporal patterns of conifer invasion over a 200-yr period in three plots totaling 4 ha. In combination, spatial and temporal patterns of establishment suggest an invasion process shaped by biotic interactions, with facilitation promoting...

[Characteristics of temporal-spatial differentiation in landscape pattern vulnerability in Nansihu Lake wetland, China.

PubMed

Liang, Jia Xin; Li, Xin Ju

2018-02-01

With remote sensing images from 1985, 2000 Lantsat 5 TM and 2015 Lantsat 8 OLI as data sources, we tried to select the suitable research scale and examine the temporal-spatial diffe-rentiation with such scale in the Nansihu Lake wetland by using landscape pattern vulnerability index constructed by sensitivity index and adaptability index, and combined with space statistics such as semivariogram and spatial autocorrelation. The results showed that 1 km × 1 km equidistant grid was the suitable research scale, which could eliminate the influence of spatial heterogeneity induced by random factors. From 1985 to 2015, the landscape pattern vulnerability in the Nansihu Lake wetland deteriorated gradually. The high-risk area of landscape pattern vulnerability dramatically expanded with time. The spatial heterogeneity of landscape pattern vulnerability increased, and the influence of non-structural factors on landscape pattern vulnerability strengthened. Spatial variability affected by spatial autocorrelation slightly weakened. Landscape pattern vulnerability had strong general spatial positive correlation, with the significant form of spatial agglomeration. The positive spatial autocorrelation continued to increase and the phenomenon of spatial concentration was more and more obvious over time. The local autocorrelation mainly based on high-high accumulation zone and low-low accumulation zone had stronger spatial autocorrelation among neighboring space units. The high-high accumulation areas showed the strongest level of significance, and the significant level of low-low accumulation zone increased with time. Natural factors, such as temperature and precipitation, affected water-level and landscape distribution, and thus changed the landscape patterns vulnerability of Nansihu Lake wetland. The dominant driver for the deterioration of landscape patterns vulnerability was human activities, including social economy activity and policy system.

Neighborhood Landscape Spatial Patterns and Land Surface Temperature: An Empirical Study on Single-Family Residential Areas in Austin, Texas.

PubMed

Kim, Jun-Hyun; Gu, Donghwan; Sohn, Wonmin; Kil, Sung-Ho; Kim, Hwanyong; Lee, Dong-Kun

2016-09-02

Rapid urbanization has accelerated land use and land cover changes, and generated the urban heat island effect (UHI). Previous studies have reported positive effects of neighborhood landscapes on mitigating urban surface temperatures. However, the influence of neighborhood landscape spatial patterns on enhancing cooling effects has not yet been fully investigated. The main objective of this study was to assess the relationships between neighborhood landscape spatial patterns and land surface temperatures (LST) by using multi-regression models considering spatial autocorrelation issues. To measure the influence of neighborhood landscape spatial patterns on LST, this study analyzed neighborhood environments of 15,862 single-family houses in Austin, Texas, USA. Using aerial photos, geographic information systems (GIS), and remote sensing, FRAGSTATS was employed to calculate values of several landscape indices used to measure neighborhood landscape spatial patterns. After controlling for the spatial autocorrelation effect, results showed that larger and better-connected landscape spatial patterns were positively correlated with lower LST values in neighborhoods, while more fragmented and isolated neighborhood landscape patterns were negatively related to the reduction of LST.

Neighborhood Landscape Spatial Patterns and Land Surface Temperature: An Empirical Study on Single-Family Residential Areas in Austin, Texas

PubMed Central

Kim, Jun-Hyun; Gu, Donghwan; Sohn, Wonmin; Kil, Sung-Ho; Kim, Hwanyong; Lee, Dong-Kun

2016-01-01

Rapid urbanization has accelerated land use and land cover changes, and generated the urban heat island effect (UHI). Previous studies have reported positive effects of neighborhood landscapes on mitigating urban surface temperatures. However, the influence of neighborhood landscape spatial patterns on enhancing cooling effects has not yet been fully investigated. The main objective of this study was to assess the relationships between neighborhood landscape spatial patterns and land surface temperatures (LST) by using multi-regression models considering spatial autocorrelation issues. To measure the influence of neighborhood landscape spatial patterns on LST, this study analyzed neighborhood environments of 15,862 single-family houses in Austin, Texas, USA. Using aerial photos, geographic information systems (GIS), and remote sensing, FRAGSTATS was employed to calculate values of several landscape indices used to measure neighborhood landscape spatial patterns. After controlling for the spatial autocorrelation effect, results showed that larger and better-connected landscape spatial patterns were positively correlated with lower LST values in neighborhoods, while more fragmented and isolated neighborhood landscape patterns were negatively related to the reduction of LST. PMID:27598186

The Drosophila Extradenticle and Homothorax selector proteins control branchless/FGF expression in mesodermal bridge-cells.

PubMed

Merabet, Samir; Ebner, Andreas; Affolter, Markus

2005-08-01

The stereotyped outgrowth of tubular branches of the Drosophila tracheal system is orchestrated by the local and highly dynamic expression profile of branchless (bnl), which encodes a secreted fibroblast growth factor (FGF)-like molecule. Despite the importance of the spatial and temporal bnl regulation, little is known about the upstream mechanisms that establish its complex expression pattern. Here, we show that the Extradenticle and Homothorax selector proteins control bnl transcription in a single cell per segment, the mesodermal bridge-cell. In addition, we observed that a key determinant of bridge-cell specification, the transcription factor Hunchback, is also required for bnl expression. Therefore, we propose that one of the functions of the bridge-cell is to synthesize and secrete the chemoattractant Bnl. These findings provide a hitherto unknown and interesting link between combinatorial inputs of transcription factors, cell-specific ligand expression and organ morphogenesis.

Multiple Spatial Coherence Resonances and Spatial Patterns in a Noise-Driven Heterogeneous Neuronal Network

NASA Astrophysics Data System (ADS)

Li, Yu-Ye; Ding, Xue-Li

2014-12-01

Heterogeneity of the neurons and noise are inevitable in the real neuronal network. In this paper, Gaussian white noise induced spatial patterns including spiral waves and multiple spatial coherence resonances are studied in a network composed of Morris—Lecar neurons with heterogeneity characterized by parameter diversity. The relationship between the resonances and the transitions between ordered spiral waves and disordered spatial patterns are achieved. When parameter diversity is introduced, the maxima of multiple resonances increases first, and then decreases as diversity strength increases, which implies that the coherence degrees induced by noise are enhanced at an intermediate diversity strength. The synchronization degree of spatial patterns including ordered spiral waves and disordered patterns is identified to be a very low level. The results suggest that the nervous system can profit from both heterogeneity and noise, and the multiple spatial coherence resonances are achieved via the emergency of spiral waves instead of synchronization patterns.

Computer Generated Holography with Intensity-Graded Patterns

PubMed Central

Conti, Rossella; Assayag, Osnath; de Sars, Vincent; Guillon, Marc; Emiliani, Valentina

2016-01-01

Computer Generated Holography achieves patterned illumination at the sample plane through phase modulation of the laser beam at the objective back aperture. This is obtained by using liquid crystal-based spatial light modulators (LC-SLMs), which modulate the spatial phase of the incident laser beam. A variety of algorithms is employed to calculate the phase modulation masks addressed to the LC-SLM. These algorithms range from simple gratings-and-lenses to generate multiple diffraction-limited spots, to iterative Fourier-transform algorithms capable of generating arbitrary illumination shapes perfectly tailored on the base of the target contour. Applications for holographic light patterning include multi-trap optical tweezers, patterned voltage imaging and optical control of neuronal excitation using uncaging or optogenetics. These past implementations of computer generated holography used binary input profile to generate binary light distribution at the sample plane. Here we demonstrate that using graded input sources, enables generating intensity graded light patterns and extend the range of application of holographic light illumination. At first, we use intensity-graded holograms to compensate for LC-SLM position dependent diffraction efficiency or sample fluorescence inhomogeneity. Finally we show that intensity-graded holography can be used to equalize photo evoked currents from cells expressing different levels of chanelrhodopsin2 (ChR2), one of the most commonly used optogenetics light gated channels, taking into account the non-linear dependence of channel opening on incident light. PMID:27799896

Structural whole-brain covariance of the anterior and posterior hippocampus: Associations with age and memory.

PubMed

Nordin, Kristin; Persson, Jonas; Stening, Eva; Herlitz, Agneta; Larsson, Elna-Marie; Söderlund, Hedvig

2018-02-01

The hippocampus (HC) interacts with distributed brain regions to support memory and shows significant volume reductions in aging, but little is known about age effects on hippocampal whole-brain structural covariance. It is also unclear whether the anterior and posterior HC show similar or distinct patterns of whole-brain covariance and to what extent these are related to memory functions organized along the hippocampal longitudinal axis. Using the multivariate approach partial least squares, we assessed structural whole-brain covariance of the HC in addition to regional volume, in young, middle-aged and older adults (n = 221), and assessed associations with episodic and spatial memory. Based on findings of sex differences in both memory and brain aging, we further considered sex as a potential modulating factor of age effects. There were two main covariance patterns: one capturing common anterior and posterior covariance, and one differentiating the two regions by capturing anterior-specific covariance only. These patterns were differentially related to associative memory while unrelated to measures of single-item memory and spatial memory. Although patterns were qualitatively comparable across age groups, participants' expression of both patterns decreased with age, independently of sex. The results suggest that the organization of hippocampal structural whole-brain covariance remains stable across age, but that the integrity of these networks decreases as the brain undergoes age-related alterations. © 2017 Wiley Periodicals, Inc.

Spatial Patterns of NLCD Land Cover Change Thematic Accuracy (2001 - 2011)

EPA Science Inventory

Research on spatial non-stationarity of land cover classification accuracy has been ongoing for over two decades. We extend the understanding of thematic map accuracy spatial patterns by: 1) quantifying spatial patterns of map-reference agreement for class-specific land cover c...

Pattern formation in Dictyostelium discoideum aggregates in confined microenvironments

NASA Astrophysics Data System (ADS)

Hallou, Adrien; Hersen, Pascal; di Meglio, Jean-Marc; Kabla, Alexandre

Dictyostelium Discoideum (Dd) is often viewed as a model system to study the complex collective cell behaviours which shape an embryo. Under starvation, Dd cells form multicellular aggregates which soon elongate, starting to display an anterior-posterior axis by differentiating into two distinct cell populations; prestalk (front) and prespore (rear) cells zones. Different models, either based on positional information or on differentiation followed up by cell sorting, have been proposed to explain the origin and the regulation of this spatial pattern.To decipher between the proposed hypotheses, we have developed am experimental platform where aggregates, made of genetically engineered Dd cells to express fluorescent reporters of cell differentiation in either prestalk or prespore cells, are allowed to develop in 20 to 400 μm wide hydrogel channels. Such a setup allows us to both mimic Dd confined natural soil environment and to follow the patterning dynamics using time-lapse microscopy. Tracking cell lineage commitments and positions in space and time, we demonstrate that Dd cells differentiate first into prestalk and prespore cells prior to sorting into an organized spatial pattern on the basis of collective motions based on differential motility and adhesion mechanisms. A. Hallou would like to thank the University of Cambridge for the Award of an ``Oliver Gatty Studentship in Biophysical and Colloid Science''.

Spatial patterns of development drive water use

USGS Publications Warehouse

Sanchez, G.M.; Smith, J.W.; Terando, Adam J.; Sun, G.; Meentemeyer, R.K.

2018-01-01

Water availability is becoming more uncertain as human populations grow, cities expand into rural regions and the climate changes. In this study, we examine the functional relationship between water use and the spatial patterns of developed land across the rapidly growing region of the southeastern United States. We quantified the spatial pattern of developed land within census tract boundaries, including multiple metrics of density and configuration. Through non‐spatial and spatial regression approaches we examined relationships and spatial dependencies between the spatial pattern metrics, socio‐economic and environmental variables and two water use variables: a) domestic water use, and b) total development‐related water use (a combination of public supply, domestic self‐supply and industrial self‐supply). Metrics describing the spatial patterns of development had the highest measure of relative importance (accounting for 53% of model's explanatory power), explaining significantly more variance in water use compared to socio‐economic or environmental variables commonly used to estimate water use. Integrating metrics characterizing the spatial pattern of development into water use models is likely to increase their utility and could facilitate water‐efficient land use planning.

Spatial Patterns of Development Drive Water Use

NASA Astrophysics Data System (ADS)

Sanchez, G. M.; Smith, J. W.; Terando, A.; Sun, G.; Meentemeyer, R. K.

2018-03-01

Water availability is becoming more uncertain as human populations grow, cities expand into rural regions and the climate changes. In this study, we examine the functional relationship between water use and the spatial patterns of developed land across the rapidly growing region of the southeastern United States. We quantified the spatial pattern of developed land within census tract boundaries, including multiple metrics of density and configuration. Through non-spatial and spatial regression approaches we examined relationships and spatial dependencies between the spatial pattern metrics, socio-economic and environmental variables and two water use variables: a) domestic water use, and b) total development-related water use (a combination of public supply, domestic self-supply and industrial self-supply). Metrics describing the spatial patterns of development had the highest measure of relative importance (accounting for 53% of model's explanatory power), explaining significantly more variance in water use compared to socio-economic or environmental variables commonly used to estimate water use. Integrating metrics characterizing the spatial pattern of development into water use models is likely to increase their utility and could facilitate water-efficient land use planning.

SNW1 Is a Critical Regulator of Spatial BMP Activity, Neural Plate Border Formation, and Neural Crest Specification in Vertebrate Embryos

PubMed Central

Wu, Mary Y.; Ramel, Marie-Christine; Howell, Michael; Hill, Caroline S.

2011-01-01

Bone morphogenetic protein (BMP) gradients provide positional information to direct cell fate specification, such as patterning of the vertebrate ectoderm into neural, neural crest, and epidermal tissues, with precise borders segregating these domains. However, little is known about how BMP activity is regulated spatially and temporally during vertebrate development to contribute to embryonic patterning, and more specifically to neural crest formation. Through a large-scale in vivo functional screen in Xenopus for neural crest fate, we identified an essential regulator of BMP activity, SNW1. SNW1 is a nuclear protein known to regulate gene expression. Using antisense morpholinos to deplete SNW1 protein in both Xenopus and zebrafish embryos, we demonstrate that dorsally expressed SNW1 is required for neural crest specification, and this is independent of mesoderm formation and gastrulation morphogenetic movements. By exploiting a combination of immunostaining for phosphorylated Smad1 in Xenopus embryos and a BMP-dependent reporter transgenic zebrafish line, we show that SNW1 regulates a specific domain of BMP activity in the dorsal ectoderm at the neural plate border at post-gastrula stages. We use double in situ hybridizations and immunofluorescence to show how this domain of BMP activity is spatially positioned relative to the neural crest domain and that of SNW1 expression. Further in vivo and in vitro assays using cell culture and tissue explants allow us to conclude that SNW1 acts upstream of the BMP receptors. Finally, we show that the requirement of SNW1 for neural crest specification is through its ability to regulate BMP activity, as we demonstrate that targeted overexpression of BMP to the neural plate border is sufficient to restore neural crest formation in Xenopus SNW1 morphants. We conclude that through its ability to regulate a specific domain of BMP activity in the vertebrate embryo, SNW1 is a critical regulator of neural plate border formation and thus neural crest specification. PMID:21358802

Comprehensive analysis of fibroblast growth factor receptor expression patterns during chick forelimb development.

PubMed

Sheeba, Caroline J; Andrade, Raquel P; Duprez, Delphine; Palmeirim, Isabel

2010-01-01

Specific interactions between fibroblast growth factors (Fgf1-22) and their tyrosine kinase receptors (FgfR1-4) activate different signalling pathways that are responsible for the biological processes in which Fgf signalling is implicated during embryonic development. In the chick, several Fgf ligands (Fgf2, 4, 8, 9, 10, 12, 13 and 18) and the four FgfRs (FgfR 1, 2, 3 and 4) have been reported to be expressed in the developing limb. The precise spatial and temporal expression of these transcripts is important to guide the limb bud to develop into a wing/leg. In this paper, we present a detailed and systematic analysis of the expression patterns of FgfR1, 2, 3 and 4 throughout chick wing development, by in situ hybridisation on whole mounts and sections. Moreover, we characterize for the first time the different isoforms of FGFR1-3 by analysing their differential expression in limb ectoderm and mesodermal tissues, using RT-PCR and in situ hybridisation on sections. Finally, isoform-specific sequences for FgfR1IIIb, FgfR1IIIc, FgfR3IIIb and FgfR3IIIc were determined and deposited in GenBank with the following accession numbers: GU053725, GU065444, GU053726, GU065445, respectively.

MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord

NASA Astrophysics Data System (ADS)

Li, Chung-Jung; Hong, Tian; Tung, Ying-Tsen; Yen, Ya-Ping; Hsu, Ho-Chiang; Lu, Ya-Lin; Chang, Mien; Nie, Qing; Chen, Jun-An

2017-03-01

The initial rostrocaudal patterning of the neural tube leads to differential expression of Hox genes that contribute to the specification of motor neuron (MN) subtype identity. Although several 3' Hox mRNAs are expressed in progenitors in a noisy manner, these Hox proteins are not expressed in the progenitors and only become detectable in postmitotic MNs. MicroRNA biogenesis impairment leads to precocious expression and propagates the noise of Hoxa5 at the protein level, resulting in an imprecise Hoxa5-Hoxc8 boundary. Here we uncover, using in silico simulation, two feed-forward Hox-miRNA loops accounting for the precocious and noisy Hoxa5 expression, as well as an ill-defined boundary phenotype in Dicer mutants. Finally, we identify mir-27 as a major regulator coordinating the temporal delay and spatial boundary of Hox protein expression. Our results provide a novel trans Hox-miRNA circuit filtering transcription noise and controlling the timing of protein expression to confer robust individual MN identity.

Laminin γ3 plays an important role in retinal lamination, photoreceptor organisation and ganglion cell differentiation.

PubMed

Dorgau, Birthe; Felemban, Majed; Sharpe, Alexander; Bauer, Roman; Hallam, Dean; Steel, David H; Lindsay, Susan; Mellough, Carla; Lako, Majlinda

2018-05-23

Laminins are heterotrimeric glycoproteins of the extracellular matrix. Eleven different laminin chains have been identified in vertebrates. They are ubiquitously expressed in the human body, with a distinct tissue distribution. Laminin expression in neural retina and their functional role during human retinogenesis is still unknown. This study investigated the laminin expression in human developing and adult retina, showing laminin α1, α5, β1, β2 and γ1 to be predominantly expressed in Bruch's membrane and the inner limiting membrane. Laminin-332 and laminin γ3 expression were mainly observed in the neural retina during retinal histogenesis. These expression patterns were largely conserved in pluripotent stem cell-derived retinal organoids. Blocking of laminin γ3 function in retinal organoids resulted in the disruption of laminar organisation and synapse formation, the loss of photoreceptor organisation and retinal ganglion cells. Our data demonstrate a unique temporal and spatial expression for laminins and reveal a novel role for laminin γ3 during human retinogenesis.

Visual information processing of faces in body dysmorphic disorder.

PubMed

Feusner, Jamie D; Townsend, Jennifer; Bystritsky, Alexander; Bookheimer, Susan

2007-12-01

Body dysmorphic disorder (BDD) is a severe psychiatric condition in which individuals are preoccupied with perceived appearance defects. Clinical observation suggests that patients with BDD focus on details of their appearance at the expense of configural elements. This study examines abnormalities in visual information processing in BDD that may underlie clinical symptoms. To determine whether patients with BDD have abnormal patterns of brain activation when visually processing others' faces with high, low, or normal spatial frequency information. Case-control study. University hospital. Twelve right-handed, medication-free subjects with BDD and 13 control subjects matched by age, sex, and educational achievement. Intervention Functional magnetic resonance imaging while performing matching tasks of face stimuli. Stimuli were neutral-expression photographs of others' faces that were unaltered, altered to include only high spatial frequency visual information, or altered to include only low spatial frequency visual information. Blood oxygen level-dependent functional magnetic resonance imaging signal changes in the BDD and control groups during tasks with each stimulus type. Subjects with BDD showed greater left hemisphere activity relative to controls, particularly in lateral prefrontal cortex and lateral temporal lobe regions for all face tasks (and dorsal anterior cingulate activity for the low spatial frequency task). Controls recruited left-sided prefrontal and dorsal anterior cingulate activity only for the high spatial frequency task. Subjects with BDD demonstrate fundamental differences from controls in visually processing others' faces. The predominance of left-sided activity for low spatial frequency and normal faces suggests detail encoding and analysis rather than holistic processing, a pattern evident in controls only for high spatial frequency faces. These abnormalities may be associated with apparent perceptual distortions in patients with BDD. The fact that these findings occurred while subjects viewed others' faces suggests differences in visual processing beyond distortions of their own appearance.

Spatial/Temporal Variations of Crime: A Routine Activity Theory Perspective.

PubMed

de Melo, Silas Nogueira; Pereira, Débora V S; Andresen, Martin A; Matias, Lindon Fonseca

2018-05-01

Temporal and spatial patterns of crime in Campinas, Brazil, are analyzed considering the relevance of routine activity theory in a Latin American context. We use geo-referenced criminal event data, 2010-2013, analyzing spatial patterns using census tracts and temporal patterns considering seasons, months, days, and hours. Our analyses include difference in means tests, count-based regression models, and Kulldorff's scan test. We find that crime in Campinas, Brazil, exhibits both temporal and spatial-temporal patterns. However, the presence of these patterns at the different temporal scales varies by crime type. Specifically, not all crime types have statistically significant temporal patterns at all scales of analysis. As such, routine activity theory works well to explain temporal and spatial-temporal patterns of crime in Campinas, Brazil. However, local knowledge of Brazilian culture is necessary for understanding a portion of these crime patterns.

Combinatorial expression of Lef1, Lhx2, Lhx5, Lhx9, Lmo3, Lmo4, and Prox1 helps to identify comparable subdivisions in the developing hippocampal formation of mouse and chicken

PubMed Central

Abellán, Antonio; Desfilis, Ester; Medina, Loreta

2014-01-01

We carried out a study of the expression patterns of seven developmental regulatory genes (Lef1, Lhx2, Lhx9, Lhx5, Lmo3, Lmo4, and Prox1), in combination with topological position, to identify the medial pallial derivatives, define its major subdivisions, and compare them between mouse and chicken. In both species, the medial pallium is defined as a pallial sector adjacent to the cortical hem and roof plate/choroid tela, showing moderate to strong ventricular zone expression of Lef1, Lhx2, and Lhx9, but not Lhx5. Based on this, the hippocampal formation (indusium griseum, dentate gyrus, Ammon's horn fields, and subiculum), the medial entorhinal cortex, and part of the amygdalo-hippocampal transition area of mouse appeared to derive from the medial pallium. In the chicken, based on the same position and gene expression profile, we propose that the hippocampus (including the V-shaped area), the parahippocampal area (including its caudolateral part), the entorhinal cortex, and the amygdalo-hippocampal transition area are medial pallial derivatives. Moreover, the combinatorial expression of Lef1, Prox1, Lmo4, and Lmo3 allowed the identification of dentate gyrus/CA3-like, CA1/subicular-like, and medial entorhinal-like comparable sectors in mouse and chicken, and point to the existence of mostly conserved molecular networks involved in hippocampal complex development. Notably, while the mouse medial entorhinal cortex derives from the medial pallium (similarly to the hippocampal formation, both being involved in spatial navigation and spatial memory), the lateral entorhinal cortex (involved in processing non-spatial, contextual information) appears to derive from a distinct dorsolateral caudal pallial sector. PMID:25071464

Virtual Human Analogs to Rodent Spatial Pattern Separation and Completion Memory Tasks

ERIC Educational Resources Information Center

Paleja, Meera; Girard, Todd A.; Christensen, Bruce K.

2011-01-01

Spatial pattern separation (SPS) and spatial pattern completion (SPC) have played an increasingly important role in computational and rodent literatures as processes underlying associative memory. SPS and SPC are complementary processes, allowing the formation of unique representations and the reconstruction of complete spatial environments based…

Cloning of an ADP-ribosylation factor gene from banana (Musa acuminata) and its expression patterns in postharvest ripening fruit.

PubMed

Wang, Yuan; Wu, Jing; Xu, Bi-Yu; Liu, Ju-Hua; Zhang, Jian-Bin; Jia, Cai-Hong; Jin, Zhi-Qiang

2010-08-15

A full-length cDNA encoding an ADP-ribosylation factor (ARF) from banana (Musa acuminata) fruit was cloned and named MaArf. It contains an open reading frame encoding a 181-amino-acid polypeptide. Sequence analysis showed that MaArf shared high similarity with ARF of other plant species. The genomic sequence of MaArf was also obtained using polymerase chain reaction (PCR). Sequence analysis showed that MaArf was a split gene containing five exons and four introns in genomic DNA. Reverse-transcriptase PCR was used to analyze the spatial expression of MaArf. The results showed that MaArf was expressed in all the organs examined: root, rhizome, leaf, flower and fruit. Real-time quantitative PCR was used to explore expression patterns of MaArf in postharvest banana. There was differential expression of MaArf associated with ethylene biosynthesis. In naturally ripened banana, expression of MaArf was in accordance with ethylene biosynthesis. However, in 1-methylcyclopropene-treated banana, the expression of MaArf was inhibited and changed little. When treated with ethylene, MaArf expression in banana fruit significantly increased in accordance with ethylene biosynthesis; the peak of MaArf was 3 d after harvest, 11 d earlier than for naturally ripened banana fruits. These results suggest that MaArf is induced by ethylene in regulating postharvest banana ripening. Finally, subcellular localization assays showed the MaArf protein in the cytoplasm. Copyright 2010 Elsevier GmbH. All rights reserved.

Analysis of Spatial Pattern and Influencing Factors of E-Commerce

NASA Astrophysics Data System (ADS)

Zhang, Y.; Chen, J.; Zhang, S.

2017-09-01

This paper aims to study the relationship between e-commerce development and geographical characteristics using data of e-commerce, economy, Internet, express delivery and population from 2011 to 2015. Moran's I model and GWR model are applied to analyze the spatial pattern of E-commerce and its influencing factors. There is a growth trend of e-commerce from west to east, and it is obvious to see that e-commerce development has a space-time clustering, especially around the Yangtze River delta. The comprehensive factors caculated through PCA are described as fundamental social productivity, resident living standard and population sex structure. The first two factors have positive correlation with e-commerce, and the intensity of effect increases yearly. However, the influence of population sex structure on the E-commerce development is not significant. Our results suggest that the clustering of e-commerce has a downward trend and the impact of driving factors on e-commerce is observably distinct from year to year in space.

The combined effects of exogenous and endogenous variability on the spatial distribution of ant communities in a forested ecosystem (Hymenoptera: Formicidae).

PubMed

Yitbarek, Senay; Vandermeer, John H; Allen, David

2011-10-01

Spatial patterns observed in ecosystems have traditionally been attributed to exogenous processes. Recently, ecologists have found that endogenous processes also have the potential to create spatial patterns. Yet, relatively few studies have attempted to examine the combined effects of exogenous and endogenous processes on the distribution of organisms across spatial and temporal scales. Here we aim to do this, by investigating whether spatial patterns of under-story tree species at a large spatial scale (18 ha) influences the spatial patterns of ground foraging ant species at a much smaller spatial scale (20 m by 20 m). At the regional scale, exogenous processes (under-story tree community) had a strong effect on the spatial patterns in the ground-foraging ant community. We found significantly more Camponotus noveboracensis, Formica subsericae, and Lasius alienus species in black cherry (Prunis serotine Ehrh.) habitats. In witch-hazel (Hamamelis virginiana L.) habitats, we similarly found significantly more Myrmica americana, Formica fusca, and Formica subsericae. At smaller spatial scales, we observed the emergence of mosaic ant patches changing rapidly in space and time. Our study reveals that spatial patterns are the result of both exogenous and endogenous forces, operating at distinct scales.

Mechanical Influences on Morphogenesis of the Knee Joint Revealed through Morphological, Molecular and Computational Analysis of Immobilised Embryos

PubMed Central

Roddy, Karen A.; Prendergast, Patrick J.; Murphy, Paula

2011-01-01

Very little is known about the regulation of morphogenesis in synovial joints. Mechanical forces generated from muscle contractions are required for normal development of several aspects of normal skeletogenesis. Here we show that biophysical stimuli generated by muscle contractions impact multiple events during chick knee joint morphogenesis influencing differential growth of the skeletal rudiment epiphyses and patterning of the emerging tissues in the joint interzone. Immobilisation of chick embryos was achieved through treatment with the neuromuscular blocking agent Decamethonium Bromide. The effects on development of the knee joint were examined using a combination of computational modelling to predict alterations in biophysical stimuli, detailed morphometric analysis of 3D digital representations, cell proliferation assays and in situ hybridisation to examine the expression of a selected panel of genes known to regulate joint development. This work revealed the precise changes to shape, particularly in the distal femur, that occur in an altered mechanical environment, corresponding to predicted changes in the spatial and dynamic patterns of mechanical stimuli and region specific changes in cell proliferation rates. In addition, we show altered patterning of the emerging tissues of the joint interzone with the loss of clearly defined and organised cell territories revealed by loss of characteristic interzone gene expression and abnormal expression of cartilage markers. This work shows that local dynamic patterns of biophysical stimuli generated from muscle contractions in the embryo act as a source of positional information guiding patterning and morphogenesis of the developing knee joint. PMID:21386908

A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis

PubMed Central

Platre, Matthieu Pierre; Barberon, Marie; Caillieux, Erwann; Colot, Vincent

2016-01-01

Summary Multicellular organisms are composed of many cell types that acquire their specific fate through a precisely controlled pattern of gene expression in time and space dictated in part by cell type-specific promoter activity. Understanding the contribution of highly specialized cell types in the development of a whole organism requires the ability to isolate or analyze different cell types separately. We have characterized and validated a large collection of root cell type-specific promoters and have generated cell type-specific marker lines. These benchmarked promoters can be readily used to evaluate cell type-specific complementation of mutant phenotypes, or to knockdown gene expression using targeted expression of artificial miRNA. We also generated vectors and characterized transgenic lines for cell type-specific induction of gene expression and cell type-specific isolation of nuclei for RNA and chromatin profiling. Vectors and seeds from transgenic Arabidopsis plants will be freely available, and will promote rapid progress in cell type-specific functional genomics. We demonstrate the power of this promoter set for analysis of complex biological processes by investigating the contribution of root cell types in the IRT1-dependent root iron uptake. Our findings revealed the complex spatial expression pattern of IRT1 in both root epidermis and phloem companion cells and the requirement for IRT1 to be expressed in both cell types for proper iron homeostasis. PMID:26662936

Quantitative assessment of Hox complex expression in the indirect development of the polychaete annelid Chaetopterus sp

NASA Technical Reports Server (NTRS)

Peterson, K. J.; Irvine, S. Q.; Cameron, R. A.; Davidson, E. H.

2000-01-01

A prediction from the set-aside theory of bilaterian origins is that pattern formation processes such as those controlled by the Hox cluster genes are required specifically for adult body plan formation. This prediction can be tested in animals that use maximal indirect development, in which the embryonic formation of the larva and the postembryonic formation of the adult body plan are temporally and spatially distinct. To this end, we quantitatively measured the amount of transcripts for five Hox genes in embryos of a lophotrochozoan, the polychaete annelid Chaetopterus sp. The polychaete Hox complex is shown not to be expressed during embryogenesis, but transcripts of all measured Hox complex genes are detected at significant levels during the initial stages of adult body plan formation. Temporal colinearity in the sequence of their activation is observed, so that activation follows the 3'-5' arrangement of the genes. Moreover, Hox gene expression is spatially localized to the region of teloblastic set-aside cells of the later-stage embryos. This study shows that an indirectly developing lophotrochozoan shares with an indirectly developing deuterostome, the sea urchin, a common mode of Hox complex utilization: construction of the larva, whether a trochophore or dipleurula, does not involve Hox cluster expression, but in both forms the complex is expressed in the set-aside cells from which the adult body plan derives.

Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus

PubMed Central

2012-01-01

Background Body coloration is an ecologically important trait that is often involved in prey-predator interactions through mimicry and crypsis. Although this subject has attracted the interest of biologists and the general public, our scientific knowledge on the subject remains fragmentary. In the caterpillar of the swallowtail butterfly Papilio xuthus, spectacular changes in the color pattern are observed; the insect mimics bird droppings (mimetic pattern) as a young larva, and switches to a green camouflage coloration (cryptic pattern) in the final instar. Despite the wide variety and significance of larval color patterns, few studies have been conducted at a molecular level compared with the number of studies on adult butterfly wing patterns. Results To obtain a catalog of genes involved in larval mimetic and cryptic pattern formation, we constructed expressed sequence tag (EST) libraries of larval epidermis for P. xuthus, and P. polytes that contained 20,736 and 5,376 clones, respectively, representing one of the largest collections available in butterflies. A comparison with silkworm epidermal EST information revealed the high expression of putative blue and yellow pigment-binding proteins in Papilio species. We also designed a microarray from the EST dataset information, analyzed more than five stages each for six markings, and confirmed spatial expression patterns by whole-mount in situ hybridization. Hence, we succeeded in elucidating many novel marking-specific genes for mimetic and cryptic pattern formation, including pigment-binding protein genes, the melanin-associated gene yellow-h3, the ecdysteroid synthesis enzyme gene 3-dehydroecdysone 3b-reductase, and Papilio-specific genes. We also found many cuticular protein genes with marking specificity that may be associated with the unique surface nanostructure of the markings. Furthermore, we identified two transcription factors, spalt and ecdysteroid signal-related E75, as genes expressed in larval eyespot markings. This finding suggests that E75 is a strong candidate mediator of the hormone-dependent coordination of larval pattern formation. Conclusions This study is one of the most comprehensive molecular analyses of complicated morphological features, and it will serve as a new resource for studying insect mimetic and cryptic pattern formation in general. The wide variety of marking-associated genes (both regulatory and structural genes) identified by our screening indicates that a similar strategy will be effective for understanding other complex traits. PMID:22651552

Spatial Pattern of Standing Timber Value across the Brazilian Amazon

PubMed Central

Ahmed, Sadia E.; Ewers, Robert M.

2012-01-01

The Amazon is a globally important system, providing a host of ecosystem services from climate regulation to food sources. It is also home to a quarter of all global diversity. Large swathes of forest are removed each year, and many models have attempted to predict the spatial patterns of this forest loss. The spatial patterns of deforestation are determined largely by the patterns of roads that open access to frontier areas and expansion of the road network in the Amazon is largely determined by profit seeking logging activities. Here we present predictions for the spatial distribution of standing value of timber across the Amazon. We show that the patterns of timber value reflect large-scale ecological gradients, determining the spatial distribution of functional traits of trees which are, in turn, correlated with timber values. We expect that understanding the spatial patterns of timber value across the Amazon will aid predictions of logging movements and thus predictions of potential future road developments. These predictions in turn will be of great use in estimating the spatial patterns of deforestation in this globally important biome. PMID:22590520

Oxytocin receptor density is associated with male mating tactics and social monogamy

PubMed Central

Ophir, Alexander G.; Gessel, Ana; Zheng, Da-Jiang; Phelps, Steven M.

2012-01-01

Despite its well-described role in female affiliation, the influence of oxytocin on male pairbonding is largely unknown. However, recent human studies indicate that this nonapeptide has a potent influence on male behaviors commonly associated with monogamy. Here we investigated the distribution of oxytocin receptors (OTR) throughout the forebrain of the socially monogamous male prairie vole (Microtus ochrogaster). Because males vary in both sexual and spatial fidelity, we explored the extent to which OTR predicted monogamous or non-monogamous patterns of space use, mating success and sexual fidelity in free-living males. We found that monogamous males expressed higher OTR density in the nucleus accumbens than non-monogamous males, a result that mirrors species differences in voles with different mating systems. OTR density in the posterior portion of the insula predicted mating success. Finally, OTR in the hippocampus and septohippocampal nucleus, which are nuclei associated with spatial memory, predicted patterns of space use and reproductive success within mating tactics. Our data highlight the importance of oxytocin receptor in neural structures associated with pairbonding and socio-spatial memory in male mating tactics. The role of memory in mating systems is often neglected, despite the fact that mating tactics impose an inherently spatial challenge for animals. Identifying mechanisms responsible for relating information about the social world with mechanisms mediating pairbonding and mating tactics is crucial to fully appreciate the suite of factors driving mating systems. PMID:22285648

Numerical investigation of aggregated fuel spatial pattern impacts on fire behavior

DOE PAGES

Parsons, Russell A.; Linn, Rodman Ray; Pimont, Francois; ...

2017-06-18

Here, landscape heterogeneity shapes species distributions, interactions, and fluctuations. Historically, in dry forest ecosystems, low canopy cover and heterogeneous fuel patterns often moderated disturbances like fire. Over the last century, however, increases in canopy cover and more homogeneous patterns have contributed to altered fire regimes with higher fire severity. Fire management strategies emphasize increasing within-stand heterogeneity with aggregated fuel patterns to alter potential fire behavior. Yet, little is known about how such patterns may affect fire behavior, or how sensitive fire behavior changes from fuel patterns are to winds and canopy cover. Here, we used a physics-based fire behavior model,more » FIRETEC, to explore the impacts of spatially aggregated fuel patterns on the mean and variability of stand-level fire behavior, and to test sensitivity of these effects to wind and canopy cover. Qualitative and quantitative approaches suggest that spatial fuel patterns can significantly affect fire behavior. Based on our results we propose three hypotheses: (1) aggregated spatial fuel patterns primarily affect fire behavior by increasing variability; (2) this variability should increase with spatial scale of aggregation; and (3) fire behavior sensitivity to spatial pattern effects should be more pronounced under moderate wind and fuel conditions.« less

Numerical investigation of aggregated fuel spatial pattern impacts on fire behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parsons, Russell A.; Linn, Rodman Ray; Pimont, Francois

Here, landscape heterogeneity shapes species distributions, interactions, and fluctuations. Historically, in dry forest ecosystems, low canopy cover and heterogeneous fuel patterns often moderated disturbances like fire. Over the last century, however, increases in canopy cover and more homogeneous patterns have contributed to altered fire regimes with higher fire severity. Fire management strategies emphasize increasing within-stand heterogeneity with aggregated fuel patterns to alter potential fire behavior. Yet, little is known about how such patterns may affect fire behavior, or how sensitive fire behavior changes from fuel patterns are to winds and canopy cover. Here, we used a physics-based fire behavior model,more » FIRETEC, to explore the impacts of spatially aggregated fuel patterns on the mean and variability of stand-level fire behavior, and to test sensitivity of these effects to wind and canopy cover. Qualitative and quantitative approaches suggest that spatial fuel patterns can significantly affect fire behavior. Based on our results we propose three hypotheses: (1) aggregated spatial fuel patterns primarily affect fire behavior by increasing variability; (2) this variability should increase with spatial scale of aggregation; and (3) fire behavior sensitivity to spatial pattern effects should be more pronounced under moderate wind and fuel conditions.« less

An orthologue of the kit-related gene fms is required for development of neural crest-derived xanthophores and a subpopulation of adult melanocytes in the zebrafish, Danio rerio.

PubMed

Parichy, D M; Ransom, D G; Paw, B; Zon, L I; Johnson, S L

2000-07-01

Developmental mechanisms underlying traits expressed in larval and adult vertebrates remain largely unknown. Pigment patterns of fishes provide an opportunity to identify genes and cell behaviors required for postembryonic morphogenesis and differentiation. In the zebrafish, Danio rerio, pigment patterns reflect the spatial arrangements of three classes of neural crest-derived pigment cells: black melanocytes, yellow xanthophores and silver iridophores. We show that the D. rerio pigment pattern mutant panther ablates xanthophores in embryos and adults and has defects in the development of the adult pattern of melanocyte stripes. We find that panther corresponds to an orthologue of the c-fms gene, which encodes a type III receptor tyrosine kinase and is the closest known homologue of the previously identified pigment pattern gene, kit. In mouse, fms is essential for the development of macrophage and osteoclast lineages and has not been implicated in neural crest or pigment cell development. In contrast, our analyses demonstrate that fms is expressed and required by D. rerio xanthophore precursors and that fms promotes the normal patterning of melanocyte death and migration during adult stripe formation. Finally, we show that fms is required for the appearance of a late developing, kit-independent subpopulation of adult melanocytes. These findings reveal an unexpected role for fms in pigment pattern development and demonstrate that parallel neural crest-derived pigment cell populations depend on the activities of two essentially paralogous genes, kit and fms.

Spatial patterns of recreational impact on experimental campsites

Treesearch

David N. Cole; Christopher A. Monz

2004-01-01

Management of camping impacts in protected areas worldwide is limited by inadequate understanding of spatial patterns of impact and attention to spatial management strategies. Spatial patterns of campsite impact were studied in two subalpine plant communities in the Wind River Mountains, Wyoming, USA (a forest and a meadow). Response to chronic disturbance and recovery...

The body electric 2.0: recent advances in developmental bioelectricity for regenerative and synthetic bioengineering.

PubMed

Mathews, Juanita; Levin, Michael

2018-04-20

Breakthroughs in biomedicine and synthetic bioengineering require predictive, rational control over anatomical structure and function. Recent successes in manipulating cellular and molecular hardware have not been matched by progress in understanding the patterning software implemented during embryogenesis and regeneration. A fundamental capability gap is driving desired changes in growth and form to address birth defects and traumatic injury. Here we review new tools, results, and conceptual advances in an exciting emerging field: endogenous non-neural bioelectric signaling, which enables cellular collectives to make global decisions and implement large-scale pattern homeostasis. Spatially distributed electric circuits regulate gene expression, organ morphogenesis, and body-wide axial patterning. Developmental bioelectricity facilitates the interface to organ-level modular control points that direct patterning in vivo. Cracking the bioelectric code will enable transformative progress in bioengineering and regenerative medicine. Copyright © 2018 Elsevier Ltd. All rights reserved.

Discover mouse gene coexpression landscapes using dictionary learning and sparse coding.

PubMed

Li, Yujie; Chen, Hanbo; Jiang, Xi; Li, Xiang; Lv, Jinglei; Peng, Hanchuan; Tsien, Joe Z; Liu, Tianming

2017-12-01

Gene coexpression patterns carry rich information regarding enormously complex brain structures and functions. Characterization of these patterns in an unbiased, integrated, and anatomically comprehensive manner will illuminate the higher-order transcriptome organization and offer genetic foundations of functional circuitry. Here using dictionary learning and sparse coding, we derived coexpression networks from the space-resolved anatomical comprehensive in situ hybridization data from Allen Mouse Brain Atlas dataset. The key idea is that if two genes use the same dictionary to represent their original signals, then their gene expressions must share similar patterns, thereby considering them as "coexpressed." For each network, we have simultaneous knowledge of spatial distributions, the genes in the network and the extent a particular gene conforms to the coexpression pattern. Gene ontologies and the comparisons with published gene lists reveal biologically identified coexpression networks, some of which correspond to major cell types, biological pathways, and/or anatomical regions.

Three-dimensional spatiotemporal focusing of holographic patterns

PubMed Central

Hernandez, Oscar; Papagiakoumou, Eirini; Tanese, Dimitrii; Fidelin, Kevin; Wyart, Claire; Emiliani, Valentina

2016-01-01

Two-photon excitation with temporally focused pulses can be combined with phase-modulation approaches, such as computer-generated holography and generalized phase contrast, to efficiently distribute light into two-dimensional, axially confined, user-defined shapes. Adding lens-phase modulations to 2D-phase holograms enables remote axial pattern displacement as well as simultaneous pattern generation in multiple distinct planes. However, the axial confinement linearly degrades with lateral shape area in previous reports where axially shifted holographic shapes were not temporally focused. Here we report an optical system using two spatial light modulators to independently control transverse- and axial-target light distribution. This approach enables simultaneous axial translation of single or multiple spatiotemporally focused patterns across the sample volume while achieving the axial confinement of temporal focusing. We use the system's capability to photoconvert tens of Kaede-expressing neurons with single-cell resolution in live zebrafish larvae. PMID:27306044

Hox gene expression in the specialized limbs of the Iberian mole (Talpa occidentalis).

PubMed

Bickelmann, Constanze; van der Vos, Wessel; de Bakker, Merijn A G; Jiménez, Rafael; Maas, Saskia; Sánchez-Villagra, Marcelo R

2017-01-01

Fossorial talpid moles use their limbs predominantly for digging, which explains their highly specialized anatomy. The humerus is particularly short and dorsoventrally rotated, with broadened distal and proximal parts where muscles attach and which facilitate powerful abductive movements. The radius and ulna are exceptionally robust and short. The ulna has an expanded olecranon process. The femur is generalized, but the fused tibia-fibula complex is short and robust. To understand the developmental bases of these specializations, we studied expression patterns of four 5' Hox genes in the fossorial Iberian mole (Talpa occidentalis). These genes are known to play major roles in patterning the developing limb skeleton in the mouse, with which comparisons were made (Mus musculus, C57BL/6Jico strain). We find that HoxA9 expression is spatially expanded in the developing stylopodial area in the mole forelimb, compared to the less specialized mouse forelimb and mole hind limb. HoxD9 expression does not extend into the thoracic body wall in the mole forelimb in contrast to the mouse, and is also reduced in the presumptive zeugopodium in mole forelimb, compared to mouse. Expression of HoxD11 is upregulated in the mole in the postaxial area of the hind limb zeugopod, compared to the mouse. On the other hand, HoxD13 is downregulated in the postaxial zeugopodial area in the forelimb of the mole, compared to the mouse. The differences in the expression patterns of these 5' Hox genes between Talpa and Mus are an indication of the developmental changes going hand in hand with anatomical digging adaptations in the mole adult. © 2016 Wiley Periodicals, Inc.

Heterogeneity in Kv2 Channel Expression Shapes Action Potential Characteristics and Firing Patterns in CA1 versus CA2 Hippocampal Pyramidal Neurons

PubMed Central

Chevaleyre, Vivien; Murray, Karl D.; Piskorowski, Rebecca A.

2017-01-01

Abstract The CA1 region of the hippocampus plays a critical role in spatial and contextual memory, and has well-established circuitry, function and plasticity. In contrast, the properties of the flanking CA2 pyramidal neurons (PNs), important for social memory, and lacking CA1-like plasticity, remain relatively understudied. In particular, little is known regarding the expression of voltage-gated K+ (Kv) channels and the contribution of these channels to the distinct properties of intrinsic excitability, action potential (AP) waveform, firing patterns and neurotransmission between CA1 and CA2 PNs. In the present study, we used multiplex fluorescence immunolabeling of mouse brain sections, and whole-cell recordings in acute mouse brain slices, to define the role of heterogeneous expression of Kv2 family Kv channels in CA1 versus CA2 pyramidal cell excitability. Our results show that the somatodendritic delayed rectifier Kv channel subunits Kv2.1, Kv2.2, and their auxiliary subunit AMIGO-1 have region-specific differences in expression in PNs, with the highest expression levels in CA1, a sharp decrease at the CA1-CA2 boundary, and significantly reduced levels in CA2 neurons. PNs in CA1 exhibit a robust contribution of Guangxitoxin-1E-sensitive Kv2-based delayed rectifier current to AP shape and after-hyperpolarization potential (AHP) relative to that seen in CA2 PNs. Our results indicate that robust Kv2 channel expression confers a distinct pattern of intrinsic excitability to CA1 PNs, potentially contributing to their different roles in hippocampal network function. PMID:28856240

Baculovirus-mediated gene transfer in butterfly wings in vivo: an efficient expression system with an anti-gp64 antibody

PubMed Central

2013-01-01

Background Candidate genes for color pattern formation in butterfly wings have been known based on gene expression patterns since the 1990s, but their functions remain elusive due to a lack of a functional assay. Several methods of transferring and expressing a foreign gene in butterfly wings have been reported, but they have suffered from low success rates or low expression levels. Here, we developed a simple, practical method to efficiently deliver and express a foreign gene using baculovirus-mediated gene transfer in butterfly wings in vivo. Results A recombinant baculovirus containing a gene for green fluorescent protein (GFP) was injected into pupae of the blue pansy butterfly Junonia orithya (Nymphalidae). GFP fluorescence was detected in the pupal wings and other body parts of the injected individuals three to five days post-injection at various degrees of fluorescence. We obtained a high GFP expression rate at relatively high virus titers, but it was associated with pupal death before color pattern formation in wings. To reduce the high mortality rate caused by the baculovirus treatment, we administered an anti-gp64 antibody, which was raised against baculovirus coat protein gp64, to infected pupae after the baculovirus injection. This treatment greatly reduced the mortality rate of the infected pupae. GFP fluorescence was observed in pupal and adult wings and other body parts of the antibody-treated individuals at various degrees of fluorescence. Importantly, we obtained completely developed wings with a normal color pattern, in which fluorescent signals originated directly from scales or the basal membrane after the removal of scales. GFP fluorescence in wing tissues spatially coincided with anti-GFP antibody staining, confirming that the fluorescent signals originated from the expressed GFP molecules. Conclusions Our baculovirus-mediated gene transfer system with an anti-gp64 antibody is reasonably efficient, and it can be an invaluable tool to transfer, express, and functionally examine foreign genes in butterfly wings and also in other non-model insect systems. PMID:23522444

In situ hybridization analysis of anterior pituitary hormone gene expression during fetal mouse development.

PubMed

Japón, M A; Rubinstein, M; Low, M J

1994-08-01

We used 35S-labeled oligonucleotides and cRNAs (riboprobes) to detect the temporal order and spatial pattern of anterior pituitary hormone gene expression in (B6CBF1 x B6CBF1)F2 fetal mice from embryonic Day 9.5 (E9.5) to postnatal Day 1 (P1). Pro-opiomelanocortin (POMC) mRNA was expressed in the basal diencephalon on Day E10.5, in the ventromedial zone of the pars distalis on Day E12.5, and in the pars intermedia on Day E14.5. The common alpha-glycoprotein subunit (alpha-GSU) mRNA first appeared in the anterior wall of Rathke's pouch on Day E11.5 and extended to the pars tuberalis and ventromedial zone of the pars distalis on Day E12.5. Thyroid-stimulating hormone-beta (TSH beta) subunit mRNA was expressed initially in both the pas tuberalis and ventromedial pars distalis on Day E14.5, with an identical spatial distribution to alpha-GSU at the time. In contrast, luteinizing hormone-beta (LH beta) subunit and follicle-stimulating hormone beta (FSH beta) subunit mRNAs were detected initially only in the ventromedial pars distalis on Days E16.5 and E17.5, respectively, in an identical distribution to each other. POMC-, alpha-GSU-, TSH beta, LH beta-, and FSH beta-positive cells within the pars distalis all increased in number and autoradiographic signal with differing degrees of spatial expansion posteriorly, laterally, and dorsally up to Day P1. POMC expression was typically the most intense and extended circumferentially to include the entire lateral and dorsal surfaces of the pars distalis. The expression of both growth hormone (GH) and prolactin (PRL) started coincidentally on Day E15.5. However PRL cells localized in the ventromedial area similarly to POMC and the glycoprotein hormone subunits, whereas GH cells were found initially in a more lateral and central distribution within the lobes of the pars distalis. Somatotrophs increased dramatically in number and autoradiographic signal, extending throughout the pars distalis except for the most peripheral layer of cells on Day E17.5. Mammotrophs also increased in number but less abundantly than somatotrophs, and PRL expression remained more confined to central-medial and ventrolateral areas of the pars distalis up to Day P1. These data demonstrate distinctive patterns of expression for each of the major anterior pituitary hormone genes during development of the mouse pituitary gland and suggest that different groups of committed cells are the immediate precursors to the terminally differentiated hormone-secreting cell types.

Spatio-temporal Analysis for New York State SPARCS Data

PubMed Central

Chen, Xin; Wang, Yu; Schoenfeld, Elinor; Saltz, Mary; Saltz, Joel; Wang, Fusheng

2017-01-01

Increased accessibility of health data provides unique opportunities to discover spatio-temporal patterns of diseases. For example, New York State SPARCS (Statewide Planning and Research Cooperative System) data collects patient level detail on patient demographics, diagnoses, services, and charges for each hospital inpatient stay and outpatient visit. Such data also provides home addresses for each patient. This paper presents our preliminary work on spatial, temporal, and spatial-temporal analysis of disease patterns for New York State using SPARCS data. We analyzed spatial distribution patterns of typical diseases at ZIP code level. We performed temporal analysis of common diseases based on 12 years’ historical data. We then compared the spatial variations for diseases with different levels of clustering tendency, and studied the evolution history of such spatial patterns. Case studies based on asthma demonstrated that the discovered spatial clusters are consistent with prior studies. We visualized our spatial-temporal patterns as animations through videos. PMID:28815148

A Method to Categorize 2-Dimensional Patterns Using Statistics of Spatial Organization.

PubMed

López-Sauceda, Juan; Rueda-Contreras, Mara D

2017-01-01

We developed a measurement framework of spatial organization to categorize 2-dimensional patterns from 2 multiscalar biological architectures. We propose that underlying shapes of biological entities can be approached using the statistical concept of degrees of freedom, defining it through expansion of area variability in a pattern. To help scope this suggestion, we developed a mathematical argument recognizing the deep foundations of area variability in a polygonal pattern (spatial heterogeneity). This measure uses a parameter called eutacticity . Our measuring platform of spatial heterogeneity can assign particular ranges of distribution of spatial areas for 2 biological architectures: ecological patterns of Namibia fairy circles and epithelial sheets. The spatial organizations of our 2 analyzed biological architectures are demarcated by being in a particular position among spatial order and disorder. We suggest that this theoretical platform can give us some insights about the nature of shapes in biological systems to understand organizational constraints.

Spatial Patterns in Water Temperature in Pacific Northwest Rivers: Diversity at Multiple Scales and Potential Influence of Climate Change

NASA Astrophysics Data System (ADS)

Torgersen, C. E.; Fullerton, A.; Lawler, J. J.; Ebersole, J. L.; Leibowitz, S. G.; Steel, E. A.; Beechie, T. J.; Faux, R.

2016-12-01

Understanding spatial patterns in water temperature will be essential for evaluating vulnerability of aquatic biota to future climate and for identifying and protecting diverse thermal habitats. We used high-resolution remotely sensed water temperature data for over 16,000 km of 2nd to 7th-order rivers throughout the Pacific Northwest and California to evaluate spatial patterns of summertime water temperature at multiple spatial scales. We found a diverse and geographically distributed suite of whole-river patterns. About half of rivers warmed asymptotically in a downstream direction, whereas the rest exhibited complex and unique spatial patterns. Patterns were associated with both broad-scale hydroclimatic variables as well as characteristics unique to each basin. Within-river thermal heterogeneity patterns were highly river-specific; across rivers, median size and spacing of cool patches <15 °C were around 250 m. Patches of this size are large enough for juvenile salmon rearing and for resting during migration, and the distance between patches is well within the movement capabilities of both juvenile and adult salmon. We found considerable thermal heterogeneity at fine spatial scales that may be important to fish that would be missed if data were analyzed at coarser scales. We estimated future thermal heterogeneity and concluded that climate change will cause warmer temperatures overall, but that thermal heterogeneity patterns may remain similar in the future for many rivers. We demonstrated considerable spatial complexity in both current and future water temperature, and resolved spatial patterns that could not have been perceived without spatially continuous data.

Quantifying seascape structure: Extending terrestrial spatial pattern metrics to the marine realm

USGS Publications Warehouse

Wedding, L.M.; Christopher, L.A.; Pittman, S.J.; Friedlander, A.M.; Jorgensen, S.

2011-01-01

Spatial pattern metrics have routinely been applied to characterize and quantify structural features of terrestrial landscapes and have demonstrated great utility in landscape ecology and conservation planning. The important role of spatial structure in ecology and management is now commonly recognized, and recent advances in marine remote sensing technology have facilitated the application of spatial pattern metrics to the marine environment. However, it is not yet clear whether concepts, metrics, and statistical techniques developed for terrestrial ecosystems are relevant for marine species and seascapes. To address this gap in our knowledge, we reviewed, synthesized, and evaluated the utility and application of spatial pattern metrics in the marine science literature over the past 30 yr (1980 to 2010). In total, 23 studies characterized seascape structure, of which 17 quantified spatial patterns using a 2-dimensional patch-mosaic model and 5 used a continuously varying 3-dimensional surface model. Most seascape studies followed terrestrial-based studies in their search for ecological patterns and applied or modified existing metrics. Only 1 truly unique metric was found (hydrodynamic aperture applied to Pacific atolls). While there are still relatively few studies using spatial pattern metrics in the marine environment, they have suffered from similar misuse as reported for terrestrial studies, such as the lack of a priori considerations or the problem of collinearity between metrics. Spatial pattern metrics offer great potential for ecological research and environmental management in marine systems, and future studies should focus on (1) the dynamic boundary between the land and sea; (2) quantifying 3-dimensional spatial patterns; and (3) assessing and monitoring seascape change. ?? Inter-Research 2011.

A novel spatial performance metric for robust pattern optimization of distributed hydrological models

NASA Astrophysics Data System (ADS)

Stisen, S.; Demirel, C.; Koch, J.

2017-12-01

Evaluation of performance is an integral part of model development and calibration as well as it is of paramount importance when communicating modelling results to stakeholders and the scientific community. There exists a comprehensive and well tested toolbox of metrics to assess temporal model performance in the hydrological modelling community. On the contrary, the experience to evaluate spatial performance is not corresponding to the grand availability of spatial observations readily available and to the sophisticate model codes simulating the spatial variability of complex hydrological processes. This study aims at making a contribution towards advancing spatial pattern oriented model evaluation for distributed hydrological models. This is achieved by introducing a novel spatial performance metric which provides robust pattern performance during model calibration. The promoted SPAtial EFficiency (spaef) metric reflects three equally weighted components: correlation, coefficient of variation and histogram overlap. This multi-component approach is necessary in order to adequately compare spatial patterns. spaef, its three components individually and two alternative spatial performance metrics, i.e. connectivity analysis and fractions skill score, are tested in a spatial pattern oriented model calibration of a catchment model in Denmark. The calibration is constrained by a remote sensing based spatial pattern of evapotranspiration and discharge timeseries at two stations. Our results stress that stand-alone metrics tend to fail to provide holistic pattern information to the optimizer which underlines the importance of multi-component metrics. The three spaef components are independent which allows them to complement each other in a meaningful way. This study promotes the use of bias insensitive metrics which allow comparing variables which are related but may differ in unit in order to optimally exploit spatial observations made available by remote sensing platforms. We see great potential of spaef across environmental disciplines dealing with spatially distributed modelling.

Comprehensive analysis and discovery of drought-related NAC transcription factors in common bean.

PubMed

Wu, Jing; Wang, Lanfen; Wang, Shumin

2016-09-07

Common bean (Phaseolus vulgaris L.) is an important warm-season food legume. Drought is the most important environmental stress factor affecting large areas of common bean via plant death or reduced global production. The NAM, ATAF1/2 and CUC2 (NAC) domain protein family are classic transcription factors (TFs) involved in a variety of abiotic stresses, particularly drought stress. However, the NAC TFs in common bean have not been characterized. In the present study, 86 putative NAC TF proteins were identified from the common bean genome database and located on 11 common bean chromosomes. The proteins were phylogenetically clustered into 8 distinct subfamilies. The gene structure and motif composition of common bean NACs were similar in each subfamily. These results suggest that NACs in the same subfamily may possess conserved functions. The expression patterns of common bean NAC genes were also characterized. The majority of NACs exhibited specific temporal and spatial expression patterns. We identified 22 drought-related NAC TFs based on transcriptome data for drought-tolerant and drought-sensitive genotypes. Quantitative real-time PCR (qRT-PCR) was performed to confirm the expression patterns of the 20 drought-related NAC genes. Based on the common bean genome sequence, we analyzed the structural characteristics, genome distribution, and expression profiles of NAC gene family members and analyzed drought-responsive NAC genes. Our results provide useful information for the functional characterization of common bean NAC genes and rich resources and opportunities for understanding common bean drought stress tolerance mechanisms.

Low-intensity focused ultrasound alters the latency and spatial patterns of sensory-evoked cortical responses in vivo

NASA Astrophysics Data System (ADS)

Fisher, Jonathan A. N.; Gumenchuk, Iryna

2018-06-01

Objective. The use of transcranial, low intensity focused ultrasound (FUS) is an emerging neuromodulation technology that shows promise for both therapeutic and research applications. Among many, one of the most exciting applications is the use of FUS to rehabilitate or augment human sensory capabilities. While there is compelling empirical evidence demonstrating this capability, basic questions regarding the spatiotemporal extent of the modulatory effects remain. Our objective was to assess the basic, yet often overlooked hypothesis that FUS in fact alters sensory-evoked neural activity within the region of the cerebral cortex at the beam’s focus. Approach. To address this knowledge gap, we developed an approach to optically interrogate patterns of neural activity in the cortex directly at the acoustic focus, in vivo. Implementing simultaneous wide-field optical imaging and FUS stimulation in mice, our experiments probed somatosensory-evoked electrical activity through the use of voltage sensitive dyes (VSDs) and, in transgenic mice expressing GCaMP6f, monitored associated Ca2+ responses. Main results. Our results demonstrate that low-intensity FUS alters both the kinetics and spatial patterns of neural activity in primary somatosensory cortex at the acoustic focus. When preceded by 1 s of pulsed ultrasound at intensities below 1 W cm‑2 (I sppa), the onset of sensory-evoked cortical responses occurred 3.0  ±  0.7 ms earlier and altered the surface spatial morphology of Ca2+ responses. Significance. These findings support the heretofore unconfirmed assumption that FUS-induced sensory modulation reflects, at least in part, altered reactivity in primary sensory cortex at the site of sonication. The findings are significant given the interest in using FUS to target and alter spatial aspects of sensory receptive fields on the cerebral cortex.

Low-intensity focused ultrasound alters the latency and spatial patterns of sensory-evoked cortical responses in vivo.

PubMed

Fisher, Jonathan A N; Gumenchuk, Iryna

2018-06-01

The use of transcranial, low intensity focused ultrasound (FUS) is an emerging neuromodulation technology that shows promise for both therapeutic and research applications. Among many, one of the most exciting applications is the use of FUS to rehabilitate or augment human sensory capabilities. While there is compelling empirical evidence demonstrating this capability, basic questions regarding the spatiotemporal extent of the modulatory effects remain. Our objective was to assess the basic, yet often overlooked hypothesis that FUS in fact alters sensory-evoked neural activity within the region of the cerebral cortex at the beam's focus. To address this knowledge gap, we developed an approach to optically interrogate patterns of neural activity in the cortex directly at the acoustic focus, in vivo. Implementing simultaneous wide-field optical imaging and FUS stimulation in mice, our experiments probed somatosensory-evoked electrical activity through the use of voltage sensitive dyes (VSDs) and, in transgenic mice expressing GCaMP6f, monitored associated Ca 2+ responses. Our results demonstrate that low-intensity FUS alters both the kinetics and spatial patterns of neural activity in primary somatosensory cortex at the acoustic focus. When preceded by 1 s of pulsed ultrasound at intensities below 1 W cm -2 (I sppa ), the onset of sensory-evoked cortical responses occurred 3.0  ±  0.7 ms earlier and altered the surface spatial morphology of Ca 2+ responses. These findings support the heretofore unconfirmed assumption that FUS-induced sensory modulation reflects, at least in part, altered reactivity in primary sensory cortex at the site of sonication. The findings are significant given the interest in using FUS to target and alter spatial aspects of sensory receptive fields on the cerebral cortex.

Throughfall and its spatial variability beneath xerophytic shrub canopies within water-limited arid desert ecosystems

NASA Astrophysics Data System (ADS)

Zhang, Ya-feng; Wang, Xin-ping; Hu, Rui; Pan, Yan-xia

2016-08-01

Throughfall is known to be a critical component of the hydrological and biogeochemical cycles of forested ecosystems with inherently temporal and spatial variability. Yet little is understood concerning the throughfall variability of shrubs and the associated controlling factors in arid desert ecosystems. Here we systematically investigated the variability of throughfall of two morphological distinct xerophytic shrubs (Caragana korshinskii and Artemisia ordosica) within a re-vegetated arid desert ecosystem, and evaluated the effects of shrub structure and rainfall characteristics on throughfall based on heavily gauged throughfall measurements at the event scale. We found that morphological differences were not sufficient to generate significant difference (P < 0.05) in throughfall between two studied shrub species under the same rainfall and meteorological conditions in our study area, with a throughfall percentage of 69.7% for C. korshinskii and 64.3% for A. ordosica. We also observed a highly variable patchy pattern of throughfall beneath individual shrub canopies, but the spatial patterns appeared to be stable among rainfall events based on time stability analysis. Throughfall linearly increased with the increasing distance from the shrub base for both shrubs, and radial direction beneath shrub canopies had a pronounced impact on throughfall. Throughfall variability, expressed as the coefficient of variation (CV) of throughfall, tended to decline with the increase in rainfall amount, intensity and duration, and stabilized passing a certain threshold. Our findings highlight the great variability of throughfall beneath the canopies of xerophytic shrubs and the time stability of throughfall pattern among rainfall events. The spatially heterogeneous and temporally stable throughfall is expected to generate a dynamic patchy distribution of soil moisture beneath shrub canopies within arid desert ecosystems.

Analysis of C. elegans VIG-1 expression.

PubMed

Shin, Kyoung-Hwa; Choi, Boram; Park, Yang-Seo; Cho, Nam Jeong

2008-12-31

Double-stranded RNA (dsRNA) induces gene silencing in a sequence-specific manner by a process known as RNA interference (RNAi). The RNA-induced silencing complex (RISC) is a multi-subunit ribonucleoprotein complex that plays a key role in RNAi. VIG (Vasa intronic gene) has been identified as a component of Drosophila RISC; however, the role VIG plays in regulating RNAi is poorly understood. Here, we examined the spatial and temporal expression patterns of VIG-1, the C. elegans ortholog of Drosophila VIG, using a vig-1::gfp fusion construct. This construct contains the 908-bp region immediately upstream of vig-1 gene translation initiation site. Analysis by confocal microscopy demonstrated GFP-VIG-1 expression in a number of tissues including the pharynx, body wall muscle, hypodermis, intestine, reproductive system, and nervous system at the larval and adult stages. Furthermore, western blot analysis showed that VIG-1 is present in each developmental stage examined. To investigate regulatory sequences for vig-1 gene expression, we generated constructs containing deletions in the upstream region. It was determined that the GFP expression pattern of a deletion construct (delta-908 to -597) was generally similar to that of the non-deletion construct. In contrast, removal of a larger segment (delta-908 to -191) resulted in the loss of GFP expression in most cell types. Collectively, these results indicate that the 406-bp upstream region (-596 to -191) contains essential regulatory sequences required for VIG-1 expression.

The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

PubMed Central

Hayamizu, Terry F; Mangan, Mary; Corradi, John P; Kadin, James A; Ringwald, Martin

2005-01-01

We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse. PMID:15774030

Accelerated recruitment of new brain development genes into the human genome.

PubMed

Zhang, Yong E; Landback, Patrick; Vibranovski, Maria D; Long, Manyuan

2011-10-01

How the human brain evolved has attracted tremendous interests for decades. Motivated by case studies of primate-specific genes implicated in brain function, we examined whether or not the young genes, those emerging genome-wide in the lineages specific to the primates or rodents, showed distinct spatial and temporal patterns of transcription compared to old genes, which had existed before primate and rodent split. We found consistent patterns across different sources of expression data: there is a significantly larger proportion of young genes expressed in the fetal or infant brain of humans than in mouse, and more young genes in humans have expression biased toward early developing brains than old genes. Most of these young genes are expressed in the evolutionarily newest part of human brain, the neocortex. Remarkably, we also identified a number of human-specific genes which are expressed in the prefrontal cortex, which is implicated in complex cognitive behaviors. The young genes upregulated in the early developing human brain play diverse functional roles, with a significant enrichment of transcription factors. Genes originating from different mechanisms show a similar expression bias in the developing brain. Moreover, we found that the young genes upregulated in early brain development showed rapid protein evolution compared to old genes also expressed in the fetal brain. Strikingly, genes expressed in the neocortex arose soon after its morphological origin. These four lines of evidence suggest that positive selection for brain function may have contributed to the origination of young genes expressed in the developing brain. These data demonstrate a striking recruitment of new genes into the early development of the human brain.

Spatially Characterizing Effective Timber Supply

NASA Technical Reports Server (NTRS)

Berry, J. K.; Sailor, J.

1982-01-01

The structure of a computer-oriented cartographic model for assessing roundwood supply for generation of base load electricity is discussed. The model provides an analytical procedure for coupling spatial information of harvesting economics and owner willingness to sell stumpages. Supply is characterized in terms of standing timber; of accessibility considering various harvesting and hauling factors; and of availability as affected by ownership and residential patterns. Factors governing accessibility to timber include effective harvesting distance to haulic roads as modified by barriers and slopes. Haul distance is expressed in units that take into account the relative ease of travel along various road types to a central processing facility. Areas of accessible timber are grouped into spatial units, termed 'timbersheds', of common access to particular haul road segments that belong to unique 'transport zones'. Timber availability considerations include size of ownership parcels, housing density and excluded areas. The analysis techniques are demonstrated for a cartographic data base in western Massachusetts.

Gene expression links functional networks across cortex and striatum.

PubMed

Anderson, Kevin M; Krienen, Fenna M; Choi, Eun Young; Reinen, Jenna M; Yeo, B T Thomas; Holmes, Avram J

2018-04-12

The human brain is comprised of a complex web of functional networks that link anatomically distinct regions. However, the biological mechanisms supporting network organization remain elusive, particularly across cortical and subcortical territories with vastly divergent cellular and molecular properties. Here, using human and primate brain transcriptional atlases, we demonstrate that spatial patterns of gene expression show strong correspondence with limbic and somato/motor cortico-striatal functional networks. Network-associated expression is consistent across independent human datasets and evolutionarily conserved in non-human primates. Genes preferentially expressed within the limbic network (encompassing nucleus accumbens, orbital/ventromedial prefrontal cortex, and temporal pole) relate to risk for psychiatric illness, chloride channel complexes, and markers of somatostatin neurons. Somato/motor associated genes are enriched for oligodendrocytes and markers of parvalbumin neurons. These analyses indicate that parallel cortico-striatal processing channels possess dissociable genetic signatures that recapitulate distributed functional networks, and nominate molecular mechanisms supporting cortico-striatal circuitry in health and disease.

Molecular analysis of the ependymin gene and functional test of its promoter region by transient expression in Brachydanio rerio.

PubMed

Rinder, H; Bayer, T A; Gertzen, E M; Hoffmann, W

1992-01-01

Ependymins are secretory products of meningeal cells and represent the predominant glycoproteins in the cerebrospinal fluid from various orders of teleost fish. In the zebrafish, their expression starts between 48 and 72 h post-fertilization. Generally, they share characteristics with proteins involved in cell-contact phenomena. Here, we characterize the ependymin gene from Brachydanio rerio and its flanking regions. The sequence was obtained from clones generated using the polymerase chain reaction (PCR), including a variation of an "anchored" PCR. Also, clones from a conventional phage library were analyzed. We found that the transcribed portion is arranged in six exons. Transient expression of an ependymin-promoter-lacZ gene fusion in zebrafish embryos revealed that the 2.0-kb upstream regulatory region used is sufficient to direct the ependymin-specific correct temporal and spatial expression pattern of the lacZ reporter gene.

Temporal and spatial expression of Drosophila DLGS97 during neural development.

PubMed

Albornoz, Valeria; Mendoza-Topaz, Carolina; Oliva, Carlos; Tello, Judith; Olguín, Patricio; Sierralta, Jimena

2008-07-01

The products of the Drosophila discs-large (dlg) gene are members of the MAGUK family of proteins, a group of proteins involved in localization, transport and recycling of receptors and channels in cell junctions, including the synapse. In vertebrates, four genes with multiple splice variants homologous to dlg are described. dlg originates two main proteins, DLGA, similar to the vertebrate neuronal protein PSD95, and DLGS97, similar to the vertebrate neuronal and epithelial protein SAP97. DLGA is expressed in epithelia, neural tissue and muscle. DLGS97 is expressed in neural tissue and muscle but not in epithelia. The distinctive difference between them is the presence in DLGS97 of an L27 domain. The differential expression between these variants makes the study of DLGS97 of key relevance to understand the in vivo role of synaptic MAGUKs in neurons. Here we present the temporal and spatial expression pattern of DLGS97 during embryonic and larval nervous system development, during eye development and in adult brain. Our results show that DLGS97 is expressed zygotically, in neurons in the embryo, larvae and adult, and is absent at all stages in glial cells. During eye development DLGS97 starts to be expressed in photoreceptor cells at early stages of differentiation and localizes basal to the basolateral junctions. In the brain, DLGS97 is expressed in the mushroom bodies and optic lobes at larval and adult stages; and in the antennal lobe in the adult stage. In addition we show that both, dlgS97 and dlgA transcripts, express during development multiple splice variants with differences in the use of exons in two sites.

Impact of scale on morphological spatial pattern of forest

Treesearch

Katarzyna Ostapowicz; Peter Vogt; Kurt H. Riitters; Jacek Kozak; Christine Estreguil

2008-01-01

Assessing and monitoring landscape pattern structure from multi-scale land-cover maps can utilize morphological spatial pattern analysis (MSPA), only if various influences of scale are known and taken into account. This paper lays part of the foundation for applying MSPA analysis in landscape monitoring by quantifying scale effects on six classes of spatial patterns...

Sequential establishment of stripe patterns in an expanding cell population.

PubMed

Liu, Chenli; Fu, Xiongfei; Liu, Lizhong; Ren, Xiaojing; Chau, Carlos K L; Li, Sihong; Xiang, Lu; Zeng, Hualing; Chen, Guanhua; Tang, Lei-Han; Lenz, Peter; Cui, Xiaodong; Huang, Wei; Hwa, Terence; Huang, Jian-Dong

2011-10-14

Periodic stripe patterns are ubiquitous in living organisms, yet the underlying developmental processes are complex and difficult to disentangle. We describe a synthetic genetic circuit that couples cell density and motility. This system enabled programmed Escherichia coli cells to form periodic stripes of high and low cell densities sequentially and autonomously. Theoretical and experimental analyses reveal that the spatial structure arises from a recurrent aggregation process at the front of the continuously expanding cell population. The number of stripes formed could be tuned by modulating the basal expression of a single gene. The results establish motility control as a simple route to establishing recurrent structures without requiring an extrinsic pacemaker.

Mutation of the murC and murB Genes Impairs Heterocyst Differentiation in Anabaena sp. Strain PCC 7120

PubMed Central

Videau, Patrick; Rivers, Orion S.; Ushijima, Blake; Oshiro, Reid T.; Kim, Min Joo; Philmus, Benjamin

2016-01-01

ABSTRACT To stabilize cellular integrity in the face of environmental perturbations, most bacteria, including cyanobacteria, synthesize and maintain a strong, flexible, three-dimensional peptidoglycan lattice. Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium capable of differentiating morphologically distinct nitrogen-fixing heterocyst cells in a periodic pattern. While heterocyst development has been shown to require proper peptidoglycan remodeling, the role of peptidoglycan synthesis has remained unclear. Here we report the identification of two peptidoglycan synthesis genes, murC (alr5065) and murB (alr5066), as required for heterocyst development. The murC and murB genes are predicted to encode a UDP-N-acetylmuramate:l-alanine ligase and a UDP-N-acetylenolpyruvoylglucosamine reductase, respectively, and we confirm enzymatic function through complementation of Escherichia coli strains deficient for these enzymes. Cells depleted of either murC or murB expression failed to differentiate heterocysts under normally inducing conditions and displayed decreased filament integrity. To identify the stage(s) of development affected by murC or murB depletion, the spatial distribution of expression of the patterning marker gene, patS, was examined. Whereas murB depletion did not affect the pattern of patS expression, murC depletion led to aberrant expression of patS in all cells of the filament. Finally, expression of gfp controlled by the region of DNA immediately upstream of murC was enriched in differentiating cells and was repressed by the transcription factor NtcA. Collectively, the data in this work provide evidence for a direct link between peptidoglycan synthesis and the maintenance of a biological pattern in a multicellular organism. IMPORTANCE Multicellular organisms that differentiate specialized cells must regulate morphological changes such that both cellular integrity and the dissemination of developmental signals are preserved. Here we show that the multicellular bacterium Anabaena, which differentiates a periodic pattern of specialized heterocyst cells, requires peptidoglycan synthesis by the murine ligase genes murC (alr5065) and murB (alr5066) for maintenance of patterned gene expression, filament integrity, and overall development. This work highlights the significant influence that intracellular structure and intercellular connections can have on the execution of a developmental program. PMID:26811320

Mutation of the murC and murB Genes Impairs Heterocyst Differentiation in Anabaena sp. Strain PCC 7120.

PubMed

Videau, Patrick; Rivers, Orion S; Ushijima, Blake; Oshiro, Reid T; Kim, Min Joo; Philmus, Benjamin; Cozy, Loralyn M

2016-04-01

To stabilize cellular integrity in the face of environmental perturbations, most bacteria, including cyanobacteria, synthesize and maintain a strong, flexible, three-dimensional peptidoglycan lattice. Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium capable of differentiating morphologically distinct nitrogen-fixing heterocyst cells in a periodic pattern. While heterocyst development has been shown to require proper peptidoglycan remodeling, the role of peptidoglycan synthesis has remained unclear. Here we report the identification of two peptidoglycan synthesis genes, murC (alr5065) and murB (alr5066), as required for heterocyst development. The murC and murB genes are predicted to encode a UDP-N-acetylmuramate:L-alanine ligase and a UDP-N-acetylenolpyruvoylglucosamine reductase, respectively, and we confirm enzymatic function through complementation of Escherichia coli strains deficient for these enzymes. Cells depleted of either murC or murB expression failed to differentiate heterocysts under normally inducing conditions and displayed decreased filament integrity. To identify the stage(s) of development affected by murC or murB depletion, the spatial distribution of expression of the patterning marker gene, patS, was examined. Whereas murB depletion did not affect the pattern of patS expression, murC depletion led to aberrant expression of patS in all cells of the filament. Finally, expression of gfp controlled by the region of DNA immediately upstream of murC was enriched in differentiating cells and was repressed by the transcription factor NtcA. Collectively, the data in this work provide evidence for a direct link between peptidoglycan synthesis and the maintenance of a biological pattern in a multicellular organism. Multicellular organisms that differentiate specialized cells must regulate morphological changes such that both cellular integrity and the dissemination of developmental signals are preserved. Here we show that the multicellular bacterium Anabaena, which differentiates a periodic pattern of specialized heterocyst cells, requires peptidoglycan synthesis by the murine ligase genes murC (alr5065) and murB (alr5066) for maintenance of patterned gene expression, filament integrity, and overall development. This work highlights the significant influence that intracellular structure and intercellular connections can have on the execution of a developmental program. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Patterning in time and space: HoxB cluster gene expression in the developing chick embryo.

PubMed

Gouveia, Analuce; Marcelino, Hugo M; Gonçalves, Lisa; Palmeirim, Isabel; Andrade, Raquel P

2015-01-01

The developing embryo is a paradigmatic model to study molecular mechanisms of time control in Biology. Hox genes are key players in the specification of tissue identity during embryo development and their expression is under strict temporal regulation. However, the molecular mechanisms underlying timely Hox activation in the early embryo remain unknown. This is hindered by the lack of a rigorous temporal framework of sequential Hox expression within a single cluster. Herein, a thorough characterization of HoxB cluster gene expression was performed over time and space in the early chick embryo. Clear temporal collinearity of HoxB cluster gene expression activation was observed. Spatial collinearity of HoxB expression was evidenced in different stages of development and in multiple tissues. Using embryo explant cultures we showed that HoxB2 is cyclically expressed in the rostral presomitic mesoderm with the same periodicity as somite formation, suggesting a link between timely tissue specification and somite formation. We foresee that the molecular framework herein provided will facilitate experimental approaches aimed at identifying the regulatory mechanisms underlying Hox expression in Time and Space.

Patterning in time and space: HoxB cluster gene expression in the developing chick embryo

PubMed Central

Gouveia, Analuce; Marcelino, Hugo M; Gonçalves, Lisa; Palmeirim, Isabel; Andrade, Raquel P

2015-01-01

The developing embryo is a paradigmatic model to study molecular mechanisms of time control in Biology. Hox genes are key players in the specification of tissue identity during embryo development and their expression is under strict temporal regulation. However, the molecular mechanisms underlying timely Hox activation in the early embryo remain unknown. This is hindered by the lack of a rigorous temporal framework of sequential Hox expression within a single cluster. Herein, a thorough characterization of HoxB cluster gene expression was performed over time and space in the early chick embryo. Clear temporal collinearity of HoxB cluster gene expression activation was observed. Spatial collinearity of HoxB expression was evidenced in different stages of development and in multiple tissues. Using embryo explant cultures we showed that HoxB2 is cyclically expressed in the rostral presomitic mesoderm with the same periodicity as somite formation, suggesting a link between timely tissue specification and somite formation. We foresee that the molecular framework herein provided will facilitate experimental approaches aimed at identifying the regulatory mechanisms underlying Hox expression in Time and Space. PMID:25602523

Expression of the beta-catenin gene in the skin of embryonic geese during feather bud development.

PubMed

Wu, W; Xu, R F; Xiao, L; Xu, H; Gao, G

2008-01-01

beta-Catenin signaling has been reported to initiate feather bud development. In the present study, beta-catenin gene was isolated and identified from a cDNA library constructed using embryonic goose skin. Expression patterns of beta-catenin gene in the dorsal skin of goose embryos were investigated using the methods of semi-quantitative reverse transcription PCR, Northern blot analysis, and in situ hybridization. The sequence of beta-catenin was found highly conserved at the amino acid level, sharing 100, 99, and 99% identity with chicken, Chinese soft-shell turtle, and human sequences, respectively. Relatively high levels (62.51 +/- 7.11% to 101.74 +/- 7.29%) of beta-catenin mRNA were detected in the dorsal skin samples. The levels of beta-catenin expression were most prominent at the early stage from embryo day (E)10 to E20 and then significantly declined with the embryonic development. In situ hybridization demonstrated that at E10, beta-catenin expression was mainly observed at the surface periderm cells and the localized region of the epidermal layer. Because feather bud forms with an anterior-posterior orientation, strong staining was observed in the periderm layer and in the ectoderm and epidermis with a diffuse distribution within the internal area of the buds. The stronger staining was seen in the barb ridges than in the center pulp of the feather follicles at E18 and E20. In this study, expression of Shh as a marker gene for the bud development was examined paralleling with expression patterns of beta-catenin. It was found that the expression pattern of beta-catenin was almost similar spatially and temporally to that of Shh mRNA at the later stages of bud development. The differential beta-catenin mRNA expression in the goose dorsal skin may be essential for promoting the normal development of embryonic feather bud.

The medial prefrontal cortex is involved in spatial memory retrieval under partial-cue conditions.

PubMed

Jo, Yong Sang; Park, Eun Hye; Kim, Il Hwan; Park, Soon Kwon; Kim, Hyun; Kim, Hyun Taek; Choi, June-Seek

2007-12-05

Brain circuits involved in pattern completion, or retrieval of memory from fragmented cues, were investigated. Using different versions of the Morris water maze, we explored the roles of the CA3 subregion of the hippocampus and the medial prefrontal cortex (mPFC) in spatial memory retrieval under various conditions. In a hidden platform task, both CA3 and mPFC lesions disrupted memory retrieval under partial-cue, but not under full-cue, conditions. For a delayed matching-to-place task, CA3 lesions produced a deficit in both forming and recalling spatial working memory regardless of extramaze cue conditions. In contrast, damage to mPFC impaired memory retrieval only when a fraction of cues was available. To corroborate the lesion study, we examined the expression of the immediate early gene c-fos in mPFC and the hippocampus. After training of spatial reference memory in full-cue conditions for 6 d, the same training procedure in the absence of all cues except one increased the number of Fos-immunoreactive cells in mPFC and CA3. Furthermore, mPFC inactivation with muscimol, a GABA agonist, blocked memory retrieval in the degraded-cue environment. However, mPFC-lesioned animals initially trained in a single-cue environment had no difficulty in retrieving spatial memory when the number of cues was increased, demonstrating that contextual change per se did not impair the behavioral performance of the mPFC-lesioned animals. Together, these findings strongly suggest that pattern completion requires interactions between mPFC and the hippocampus, in which mPFC plays significant roles in retrieving spatial information maintained in the hippocampus for efficient navigation.

Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems.

PubMed

Woolley, Thomas E; Baker, Ruth E; Gaffney, Eamonn A; Maini, Philip K; Seirin-Lee, Sungrim

2012-05-01

Cellular gene expression is a complex process involving many steps, including the transcription of DNA and translation of mRNA; hence the synthesis of proteins requires a considerable amount of time, from ten minutes to several hours. Since diffusion-driven instability has been observed to be sensitive to perturbations in kinetic delays, the application of Turing patterning mechanisms to the problem of producing spatially heterogeneous differential gene expression has been questioned. In deterministic systems a small delay in the reactions can cause a large increase in the time it takes a system to pattern. Recently, it has been observed that in undelayed systems intrinsic stochasticity can cause pattern initiation to occur earlier than in the analogous deterministic simulations. Here we are interested in adding both stochasticity and delays to Turing systems in order to assess whether stochasticity can reduce the patterning time scale in delayed Turing systems. As analytical insights to this problem are difficult to attain and often limited in their use, we focus on stochastically simulating delayed systems. We consider four different Turing systems and two different forms of delay. Our results are mixed and lead to the conclusion that, although the sensitivity to delays in the Turing mechanism is not completely removed by the addition of intrinsic noise, the effects of the delays are clearly ameliorated in certain specific cases.

WEREWOLF and ENHANCER of GLABRA3 are interdependent regulators of the spatial expression pattern of GLABRA2 in Arabidopsis.

PubMed

Song, Sang-Kee; Kwak, Su-Hwan; Chang, Soo Chul; Schiefelbein, John; Lee, Myeong Min

2015-11-06

In multicellular organisms, cell fates are specified through differential regulation of transcription. Epidermal cell fates in the Arabidopsis thaliana root are precisely specified by several transcription factors, with the GLABRA2 (GL2) homeodomain protein acting at the farthest downstream in this process. To better understand the regulation of GL2 expression, we ectopically expressed WEREWOLF (WER) and ENHANCER OF GLABRA3 (EGL3) in various tissues and examined GL2 expression. Here we show that WER expressed ubiquitously in the root induced GL2 expression only in the root epidermis, whereas co-expression of WER and EGL3 induced GL2 expression in the corresponding tissues. We also found that GL3 accumulated in the nucleus at the early meristematic region and EGL3 accumulated later in the nucleus of epidermal cells. We further found that ectopic expression of WER and EGL3 in ground tissues inhibited GL2 expression in the epidermis. Our results suggest that the co-expression of WER and EGL3 is sufficient for driving GL2 and CPC expression. Copyright © 2015 Elsevier Inc. All rights reserved.

Investigating circular patterns in linear polarization observations of Venus

NASA Astrophysics Data System (ADS)

Mahapatra, Gourav; Stam, Daphne; Rossi, Loic; Rodenhuis, Michiel; Snik, Frans

2017-04-01

ESA's Venus Express mission has revealed our neighbouring planet to be a highly dynamic world, with ever-changing cloud properties and structures, wind speeds that increase in time, and variable concentrations of atmospheric trace gases such as SO2. The SPICAV-IR instrument on Venus Express has provided us with close-up linear polarization data of sunlight reflected by Venus's clouds and hazes, that allows a characterisation of their composition and particle sizes. Here, we analyse linear polarization data of the planet at a distance, obtained with the Extreme Polarimeter (ExPo) on the William Herschel Telescope on La Palma. These spatially resolved, high-accuracy polarization observations of Venus show faint circular patterns centered on the sub-solar point that are absent in the flux observations. So far, careful analyses have ruled out instrumental effects which leaves us to wonder about atmospheric properties as the cause of the circular patterns. Using numerical simulations of the flux and polarization of sunlight that is reflected by Venus, we have investigated the relation between the observed patterns and several atmospheric properties, such as variations in particle sizes, composition, density and altitude. We discuss the plausibility of the possible causes in the view of the current knowledge of the composition and dynamical processes in Venus's atmosphere.

COMPARISON OF SPATIAL PATTERNS OF POLLUTANT DISTRIBUTION WITH CMAQ PREDICTIONS

EPA Science Inventory

To evaluate the Models-3/Community Multiscale Air Quality (CMAQ) modeling system in reproducing the spatial patterns of aerosol concentrations over the country on timescales of months and years, the spatial patterns of model output are compared with those derived from observation...

Erythropoietin and engineered innate repair activators.

PubMed

Brines, Michael; Cerami, Anthony

2013-01-01

Erythropoietin (EPO) is a pleiotropic type I cytokine that has been identified as a major endogenous tissue protective molecule. In response to injury, EPO and a distinct receptor are expressed with a characteristic temporal and spatial expression pattern. Together, these serve to limit injury and to initiate repair. Administration of EPO in the setting of injury has been shown to be beneficial in a multitude of preclinical models. However, translation into the clinic has been hampered by EPO's adverse effects, including promotion of thrombosis. Recently, engineered molecules based on EPO's structure-activity relationships have been developed that are devoid of hematopoietic effects. These compounds are promising candidates for treatment of a wide variety of acute and chronic diseases.

Spatial Patterns in Alternative States and Thresholds: A Missing Link for Management of Landscapes?

USDA-ARS?s Scientific Manuscript database

The detection of threshold dynamics (and other dynamics of interest) would benefit from explicit representations of spatial patterns of disturbance, spatial dependence in responses to disturbance, and the spatial structure of feedbacks in the design of monitoring and management strategies. Spatially...

Contributions of ignitions, fuels, and weather to the spatial patterns of burn probability of a boreal landscape

Treesearch

Marc-Andre Parisien; Sean A. Parks; Carol Miller; Meg A. Krawchuck; Mark Heathcott; Max A. Moritz

2011-01-01

The spatial pattern of fire observed across boreal landscapes is the outcome of complex interactions among components of the fire environment. We investigated how the naturally occurring patterns of ignitions, fuels, and weather generate spatial pattern of burn probability (BP) in a large and highly fireprone boreal landscape of western Canada, Wood Buffalo National...

Spatial arrangement of faults and opening-mode fractures

NASA Astrophysics Data System (ADS)

Laubach, S. E.; Lamarche, J.; Gauthier, B. D. M.; Dunne, W. M.; Sanderson, David J.

2018-03-01

Spatial arrangement is a fundamental characteristic of fracture arrays. The pattern of fault and opening-mode fracture positions in space defines structural heterogeneity and anisotropy in a rock volume, governs how faults and fractures affect fluid flow, and impacts our understanding of the initiation, propagation and interactions during the formation of fracture patterns. This special issue highlights recent progress with respect to characterizing and understanding the spatial arrangements of fault and fracture patterns, providing examples over a wide range of scales and structural settings. Five papers describe new methods and improvements of existing techniques to quantify spatial arrangement. One study unravels the time evolution of opening-mode fracture spatial arrangement, which are data needed to compare natural patterns with progressive fracture growth in kinematic and mechanical models. Three papers investigate the role of evolving diagenesis in localizing fractures by mechanical stratigraphy and nine discuss opening-mode fracture spatial arrangement. Two papers show the relevance of complex cluster patterns to unconventional reservoirs through examples of fractures in tight gas sandstone horizontal wells, and a study of fracture arrangement in shale. Four papers demonstrate the roles of folds in fracture localization and the development spatial patterns. One paper models along-fault friction and fluid pressure and their effects on fault-related fracture arrangement. Contributions address deformation band patterns in carbonate rocks and fault size and arrangement above a detachment fault. Three papers describe fault and fracture arrangements in basement terrains, and three document fracture patterns in shale. This collection of papers points toward improvement in field methods, continuing improvements in computer-based data analysis and creation of synthetic fracture patterns, and opportunities for further understanding fault and fracture attributes in the subsurface through coupled spatial, size, and pattern analysis.

Evolving doublesex expression correlates with the origin and diversification of male sexual ornaments in the Drosophila immigrans species group.

PubMed

Rice, Gavin; Barmina, Olga; Hu, Kevin; Kopp, Artyom

2018-03-01

Male ornaments and other sex-specific traits present some of the most dramatic examples of evolutionary innovations. Comparative studies of similar but independently evolved traits are particularly important for identifying repeated patterns in the evolution of these traits. Male-specific modifications of the front legs have evolved repeatedly in Drosophilidae and other Diptera. The best understood of these novel structures is the sex comb of Drosophila melanogaster and its close relatives. Here, we examine the evolution of another male foreleg modification, the sex brush, found in the distantly related Drosophila immigrans species group. Similar to the sex comb, we find that the origin of the sex brush correlates with novel, spatially restricted expression of the doublesex (dsx) transcription factor, the primary effector of the Drosophila sex determination pathway. The diversity of Dsx expression patterns in the immigrans species group closely reflects the differences in the presence, position, and size of the sex brush. Together with previous work on sex comb evolution, these observations suggest that tissue-specific activation of dsx expression may be a common mechanism responsible for the evolution of sexual dimorphism and particularly for the origin of novel male-specific ornaments. © 2018 Wiley Periodicals, Inc.

Changing pattern of the subcellular distribution of erythroblast macrophage protein (Emp) during macrophage differentiation.

PubMed

Soni, Shivani; Bala, Shashi; Kumar, Ajay; Hanspal, Manjit

2007-01-01

Erythroblast macrophage protein (Emp) mediates the attachment of erythroid cells to macrophages and is required for normal differentiation of both cell lineages. In erythroid cells, Emp is believed to be involved in nuclear extrusion, however, its role in macrophage differentiation is unknown. Information on the changes in the expression level and subcellular distribution of Emp in differentiating macrophages is essential for understanding the function of Emp. Macrophages of varying maturity were examined by immunofluorescence microscopy and biochemical methods. Our data show that Emp is expressed in all stages of maturation, but its localization pattern changes dramatically during maturation: in immature macrophages, a substantial fraction of Emp is associated with the nuclear matrix, whereas in more mature cells, Emp is expressed largely at cell surface. Pulse-chase experiments show that nascent Emp migrates intracellularly from the cytoplasm to the plasma membrane more efficiently in mature macrophages than in immature cells. Incubation of erythroid cells with macrophages in culture shows that erythroid cells attach to mature macrophages but not to immature macrophage precursors. Together, our data show that the temporal and spatial expression of Emp correlates with its role in erythroblastic island formation and suggest that Emp may be involved in multiple cellular functions.

*CHANGING PATTERN OF THE SUBCELLULAR DISTRIBUTION OF ERYTHROBLAST MACROPHAGE PROTEIN (EMP) DURING MACROPHAGE DIFFERENTIATION

PubMed Central

Soni, Shivani; Bala, Shashi; Kumar, Ajay; Hanspal, Manjit

2007-01-01

Erythroblast macrophage protein (Emp), mediates the attachment of erythroid cells to macrophages, and is required for normal differentiation of both cell lineages. In erythroid cells Emp is believed to be involved in nuclear extrusion however, its role in macrophage differentiation is unknown. Information on the changes in the expression level and subcellular distribution of Emp in differentiating macrophages is essential for understanding the function of Emp. Macrophages of varying maturity were examined by immunofluorescence microscopy and biochemical methods. Our data shows that Emp is expressed in all stages of maturation, but its localization pattern changes dramatically during maturation: in immature macrophages, a substantial fraction of Emp is associated with the nuclear matrix, whereas in more mature cells, Emp is expressed largely at cell surface. Pulse-chase experiments show that nascent Emp migrates intracellularly from the cytoplasm to the plasma membrane more efficiently in mature macrophages than in immature cells. Incubation of erythroid cells with macrophages in culture show that erythroid cells attach to mature macrophages but not to immature macrophage precursors. Together, our data shows that the temporal and spatial expression of Emp correlates with its role in erythroblastic island formation, and suggests that Emp may be involved in multiple cellular functions. PMID:17071116

Introduction of the human AVPR1A gene substantially alters brain receptor expression patterns and enhances aspects of social behavior in transgenic mice

PubMed Central

Charles, Rhonda; Sakurai, Takeshi; Takahashi, Nagahide; Elder, Gregory A.; Gama Sosa, Miguel A.; Young, Larry J.; Buxbaum, Joseph D.

2014-01-01

Central arginine vasopressin receptor 1A (AVPR1A) modulates a wide range of behaviors, including stress management and territorial aggression, as well as social bonding and recognition. Inter- and intra-species variations in the expression pattern of AVPR1A in the brain and downstream differential behavioral phenotypes have been attributed to differences in the non-coding regions of the AVPR1A gene, including polymorphic elements within upstream regulatory areas. Gene association studies have suggested a link between AVPR1A polymorphisms and autism, and AVPR1A has emerged as a potential pharmacological target for treatment of social cognitive impairments and mood and anxiety disorders. To further investigate the genetic mechanism giving rise to species differences in AVPR1A expression patterns and associated social behaviors, and to create a preclinical mouse model useful for screening drugs targeting AVPR1A, we engineered and extensively characterized bacterial artificial chromosome (BAC) transgenic mice harboring the entire human AVPR1A locus with the surrounding regulatory elements. Compared with wild-type animals, the humanized mice displayed a more widely distributed ligand-AVPR1A binding pattern, which overlapped with that of primates. Furthermore, humanized AVPR1A mice displayed increased reciprocal social interactions compared with wild-type animals, but no differences in social approach and preference for social novelty were observed. Aspects of learning and memory, specifically novel object recognition and spatial relocation recognition, were unaffected. The biological alterations in humanized AVPR1A mice resulted in the rescue of the prepulse inhibition impairments that were observed in knockout mice, indicating conserved functionality. Although further behavioral paradigms and additional cohorts need to be examined in humanized AVPR1A mice, the results demonstrate that species-specific variations in the genomic content of regulatory regions surrounding the AVPR1A locus are responsible for differential receptor protein expression patterns across species and that they are likely to contribute to species-specific behavioral variation. The humanized AVPR1A mouse is a potential preclinical model for further understanding the regulation of receptor gene expression and the impact of variation in receptor expression on behaviors, and should be useful for screening drugs targeting human AVPR1A, taking advantage of the expression of human AVPR1A in human-relevant brain regions. PMID:24924430

The role of spatial frequency information for ERP components sensitive to faces and emotional facial expression.

PubMed

Holmes, Amanda; Winston, Joel S; Eimer, Martin

2005-10-01

To investigate the impact of spatial frequency on emotional facial expression analysis, ERPs were recorded in response to low spatial frequency (LSF), high spatial frequency (HSF), and unfiltered broad spatial frequency (BSF) faces with fearful or neutral expressions, houses, and chairs. In line with previous findings, BSF fearful facial expressions elicited a greater frontal positivity than BSF neutral facial expressions, starting at about 150 ms after stimulus onset. In contrast, this emotional expression effect was absent for HSF and LSF faces. Given that some brain regions involved in emotion processing, such as amygdala and connected structures, are selectively tuned to LSF visual inputs, these data suggest that ERP effects of emotional facial expression do not directly reflect activity in these regions. It is argued that higher order neocortical brain systems are involved in the generation of emotion-specific waveform modulations. The face-sensitive N170 component was neither affected by emotional facial expression nor by spatial frequency information.

Evidence for self-organization in determining spatial patterns of stream nutrients, despite primacy of the geomorphic template

PubMed Central

Dong, Xiaoli; Grimm, Nancy B.

2017-01-01

Nutrients in freshwater ecosystems are highly variable in space and time. Nevertheless, the variety of processes contributing to nutrient patchiness, and the wide range of spatial and temporal scales at which these processes operate, obfuscate how this spatial heterogeneity is generated. Here, we describe the spatial structure of stream nutrient concentration, quantify the relative importance of the physical template and biological processes, and detect and evaluate the role of self-organization in driving such patterns. We examined nutrient spatial patterns in Sycamore Creek, an intermittent desert stream in Arizona that experienced an ecosystem regime shift [from a gravel/algae-dominated to a vascular plant-dominated (hereafter, “wetland”) system] in 2000 when cattle grazing ceased. We conducted high-resolution nutrient surveys in surface water along a 10-km stream reach over four visits spanning 18 y (1995–2013) that represent different successional stages and prewetland stage vs. postwetland state. As expected, groundwater upwelling had a major influence on nutrient spatial patterns. However, self-organization realized by the mechanism of spatial feedbacks also was significant and intensified over ecosystem succession, as a resource (nitrogen) became increasingly limiting. By late succession, the effects of internal spatial feedbacks and groundwater upwelling were approximately equal in magnitude. Wetland establishment influenced nutrient spatial patterns only indirectly, by modifying the extent of surface water/groundwater exchange. This study illustrates that multiple mechanisms interact in a dynamic way to create spatial heterogeneity in riverine ecosystems, and provides a means to detect spatial self-organization against physical template heterogeneity as a dominant driver of spatial patterns. PMID:28559326

Evidence for self-organization in determining spatial patterns of stream nutrients, despite primacy of the geomorphic template.

PubMed

Dong, Xiaoli; Ruhí, Albert; Grimm, Nancy B

2017-06-13

Nutrients in freshwater ecosystems are highly variable in space and time. Nevertheless, the variety of processes contributing to nutrient patchiness, and the wide range of spatial and temporal scales at which these processes operate, obfuscate how this spatial heterogeneity is generated. Here, we describe the spatial structure of stream nutrient concentration, quantify the relative importance of the physical template and biological processes, and detect and evaluate the role of self-organization in driving such patterns. We examined nutrient spatial patterns in Sycamore Creek, an intermittent desert stream in Arizona that experienced an ecosystem regime shift [from a gravel/algae-dominated to a vascular plant-dominated (hereafter, "wetland") system] in 2000 when cattle grazing ceased. We conducted high-resolution nutrient surveys in surface water along a 10-km stream reach over four visits spanning 18 y (1995-2013) that represent different successional stages and prewetland stage vs. postwetland state. As expected, groundwater upwelling had a major influence on nutrient spatial patterns. However, self-organization realized by the mechanism of spatial feedbacks also was significant and intensified over ecosystem succession, as a resource (nitrogen) became increasingly limiting. By late succession, the effects of internal spatial feedbacks and groundwater upwelling were approximately equal in magnitude. Wetland establishment influenced nutrient spatial patterns only indirectly, by modifying the extent of surface water/groundwater exchange. This study illustrates that multiple mechanisms interact in a dynamic way to create spatial heterogeneity in riverine ecosystems, and provides a means to detect spatial self-organization against physical template heterogeneity as a dominant driver of spatial patterns.

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.

PubMed

Oosterveen, Tony; Kurdija, Sanja; Ensterö, Mats; Uhde, Christopher W; Bergsland, Maria; Sandberg, Magnus; Sandberg, Rickard; Muhr, Jonas; Ericson, Johan

2013-04-30

The reiterative deployment of a small cadre of morphogen signals underlies patterning and growth of most tissues during embyogenesis, but how such inductive events result in tissue-specific responses remains poorly understood. By characterizing cis-regulatory modules (CRMs) associated with genes regulated by Sonic hedgehog (Shh), retinoids, or bone morphogenetic proteins in the CNS, we provide evidence that the neural-specific interpretation of morphogen signaling reflects a direct integration of these pathways with SoxB1 proteins at the CRM level. Moreover, expression of SoxB1 proteins in the limb bud confers on mesodermal cells the potential to activate neural-specific target genes upon Shh, retinoid, or bone morphogenetic protein signaling, and the collocation of binding sites for SoxB1 and morphogen-mediatory transcription factors in CRMs faithfully predicts neural-specific gene activity. Thus, an unexpectedly simple transcriptional paradigm appears to conceptually explain the neural-specific interpretation of pleiotropic signaling during vertebrate development. Importantly, genes induced in a SoxB1-dependent manner appear to constitute repressive gene regulatory networks that are directly interlinked at the CRM level to constrain the regional expression of patterning genes. Accordingly, not only does the topology of SoxB1-driven gene regulatory networks provide a tissue-specific mode of gene activation, but it also determines the spatial expression pattern of target genes within the developing neural tube.

Mapping spatial patterns with morphological image processing

Treesearch

Peter Vogt; Kurt H. Riitters; Christine Estreguil; Jacek Kozak; Timothy G. Wade; James D. Wickham

2006-01-01

We use morphological image processing for classifying spatial patterns at the pixel level on binary land-cover maps. Land-cover pattern is classified as 'perforated,' 'edge,' 'patch,' and 'core' with higher spatial precision and thematic accuracy compared to a previous approach based on image convolution, while retaining the...

Ecological and evolutionary drivers of the elevational gradient of diversity.

PubMed

Laiolo, Paola; Pato, Joaquina; Obeso, José Ramón

2018-05-02

Ecological, evolutionary, spatial and neutral theories make distinct predictions and provide distinct explanations for the mechanisms that control the relationship between diversity and the environment. Here, we test predictions of the elevational diversity gradient focusing on Iberian bumblebees, grasshoppers and birds. Processes mediated by local abundance and regional diversity concur in explaining local diversity patterns along elevation. Effects expressed through variation in abundance were similar among taxa and point to the overriding role of a physical factor, temperature. This determines how energy is distributed among individuals and ultimately how the resulting pattern of abundance affects species incidence. Effects expressed through variation in regional species pools depended instead on taxon-specific evolutionary history, and lead to diverging responses under similar environmental pressures. Local filters and regional variation also explain functional diversity gradients, in line with results from species richness that indicate an (local) ecological and (regional) historical unfolding of diversity-elevation relationships. © 2018 John Wiley & Sons Ltd/CNRS.

Transcriptional architecture of the primate neocortex.

PubMed

Bernard, Amy; Lubbers, Laura S; Tanis, Keith Q; Luo, Rui; Podtelezhnikov, Alexei A; Finney, Eva M; McWhorter, Mollie M E; Serikawa, Kyle; Lemon, Tracy; Morgan, Rebecca; Copeland, Catherine; Smith, Kimberly; Cullen, Vivian; Davis-Turak, Jeremy; Lee, Chang-Kyu; Sunkin, Susan M; Loboda, Andrey P; Levine, David M; Stone, David J; Hawrylycz, Michael J; Roberts, Christopher J; Jones, Allan R; Geschwind, Daniel H; Lein, Ed S

2012-03-22

Genome-wide transcriptional profiling was used to characterize the molecular underpinnings of neocortical organization in rhesus macaque, including cortical areal specialization and laminar cell-type diversity. Microarray analysis of individual cortical layers across sensorimotor and association cortices identified robust and specific molecular signatures for individual cortical layers and areas, prominently involving genes associated with specialized neuronal function. Overall, transcriptome-based relationships were related to spatial proximity, being strongest between neighboring cortical areas and between proximal layers. Primary visual cortex (V1) displayed the most distinctive gene expression compared to other cortical regions in rhesus and human, both in the specialized layer 4 as well as other layers. Laminar patterns were more similar between macaque and human compared to mouse, as was the unique V1 profile that was not observed in mouse. These data provide a unique resource detailing neocortical transcription patterns in a nonhuman primate with great similarity in gene expression to human. Copyright © 2012 Elsevier Inc. All rights reserved.

Hierarchical analysis of spatial pattern and processes of Douglas-fir forests. Ph.D. Thesis, 10 Sep. 1991 Abstract Only

NASA Technical Reports Server (NTRS)

Bradshaw, G. A.

1995-01-01

There has been an increased interest in the quantification of pattern in ecological systems over the past years. This interest is motivated by the desire to construct valid models which extend across many scales. Spatial methods must quantify pattern, discriminate types of pattern, and relate hierarchical phenomena across scales. Wavelet analysis is introduced as a method to identify spatial structure in ecological transect data. The main advantage of the wavelet transform over other methods is its ability to preserve and display hierarchical information while allowing for pattern decomposition. Two applications of wavelet analysis are illustrated, as a means to: (1) quantify known spatial patterns in Douglas-fir forests at several scales, and (2) construct spatially-explicit hypotheses regarding pattern generating mechanisms. Application of the wavelet variance, derived from the wavelet transform, is developed for forest ecosystem analysis to obtain additional insight into spatially-explicit data. Specifically, the resolution capabilities of the wavelet variance are compared to the semi-variogram and Fourier power spectra for the description of spatial data using a set of one-dimensional stationary and non-stationary processes. The wavelet cross-covariance function is derived from the wavelet transform and introduced as a alternative method for the analysis of multivariate spatial data of understory vegetation and canopy in Douglas-fir forests of the western Cascades of Oregon.

Long-term consistency in spatial patterns of primate seed dispersal.

PubMed

Heymann, Eckhard W; Culot, Laurence; Knogge, Christoph; Noriega Piña, Tony Enrique; Tirado Herrera, Emérita R; Klapproth, Matthias; Zinner, Dietmar

2017-03-01

Seed dispersal is a key ecological process in tropical forests, with effects on various levels ranging from plant reproductive success to the carbon storage potential of tropical rainforests. On a local and landscape scale, spatial patterns of seed dispersal create the template for the recruitment process and thus influence the population dynamics of plant species. The strength of this influence will depend on the long-term consistency of spatial patterns of seed dispersal. We examined the long-term consistency of spatial patterns of seed dispersal with spatially explicit data on seed dispersal by two neotropical primate species, Leontocebus nigrifrons and Saguinus mystax (Callitrichidae), collected during four independent studies between 1994 and 2013. Using distributions of dispersal probability over distances independent of plant species, cumulative dispersal distances, and kernel density estimates, we show that spatial patterns of seed dispersal are highly consistent over time. For a specific plant species, the legume Parkia panurensis , the convergence of cumulative distributions at a distance of 300 m, and the high probability of dispersal within 100 m from source trees coincide with the dimension of the spatial-genetic structure on the embryo/juvenile (300 m) and adult stage (100 m), respectively, of this plant species. Our results are the first demonstration of long-term consistency of spatial patterns of seed dispersal created by tropical frugivores. Such consistency may translate into idiosyncratic patterns of regeneration.

Autoregressive modelling of species richness in the Brazilian Cerrado.

PubMed

Vieira, C M; Blamires, D; Diniz-Filho, J A F; Bini, L M; Rangel, T F L V B

2008-05-01

Spatial autocorrelation is the lack of independence between pairs of observations at given distances within a geographical space, a phenomenon commonly found in ecological data. Taking into account spatial autocorrelation when evaluating problems in geographical ecology, including gradients in species richness, is important to describe both the spatial structure in data and to correct the bias in Type I errors of standard statistical analyses. However, to effectively solve these problems it is necessary to establish the best way to incorporate the spatial structure to be used in the models. In this paper, we applied autoregressive models based on different types of connections and distances between 181 cells covering the Cerrado region of Central Brazil to study the spatial variation in mammal and bird species richness across the biome. Spatial structure was stronger for birds than for mammals, with R(2) values ranging from 0.77 to 0.94 for mammals and from 0.77 to 0.97 for birds, for models based on different definitions of spatial structures. According to the Akaike Information Criterion (AIC), the best autoregressive model was obtained by using the rook connection. In general, these results furnish guidelines for future modelling of species richness patterns in relation to environmental predictors and other variables expressing human occupation in the biome.

Age, state, environment, and season dependence of senescence in body mass.

PubMed

Kroeger, Svenja B; Blumstein, Daniel T; Armitage, Kenneth B; Reid, Jane M; Martin, Julien G A

2018-02-01

Senescence is a highly variable process that comprises both age-dependent and state-dependent components and can be greatly affected by environmental conditions. However, few studies have quantified the magnitude of age-dependent and state-dependent senescence in key life-history traits across individuals inhabiting different spatially structured and seasonal environments. We used longitudinal data from wild female yellow-bellied marmots ( Marmota flaviventer ), living in two adjacent environments that differ in elevation and associated phenology, to quantify how age and individual state, measured as "time to death," affect body mass senescence in different environments. Further, we quantified how patterns of senescence differed between two biologically distinct seasons, spring, and late summer. Body mass senescence had an age-dependent component, expressed as a decrease in mass in old age. Overall, estimated age-dependent senescence was greater in females living in the more favorable lower elevation environment, than in the harsher higher elevation environment, and greater in late summer than in spring. Body mass senescence also had a state-dependent component, captured by effects of time to death, but only in the more favorable lower elevation environment. In spring, body mass gradually decreased from 2 years before death, whereas in late summer, state-dependent effects were expressed as a terminal decrease in body mass in the last year of life. Contrary to expectations, we found that senescence was more likely to be observed under more favorable environmental conditions, rather than under harsher conditions. By further demonstrating that senescence patterns differ among seasons, our results imply that within-year temporal environmental variation must be considered alongside spatial environmental variation in order to characterize and understand the pattern and magnitude of senescence in wild populations.

Discovering biclusters in gene expression data based on high-dimensional linear geometries

PubMed Central

Gan, Xiangchao; Liew, Alan Wee-Chung; Yan, Hong

2008-01-01

Background In DNA microarray experiments, discovering groups of genes that share similar transcriptional characteristics is instrumental in functional annotation, tissue classification and motif identification. However, in many situations a subset of genes only exhibits consistent pattern over a subset of conditions. Conventional clustering algorithms that deal with the entire row or column in an expression matrix would therefore fail to detect these useful patterns in the data. Recently, biclustering has been proposed to detect a subset of genes exhibiting consistent pattern over a subset of conditions. However, most existing biclustering algorithms are based on searching for sub-matrices within a data matrix by optimizing certain heuristically defined merit functions. Moreover, most of these algorithms can only detect a restricted set of bicluster patterns. Results In this paper, we present a novel geometric perspective for the biclustering problem. The biclustering process is interpreted as the detection of linear geometries in a high dimensional data space. Such a new perspective views biclusters with different patterns as hyperplanes in a high dimensional space, and allows us to handle different types of linear patterns simultaneously by matching a specific set of linear geometries. This geometric viewpoint also inspires us to propose a generic bicluster pattern, i.e. the linear coherent model that unifies the seemingly incompatible additive and multiplicative bicluster models. As a particular realization of our framework, we have implemented a Hough transform-based hyperplane detection algorithm. The experimental results on human lymphoma gene expression dataset show that our algorithm can find biologically significant subsets of genes. Conclusion We have proposed a novel geometric interpretation of the biclustering problem. We have shown that many common types of bicluster are just different spatial arrangements of hyperplanes in a high dimensional data space. An implementation of the geometric framework using the Fast Hough transform for hyperplane detection can be used to discover biologically significant subsets of genes under subsets of conditions for microarray data analysis. PMID:18433477

Travelling and splitting of a wave of hedgehog expression involved in spider-head segmentation.

PubMed

Kanayama, Masaki; Akiyama-Oda, Yasuko; Nishimura, Osamu; Tarui, Hiroshi; Agata, Kiyokazu; Oda, Hiroki

2011-10-11

During development segmentation is a process that generates a spatial periodic pattern. Peak splitting of waves of gene expression is a mathematically predicted, simple strategy accounting for this type of process, but it has not been well characterized biologically. Here we show temporally repeated splitting of gene expression into stripes that is associated with head axis growth in the spider Achaearanea embryo. Preceding segmentation, a wave of hedgehog homologue gene expression is observed to travel posteriorly during development stage 6. This stripe, co-expressing an orthodenticle homologue, undergoes two cycles of splitting and shifting accompanied by convergent extension, serving as a generative zone for the head segments. The two orthodenticle and odd-paired homologues are identified as targets of Hedgehog signalling, and evidence suggests that their activities mediate feedback to maintain the head generative zone and to promote stripe splitting in this zone. We propose that the 'stripe-splitting' strategy employs genetic components shared with Drosophila blastoderm subdivision, which are required for participation in an autoregulatory signalling network.

Mosaic expression of claudins in thick ascending limbs of Henle results in spatial separation of paracellular Na+ and Mg2+ transport

PubMed Central

Wulfmeyer, Vera Christine; Drewell, Hoora; Mutig, Kerim; Hou, Jianghui; Breiderhoff, Tilman; Müller, Dominik; Fromm, Michael; Bleich, Markus; Günzel, Dorothee

2017-01-01

The thick ascending limb (TAL) of Henle’s loop drives paracellular Na+, Ca2+, and Mg2+ reabsorption via the tight junction (TJ). The TJ is composed of claudins that consist of four transmembrane segments, two extracellular segments (ECS1 and -2), and one intracellular loop. Claudins interact within the same (cis) and opposing (trans) plasma membranes. The claudins Cldn10b, -16, and -19 facilitate cation reabsorption in the TAL, and their absence leads to a severe disturbance of renal ion homeostasis. We combined electrophysiological measurements on microperfused mouse TAL segments with subsequent analysis of claudin expression by immunostaining and confocal microscopy. Claudin interaction properties were examined using heterologous expression in the TJ-free cell line HEK 293, live-cell imaging, and Förster/FRET. To reveal determinants of interaction properties, a set of TAL claudin protein chimeras was created and analyzed. Our main findings are that (i) TAL TJs show a mosaic expression pattern of either cldn10b or cldn3/cldn16/cldn19 in a complex; (ii) TJs dominated by cldn10b prefer Na+ over Mg2+, whereas TJs dominated by cldn16 favor Mg2+ over Na+; (iii) cldn10b does not interact with other TAL claudins, whereas cldn3 and cldn16 can interact with cldn19 to form joint strands; and (iv) further claudin segments in addition to ECS2 are crucial for trans interaction. We suggest the existence of at least two spatially distinct types of paracellular channels in TAL: a cldn10b-based channel for monovalent cations such as Na+ and a spatially distinct site for reabsorption of divalent cations such as Ca2+ and Mg2+. PMID:28028216

Tree species exhibit complex patterns of distribution in bottomland hardwood forests

Treesearch

Luben D Dimov; Jim L Chambers; Brian R. Lockhart

2013-01-01

& Context Understanding tree interactions requires an insight into their spatial distribution. & Aims We looked for presence and extent of tree intraspecific spatial point pattern (random, aggregated, or overdispersed) and interspecific spatial point pattern (independent, aggregated, or segregated). & Methods We established twelve 0.64-ha plots in natural...

Spatial image modulation to improve performance of computed tomography imaging spectrometer

NASA Technical Reports Server (NTRS)

Bearman, Gregory H. (Inventor); Wilson, Daniel W. (Inventor); Johnson, William R. (Inventor)

2010-01-01

Computed tomography imaging spectrometers ("CTIS"s) having patterns for imposing spatial structure are provided. The pattern may be imposed either directly on the object scene being imaged or at the field stop aperture. The use of the pattern improves the accuracy of the captured spatial and spectral information.

Mapping the bycatch seascape: multispecies and multi-scale spatial patterns of fisheries bycatch.

PubMed

Lewison, Rebecca L; Soykan, Candan U; Franklin, Janet

2009-06-01

Fisheries bycatch is a worldwide conservation issue. Despite a growing awareness of bycatch problems in particular ocean regions, there have been few efforts to identify spatial patterns in bycatch events. Furthermore, many studies of fisheries bycatch have been myopic, focusing on a single species or a single region. Using a range of analytical approaches to identify spatial patterns in bycatch data, we demonstrate the utility and applications of area and point pattern analyses to single and multispecies bycatch seascapes of pelagic longline fisheries in the Atlantic and Pacific Oceans. We find clear evidence of spatial clustering within bycatch species in both ocean basins, both in terms of the underlying pattern of the locations of bycatch events relative to fishing locations and for areas of high bycatch rates. Furthermore, we find significant spatial overlap in the pattern of bycatch across species relative to the spatial distribution in fishing effort and target catch. These results point to the importance of considering spatial patterns of both single and multispecies bycatch to meet the ultimate goal of reducing bycatch encounters. These analyses also highlight the importance of considering bycatch relative to target catch as a way of identifying areas where fishing effort reduction may help to reduce multispecies bycatch with minimal impact on target catch.

Development, survival and fitness performance of Helicoverpa zea (Lepidoptera: Noctuidae) in MON810 Bt field corn.

PubMed

Horner, T A; Dively, G P; Herbert, D A

2003-06-01

Helicoverpa zea (Boddie) development, survival, and feeding injury in MON810 transgenic ears of field corn (Zea mays L.) expressing Bacillus thuringiensis variety kurstaki (Bt) Cry1Ab endotoxins were compared with non-Bt ears at four geographic locations over two growing seasons. Expression of Cry1Ab endotoxin resulted in overall reductions in the percentage of damaged ears by 33% and in the amount of kernels consumed by 60%. Bt-induced effects varied significantly among locations, partly because of the overall level and timing of H. zea infestations, condition of silk tissue at the time of egg hatch, and the possible effects of plant stress. Larvae feeding on Bt ears produced scattered, discontinuous patches of partially consumed kernels, which were arranged more linearly than the compact feeding patterns in non-Bt ears. The feeding patterns suggest that larvae in Bt ears are moving about sampling kernels more frequently than larvae in non-Bt ears. Because not all kernels express the same level of endotoxin, the spatial heterogeneity of toxin distribution within Bt ears may provide an opportunity for development of behavioral responses in H. zea to avoid toxin. MON810 corn suppressed the establishment and development of H. zea to late instars by at least 75%. This level of control is considered a moderate dose, which may increase the risk of resistance development in areas where MON810 corn is widely adopted and H. zea overwinters successfully. Sublethal effects of MON810 corn resulted in prolonged larval and prepupal development, smaller pupae, and reduced fecundity of H. zea. The moderate dose effects and the spatial heterogeneity of toxin distribution among kernels could increase the additive genetic variance for both physiological and behavioral resistance in H. zea populations. Implications of localized population suppression are discussed.

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice.

PubMed

Dong, Qianli; Li, Ning; Li, Xiaochong; Yuan, Zan; Xie, Dejian; Wang, Xiaofei; Li, Jianing; Yu, Yanan; Wang, Jinbin; Ding, Baoxu; Zhang, Zhibin; Li, Changping; Bian, Yao; Zhang, Ai; Wu, Ying; Liu, Bao; Gong, Lei

2018-06-01

The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants. © 2018 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Exploring the Role of Spatial Frequency Information during Neural Emotion Processing in Human Infants.

PubMed

Jessen, Sarah; Grossmann, Tobias

2017-01-01

Enhanced attention to fear expressions in adults is primarily driven by information from low as opposed to high spatial frequencies contained in faces. However, little is known about the role of spatial frequency information in emotion processing during infancy. In the present study, we examined the role of low compared to high spatial frequencies in the processing of happy and fearful facial expressions by using filtered face stimuli and measuring event-related brain potentials (ERPs) in 7-month-old infants ( N = 26). Our results revealed that infants' brains discriminated between emotional facial expressions containing high but not between expressions containing low spatial frequencies. Specifically, happy faces containing high spatial frequencies elicited a smaller Nc amplitude than fearful faces containing high spatial frequencies and happy and fearful faces containing low spatial frequencies. Our results demonstrate that already in infancy spatial frequency content influences the processing of facial emotions. Furthermore, we observed that fearful facial expressions elicited a comparable Nc response for high and low spatial frequencies, suggesting a robust detection of fearful faces irrespective of spatial frequency content, whereas the detection of happy facial expressions was contingent upon frequency content. In summary, these data provide new insights into the neural processing of facial emotions in early development by highlighting the differential role played by spatial frequencies in the detection of fear and happiness.

Sense and antisense transcripts of the developmentally regulated murine hsp70.2 gene are expressed in distinct and only partially overlapping areas in the adult brain

NASA Technical Reports Server (NTRS)

Murashov, A. K.; Wolgemuth, D. J.

1996-01-01

We have examined the spatial pattern of expression of a member of the hsp70 gene family, hsp70.2, in the mouse central nervous system. Surprisingly, RNA blot analysis and in situ hybridization revealed abundant expression of an 'antisense' hsp70.2 transcript in several areas of adult mouse brain. Two different transcripts recognized by sense and antisense riboprobes for the hsp70.2 gene were expressed in distinct and only partially overlapping neuronal populations. RNA blot analysis revealed low levels of the 2.7 kb transcript of hsp70.2 in several areas of the brain, with highest signal in the hippocampus. Abundant expression of a slightly larger (approximately 2.8 kb) 'antisense' transcript was detected in several brain regions, notably in the brainstem, cerebellum, mesencephalic tectum, thalamus, cortex, and hippocampus. In situ hybridization revealed that the sense and antisense transcripts were both predominantly neuronal and localized to the same cell types in the granular layer of the cerebellum, trapezoid nucleus of the superior olivary complex, locus coeruleus and hippocampus. The hsp70.2 antisense transcripts were particularly abundant in the frontal cortex, dentate gyrus, subthalamic nucleus, zona incerta, superior and inferior colliculi, central gray, brainstem, and cerebellar Purkinje cells. Our findings have revealed a distinct cellular and spatial localization of both sense and antisense transcripts, demonstrating a new level of complexity in the function of the heat shock genes.

Developmental expression and function analysis of protein tyrosine phosphatase receptor type D in oligodendrocyte myelination

PubMed Central

Zhu, Qiang; Tan, Zhou; Zhao, Shufang; Huang, Hao; Zhao, Xiaofeng; Hu, Xuemei; Zhang, Yiping; Shields, Christopher B; Uetani, Noriko; Qiu, Mengsheng

2015-01-01

Receptor protein tyrosine phosphatases (RPTPs) are extensively expressed in the central nervous system (CNS), and have distinct spatial and temporal patterns in different cell types during development. Previous studies have demonstrated possible roles for RPTPs in axon outgrowth, guidance, and synaptogenesis. In the present study, our results revealed that protein tyrosine phosphatase, receptor type D (PTPRD) was initially expressed in mature neurons in embryonic CNS, and later in oligodendroglial cells at postnatal stages when oligodendrocyte undergo active axonal myelination process. In PTPRD mutants, oligodendrocyte differentiation was normal and a transient myelination delay occurred at early postnatal stages, indicating the contribution of PTPRD to the initiation of axonal myelination. Our results also showed that the remyelination process was not affected in the absence of PTPRD function after a cuprizone-induced demyelination in adult animals. PMID:26341907

Oxytocin receptor density is associated with male mating tactics and social monogamy.

PubMed

Ophir, Alexander G; Gessel, Ana; Zheng, Da-Jiang; Phelps, Steven M

2012-03-01

Despite its well-described role in female affiliation, the influence of oxytocin on male pairbonding is largely unknown. However, recent human studies indicate that this nonapeptide has a potent influence on male behaviors commonly associated with monogamy. Here we investigated the distribution of oxytocin receptors (OTR) throughout the forebrain of the socially monogamous male prairie vole (Microtus ochrogaster). Because males vary in both sexual and spatial fidelity, we explored the extent to which OTR predicted monogamous or non-monogamous patterns of space use, mating success and sexual fidelity in free-living males. We found that monogamous males expressed higher OTR density in the nucleus accumbens than non-monogamous males, a result that mirrors species differences in voles with different mating systems. OTR density in the posterior portion of the insula predicted mating success. Finally, OTR in the hippocampus and septohippocampal nucleus, which are nuclei associated with spatial memory, predicted patterns of space use and reproductive success within mating tactics. Our data highlight the importance of oxytocin receptor in neural structures associated with pairbonding and socio-spatial memory in male mating tactics. The role of memory in mating systems is often neglected, despite the fact that mating tactics impose an inherently spatial challenge for animals. Identifying mechanisms responsible for relating information about the social world with mechanisms mediating pairbonding and mating tactics is crucial to fully appreciate the suite of factors driving mating systems. This article is part of a Special Issue entitled Oxytocin, Vasopressin, and Social Behavior. Published by Elsevier Inc.

[Spatial point patterns of Antarctic krill fishery in the northern Antarctic Peninsula].

PubMed

Yang, Xiao Ming; Li, Yi Xin; Zhu, Guo Ping

2016-12-01

As a key species in the Antarctic ecosystem, the spatial distribution of Antarctic krill (thereafter krill) often tends to present aggregation characteristics, which therefore reflects the spatial patterns of krill fishing operation. Based on the fishing data collected from Chinese krill fishing vessels, of which vessel A was professional krill fishing vessel and Vessel B was a fishing vessel which shifted between Chilean jack mackerel (Trachurus murphyi) fishing ground and krill fishing ground. In order to explore the characteristics of spatial distribution pattern and their ecological effects of two obvious different fishing fleets under a high and low nominal catch per unit effort (CPUE), from the viewpoint of spatial point pattern, the present study analyzed the spatial distribution characteristics of krill fishery in the northern Antarctic Peninsula from three aspects: (1) the two vessels' point pattern characteristics of higher CPUEs and lower CPUEs at different scales; (2) correlation of the bivariate point patterns between these points of higher CPUE and lower CPUE; and (3) correlation patterns of CPUE. Under the analysis derived from the Ripley's L function and mark correlation function, the results showed that the point patterns of the higher/lo-wer catch available were similar, both showing an aggregation distribution in this study windows at all scale levels. The aggregation intensity of krill fishing was nearly maximum at 15 km spatial scale, and kept stably higher values at the scale of 15-50 km. The aggregation intensity of krill fishery point patterns could be described in order as higher CPUE of vessel A > lower CPUE of vessel B >higher CPUE of vessel B > higher CPUE of vessel B. The relationship of the higher and lo-wer CPUEs of vessel A showed positive correlation at the spatial scale of 0-75 km, and presented stochastic relationship after 75 km scale, whereas vessel B showed positive correlation at all spatial scales. The point events of higher and lower CPUEs were synchronized, showing significant correlations at most of spatial scales because of the dynamics nature and complex of krill aggregation patterns. The distribution of vessel A's CPUEs was positively correlated at scales of 0-44 km, but negatively correlated at the scales of 44-80 km. The distribution of vessel B's CPUEs was negatively correlated at the scales of 50-70 km, but no significant correlations were found at other scales. The CPUE mark point patterns showed a negative correlation, which indicated that intraspecific competition for space and prey was significant. There were significant differences in spatial point pattern distribution between vessel A with higher fishing capacity and vessel B with lower fishing capacity. The results showed that the professional krill fishing vessel is suitable to conduct the analysis of spatial point pattern and scientific fishery survey.

A rapidly evolving secretome builds and patterns a sea shell

PubMed Central

Jackson, Daniel J; McDougall, Carmel; Green, Kathryn; Simpson, Fiona; Wörheide, Gert; Degnan, Bernard M

2006-01-01

Background Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. Conclusion The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells. PMID:17121673

Molecular cloning and expression of nanos in the Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae).

PubMed

Ogaugwu, Christian E; Wimmer, Ernst A

2013-01-01

The gene nanos (nos) is a maternal-effect gene that plays an important role in posterior patterning and germ cell development in early stage embryos. nos is known from several diverse insect species, but has so far not been described for any Tephritid fruit fly. Here, we report the molecular cloning and expression pattern of the nos orthologous gene, Ccnos, in the Mediterranean fruit fly Ceratitis capitata, which is a destructive pest of high agricultural importance. CcNOS contains 398 amino acids and has a C-terminal region with two conserved CCHC zinc-binding motifs known to be essential for NOS function. Transcripts of Ccnos were confirmed by in situ hybridization to be maternally-derived and localized to the posterior pole of early stage embryos. Regulatory regions of nos have been employed in genetic engineering in some dipterans such as Drosophila and mosquitoes. Given the similarity in spatial and temporal expression between Ccnos and nos orthologs from other dipterans, its regulatory regions will be valuable to generate additional genetic tools that can be applied for engineering purposes to improve the fight against this devastating pest. Copyright © 2013 Elsevier B.V. All rights reserved.

FracPaQ: a MATLAB™ toolbox for the quantification of fracture patterns

NASA Astrophysics Data System (ADS)

Healy, David; Rizzo, Roberto; Farrell, Natalie; Watkins, Hannah; Cornwell, David; Gomez-Rivas, Enrique; Timms, Nick

2017-04-01

The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, shapes and spatial distributions often exhibit some kind of order. In detail, there may be relationships among the different fracture attributes e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture patterns and fracture attributes. This presentation describes an open source toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales. Our current focus for the application of the software is on quantifying crack and fracture patterns in and around fault zones. There is a large body of published work on the quantification of relatively simple joint patterns, but fault zones present a bigger, and arguably more important, challenge. The methods presented are inherently scale independent, and a key task will be to analyse and integrate quantitative fracture pattern data from micro- to macro-scales. New features in this release include multi-scale analyses based on a wavelet method to look for scale transitions, support for multi-colour traces in the input file processed as separate fracture sets, and combining fracture traces from multiple 2-D images to derive the statistically equivalent 3-D fracture pattern expressed as a 2nd rank crack tensor.

Wnt5 and Drl/Ryk Gradients Pattern the Drosophila Olfactory Dendritic Map

PubMed Central

Wu, Yuping; Helt, Jay-Christian; Wexler, Emily; Petrova, Iveta M.; Noordermeer, Jasprina N.; Fradkin, Lee G.

2014-01-01

During development, dendrites migrate to their correct locations in response to environmental cues. The mechanisms of dendritic guidance are poorly understood. Recent work has shown that the Drosophila olfactory map is initially formed by the spatial segregation of the projection neuron (PN) dendrites in the developing antennal lobe (AL). We report here that between 16 and 30 h after puparium formation, the PN dendrites undergo dramatic rotational reordering to achieve their final glomerular positions. During this period, a novel set of AL-extrinsic neurons express high levels of the Wnt5 protein and are tightly associated with the dorsolateral edge of the AL. Wnt5 forms a dorsolateral-high to ventromedial-low pattern in the antennal lobe neuropil. Loss of Wnt5 prevents the ventral targeting of the dendrites, whereas Wnt5 overexpression disrupts dendritic patterning. We find that Drl/Ryk, a known Wnt5 receptor, is expressed in a dorsolateral-to-ventromedial (DL > VM) gradient by the PN dendrites. Loss of Drl in the PNs results in the aberrant ventromedial targeting of the dendrites, a defect that is suppressed by reduction in Wnt5 gene dosage. Conversely, overexpression of Drl in the PNs results in the dorsolateral targeting of their dendrites, an effect that requires Drl's cytoplasmic domain. We propose that Wnt5 acts as a repulsive guidance cue for the PN dendrites, whereas Drl signaling in the dendrites inhibits Wnt5 signaling. In this way, the precise expression patterns of Wnt5 and Drl orient the PN dendrites allowing them to target their final glomerular positions. PMID:25378162

Crop yield response to climate change varies with crop spatial distribution pattern

DOE PAGES

Leng, Guoyong; Huang, Maoyi

2017-05-03

The linkage between crop yield and climate variability has been confirmed in numerous studies using statistical approaches. A crucial assumption in these studies is that crop spatial distribution pattern is constant over time. Here, we explore how changes in county-level corn spatial distribution pattern modulate the response of its yields to climate change at the state level over the Contiguous United States. Our results show that corn yield response to climate change varies with crop spatial distribution pattern, with distinct impacts on the magnitude and even the direction at the state level. Corn yield is predicted to decrease by 20~40%more » by 2050s when considering crop spatial distribution pattern changes, which is 6~12% less than the estimates with fixed cropping pattern. The beneficial effects are mainly achieved by reducing the negative impacts of daily maximum temperature and strengthening the positive impacts of precipitation. Our results indicate that previous empirical studies could be biased in assessing climate change impacts by ignoring the changes in crop spatial distribution pattern. As a result, this has great implications for understanding the increasing debates on whether climate change will be a net gain or loss for regional agriculture.« less

Crop yield response to climate change varies with crop spatial distribution pattern

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leng, Guoyong; Huang, Maoyi

The linkage between crop yield and climate variability has been confirmed in numerous studies using statistical approaches. A crucial assumption in these studies is that crop spatial distribution pattern is constant over time. Here, we explore how changes in county-level corn spatial distribution pattern modulate the response of its yields to climate change at the state level over the Contiguous United States. Our results show that corn yield response to climate change varies with crop spatial distribution pattern, with distinct impacts on the magnitude and even the direction at the state level. Corn yield is predicted to decrease by 20~40%more » by 2050s when considering crop spatial distribution pattern changes, which is 6~12% less than the estimates with fixed cropping pattern. The beneficial effects are mainly achieved by reducing the negative impacts of daily maximum temperature and strengthening the positive impacts of precipitation. Our results indicate that previous empirical studies could be biased in assessing climate change impacts by ignoring the changes in crop spatial distribution pattern. As a result, this has great implications for understanding the increasing debates on whether climate change will be a net gain or loss for regional agriculture.« less

Large-area imaging reveals biologically driven non-random spatial patterns of corals at a remote reef

NASA Astrophysics Data System (ADS)

Edwards, Clinton B.; Eynaud, Yoan; Williams, Gareth J.; Pedersen, Nicole E.; Zgliczynski, Brian J.; Gleason, Arthur C. R.; Smith, Jennifer E.; Sandin, Stuart A.

2017-12-01

For sessile organisms such as reef-building corals, differences in the degree of dispersion of individuals across a landscape may result from important differences in life-history strategies or may reflect patterns of habitat availability. Descriptions of spatial patterns can thus be useful not only for the identification of key biological and physical mechanisms structuring an ecosystem, but also by providing the data necessary to generate and test ecological theory. Here, we used an in situ imaging technique to create large-area photomosaics of 16 plots at Palmyra Atoll, central Pacific, each covering 100 m2 of benthic habitat. We mapped the location of 44,008 coral colonies and identified each to the lowest taxonomic level possible. Using metrics of spatial dispersion, we tested for departures from spatial randomness. We also used targeted model fitting to explore candidate processes leading to differences in spatial patterns among taxa. Most taxa were clustered and the degree of clustering varied by taxon. A small number of taxa did not significantly depart from randomness and none revealed evidence of spatial uniformity. Importantly, taxa that readily fragment or tolerate stress through partial mortality were more clustered. With little exception, clustering patterns were consistent with models of fragmentation and dispersal limitation. In some taxa, dispersion was linearly related to abundance, suggesting density dependence of spatial patterning. The spatial patterns of stony corals are non-random and reflect fundamental life-history characteristics of the taxa, suggesting that the reef landscape may, in many cases, have important elements of spatial predictability.

Gene expression patterns and dynamics of the colonization of common bean (Phaseolus vulgaris L.) by highly virulent and weakly virulent strains of Fusarium oxysporum

PubMed Central

Niño-Sánchez, Jonathan; Tello, Vega; Casado-del Castillo, Virginia; Thon, Michael R.; Benito, Ernesto P.; Díaz-Mínguez, José María

2015-01-01

The dynamics of root and hypocotyl colonization, and the gene expression patterns of several fungal virulence factors and plant defense factors have been analyzed and compared in the interaction of two Fusarium oxysporum f. sp. phaseoli strains displaying clear differences in virulence, with a susceptible common bean cultivar. The growth of the two strains on the root surface and the colonization of the root was quantitatively similar although the highly virulent (HV) strain was more efficient reaching the central root cylinder. The main differences between both strains were found in the temporal and spatial dynamics of crown root and hypocotyl colonization. The increase of fungal biomass in the crown root was considerably larger for the HV strain, which, after an initial stage of global colonization of both the vascular cylinder and the parenchymal cells, restricted its growth to the newly differentiated xylem vessels. The weakly virulent (WV) strain was a much slower and less efficient colonizer of the xylem vessels, showing also growth in the intercellular spaces of the parenchyma. Most of the virulence genes analyzed showed similar expression patterns in both strains, except SIX1, SIX6 and the gene encoding the transcription factor FTF1, which were highly upregulated in root crown and hypocotyl. The response induced in the infected plant showed interesting differences for both strains. The WV strain induced an early and strong transcription of the PR1 gene, involved in SAR response, while the HV strain preferentially induced the early expression of the ethylene responsive factor ERF2. PMID:25883592

Identification and expression analysis of zebrafish polypeptide α-N-acetylgalactosaminyltransferase Y-subfamily genes during embryonic development.

PubMed

Nakayama, Yoshiaki; Nakamura, Naosuke; Kawai, Tamiko; Kaneda, Eiichi; Takahashi, Yui; Miyake, Ayumi; Itoh, Nobuyuki; Kurosaka, Akira

2014-09-01

Mucin-type glycosylation is one of the most common posttranslational modifications of secretory and membrane proteins and has diverse physiological functions. The initial biosynthesis of mucin-type carbohydrates is catalyzed by UDP-GalNAc: polypeptide α-N-acetylgalactosaminyltransferases (GalNAc-Ts) encoded by GALNT genes. Among these, GalNAc-T8, -T9, -T17, and -T18 form a characteristic subfamily called "Y-subfamily" and have no or very low in vitro transferase activities when assayed with typical mucin peptides as acceptor substrates. Although the Y-subfamily isozymes have been reported to be possibly involved in various diseases, their in vivo functions have not been reported. Here, we isolated zebrafish Y-subfamily galnt genes, and determined their spatial and temporal expressions during the early development of zebrafish. Our study demonstrated that all the Y-subfamily isozymes were well conserved in zebrafish with GalNAc-T18 having two orthologs, galnt18a and galnt18b, and with the other three isozymes each having a corresponding ortholog, galnt8, galnt9, and galnt17. The galnt8 was expressed in the cephalic mesoderm and hatching gland during early developmental stages, and differently expressed in the head, somatic muscles, and liver in the later stages. The other three orthologs also exhibited the characteristic expression patterns, although their expressions were generally strong in the nervous systems. In addition to the expression in the brain, galnt17 and galnt18a were expressed in the somitic muscles, and galnt18a and galnt18b in the notochord. These expression patterns may contribute to the functional analysis of the Y-subfamily, whose physiological roles still remain to be elucidated. Copyright © 2014 Elsevier B.V. All rights reserved.

Spatial patterns of development drive water use

Treesearch

G. M. Sanchez; J. W. Smith; A. Terando; G. Sun; R. K. Meentemeyer

2018-01-01

Water availability is becoming more uncertain as human populations grow, cities expand into rural regions and the climate changes. In this study, we examine the functional relationship between water use and the spatial patterns of developed land across the rapidly growing region of the southeastern United States. We quantified the spatial pattern of developed land...

Visually Guided Avoidance in the Chameleon (Chamaeleo chameleon): Response Patterns and Lateralization

PubMed Central

Lustig, Avichai; Ketter-Katz, Hadas; Katzir, Gadi

2012-01-01

The common chameleon, Chamaeleo chameleon, is an arboreal lizard with highly independent, large-amplitude eye movements. In response to a moving threat, a chameleon on a perch responds with distinct avoidance movements that are expressed in its continuous positioning on the side of the perch distal to the threat. We analyzed body-exposure patterns during threat avoidance for evidence of lateralization, that is, asymmetry at the functional/behavioral levels. Chameleons were exposed to a threat approaching horizontally from the left or right, as they held onto a vertical pole that was either wider or narrower than the width of their head, providing, respectively, monocular or binocular viewing of the threat. We found two equal-sized sub-groups, each displaying lateralization of motor responses to a given direction of stimulus approach. Such an anti-symmetrical distribution of lateralization in a population may be indicative of situations in which organisms are regularly exposed to crucial stimuli from all spatial directions. This is because a bimodal distribution of responses to threat in a natural population will reduce the spatial advantage of predators. PMID:22685546

Visually guided avoidance in the chameleon (Chamaeleo chameleon): response patterns and lateralization.

PubMed

Lustig, Avichai; Ketter-Katz, Hadas; Katzir, Gadi

2012-01-01

The common chameleon, Chamaeleo chameleon, is an arboreal lizard with highly independent, large-amplitude eye movements. In response to a moving threat, a chameleon on a perch responds with distinct avoidance movements that are expressed in its continuous positioning on the side of the perch distal to the threat. We analyzed body-exposure patterns during threat avoidance for evidence of lateralization, that is, asymmetry at the functional/behavioral levels. Chameleons were exposed to a threat approaching horizontally from the left or right, as they held onto a vertical pole that was either wider or narrower than the width of their head, providing, respectively, monocular or binocular viewing of the threat. We found two equal-sized sub-groups, each displaying lateralization of motor responses to a given direction of stimulus approach. Such an anti-symmetrical distribution of lateralization in a population may be indicative of situations in which organisms are regularly exposed to crucial stimuli from all spatial directions. This is because a bimodal distribution of responses to threat in a natural population will reduce the spatial advantage of predators.

Nonlinear periodic wavetrains in thin liquid films falling on a uniformly heated horizontal plate

NASA Astrophysics Data System (ADS)

Issokolo, Remi J. Noumana; Dikandé, Alain M.

2018-05-01

A thin liquid film falling on a uniformly heated horizontal plate spreads into fingering ripples that can display a complex dynamics ranging from continuous waves, nonlinear spatially localized periodic wave patterns (i.e., rivulet structures) to modulated nonlinear wavetrain structures. Some of these structures have been observed experimentally; however, conditions under which they form are still not well understood. In this work, we examine profiles of nonlinear wave patterns formed by a thin liquid film falling on a uniformly heated horizontal plate. For this purpose, the Benney model is considered assuming a uniform temperature distribution along the film propagation on the horizontal surface. It is shown that for strong surface tension but a relatively small Biot number, spatially localized periodic-wave structures can be analytically obtained by solving the governing equation under appropriate conditions. In the regime of weak nonlinearity, a multiple-scale expansion combined with the reductive perturbation method leads to a complex Ginzburg-Landau equation: the solutions of which are modulated periodic pulse trains which amplitude and width and period are expressed in terms of characteristic parameters of the model.

Memory under pressure: secondary-task effects on contextual cueing of visual search.

PubMed

Annac, Efsun; Manginelli, Angela A; Pollmann, Stefan; Shi, Zhuanghua; Müller, Hermann J; Geyer, Thomas

2013-11-04

Repeated display configurations improve visual search. Recently, the question has arisen whether this contextual cueing effect (Chun & Jiang, 1998) is itself mediated by attention, both in terms of selectivity and processing resources deployed. While it is accepted that selective attention modulates contextual cueing (Jiang & Leung, 2005), there is an ongoing debate whether the cueing effect is affected by a secondary working memory (WM) task, specifically at which stage WM influences the cueing effect: the acquisition of configural associations (e.g., Travis, Mattingley, & Dux, 2013) versus the expression of learned associations (e.g., Manginelli, Langer, Klose, & Pollmann, 2013). The present study re-investigated this issue. Observers performed a visual search in combination with a spatial WM task. The latter was applied on either early or late search trials--so as to examine whether WM load hampers the acquisition of or retrieval from contextual memory. Additionally, the WM and search tasks were performed either temporally in parallel or in succession--so as to permit the effects of spatial WM load to be dissociated from those of executive load. The secondary WM task was found to affect cueing in late, but not early, experimental trials--though only when the search and WM tasks were performed in parallel. This pattern suggests that contextual cueing involves a spatial WM resource, with spatial WM providing a workspace linking the current search array with configural long-term memory; as a result, occupying this workspace by a secondary WM task hampers the expression of learned configural associations.

Behavioral states may be associated with distinct spatial patterns in electrocorticogram.

PubMed

Panagiotides, Heracles; Freeman, Walter J; Holmes, Mark D; Pantazis, Dimitrios

2011-03-01

To determine if behavioral states are associated with unique spatial electrocorticographic (ECoG) patterns, we obtained recordings with a microgrid electrode array applied to the cortical surface of a human subject. The array was constructed with the intent of extracting maximal spatial information by optimizing interelectrode distances. A 34-year-old patient with intractable epilepsy underwent intracranial ECoG monitoring after standard methods failed to reveal localization of seizures. During the 8-day period of invasive recording, in addition to standard clinical electrodes a square 1 × 1 cm microgrid array with 64 electrodes (1.25 mm separation) was placed on the right inferior temporal gyrus. Careful review of video recordings identified four extended naturalistic behaviors: reading, conversing on the telephone, looking at photographs, and face-to-face interactions. ECoG activity recorded with the microgrid that corresponded to these behaviors was collected and ECoG spatial patterns were analyzed. During periods of ECoG selected for analysis, no electrographic seizures or epileptiform patterns were present. Moments of maximal spatial variance are shown to cluster by behavior. Comparisons between conditions using a permutation test reveal significantly different spatial patterns for each behavior. We conclude that ECoG recordings obtained on the cortical surface with optimal high spatial frequency resolution reveal distinct local spatial patterns that reflect different behavioral states, and we predict that similar patterns will be found in many if not most cortical areas on which a microgrid is placed.

Seed-Specific Stable Expression of the α-AI1 Inhibitor in Coffee Grains and the In Vivo Implications for the Development of the Coffee Berry Borer.

PubMed

Albuquerque, Érika V S; Bezerra, Caroline A; Romero, Juan V; Valencia, Jorge W A; Valencia-Jiménez, Arnubio; Pimenta, Lucas M; Barbosa, Aulus E A D; Silva, Maria C M; Meneguim, Ana M; Sá, Maria Eugênia L; Engler, Gilbert; de Almeida-Engler, Janice; Fernandez, Diana; Grossi-de-Sá, Maria F

Genetic transformation of coffee ( Coffea spp.), the second most traded commodity worldwide, is an alternative approach to introducing features that cannot be introgressed by traditional crossings. The transgenic stability, heritability and quantitative and spatial expression patterns of the seed-specific promoter phytohemagglutinin (PHA-L) from Phaseolus vulgaris were characterized in genetically modified C. arabica expressing the α-amylase inhibitor-1 ( α-AI1 ) gene. The α-AI1 inhibitor shows considerable activity toward digestive enzymes of the coffee berry borer (CBB) Hypothenemus hampei . This insect pest expends its life cycle almost entirely in coffee berries. Transgene containment in the fruit is important to meeting food and environmental safety requirements for releasing genetically modified (GM) crops. PCR analysis of T2 coffee plants showed a Mendelian single-copy segregation pattern. Ectopic transgene expression was only detected in coffee grains, as demonstrated by reverse transcription-PCR analysis of different plant tissues. An intense immunocytochemical signal associated with α-AI1 protein expression was localized to endospermic cells. In addition, a delay in the larval development of CBB was observed after challenging transgenic coffee seeds with the insect. These results indicate that the PHA-L promoter might be a useful tool in coffee for the seed-specific expression of genes related to coffee bean productivity, quality and pest protection. The biotechnological applicability of the α-AI1 gene for controlling CBB is also discussed. This work is the first report showing a seed-specific transgene expression in coffee plants.

Temporal consistency of spatial pattern in growth of the mussel, Mytilus edulis: Implications for predictive modelling

NASA Astrophysics Data System (ADS)

Bergström, Per; Lindegarth, Susanne; Lindegarth, Mats

2013-10-01

Human pressures on coastal seas are increasing and methods for sustainable management, including spatial planning and mitigative actions, are therefore needed. In coastal areas worldwide, the development of mussel farming as an economically and ecologically sustainable industry requires geographic information on the growth and potential production capacity. In practice this means that coherent maps of temporally stable spatial patterns of growth need to be available in the planning process and that maps need to be based on mechanistic or empirical models. Therefore, as a first step towards development of models of growth, we assessed empirically the fundamental requirement that there are temporally consistent spatial patterns of growth in the blue mussel, Mytilus edulis. Using a pilot study we designed and dimensioned a transplant experiment, where the spatial consistency in the growth of mussels was evaluated at two resolutions. We found strong temporal and scale-dependent spatial variability in growth but patterns suggested that spatial patterns were uncoupled between growth of shell and that of soft tissue. Spatial patterns of shell growth were complex and largely inconsistent among years. Importantly, however, the growth of soft tissue was qualitatively consistent among years at the scale of km. The results suggest that processes affecting the whole coastal area cause substantial differences in growth of soft tissue among years but that factors varying at the scale of km create strong and persistent spatial patterns of growth, with a potential doubling of productivity by identifying the most suitable locations. We conclude that the observed spatial consistency provides a basis for further development of predictive modelling and mapping of soft tissue growth in these coastal areas. Potential causes of observed patterns, consequences for mussel-farming as a tool for mitigating eutrophication, aspects of precision of modelling and sampling of mussel growth as well as ecological functions in general are discussed.

Spatial Patterns of Inshore Marine Soundscapes.

PubMed

McWilliam, Jamie

2016-01-01

Passive acoustic monitoring was employed to investigate spatial patterns of soundscapes within a marine reserve. High energy level broadband snaps dominated nearly all habitat soundscapes. Snaps, the principal acoustic feature of soundscapes, were primarily responsible for the observed spatial patterns, and soundscapes appeared to retain a level of compositional and configurational stability. In the presence of high-level broadband snaps, soundscape composition was more influenced by geographic location than habitat type. Future research should focus on investigating the spatial patterns of soundscapes across a wider range of coastal and offshore seascapes containing a variety of distinct ecosystems and habitats.

Boundary-induced pattern formation from uniform temporal oscillation

NASA Astrophysics Data System (ADS)

Kohsokabe, Takahiro; Kaneko, Kunihiko

2018-04-01

Pattern dynamics triggered by fixing a boundary is investigated. By considering a reaction-diffusion equation that has a unique spatially uniform and limit cycle attractor under a periodic or Neumann boundary condition, and then by choosing a fixed boundary condition, we found three novel phases depending on the ratio of diffusion constants of activator to inhibitor: transformation of temporally periodic oscillation into a spatially periodic fixed pattern, travelling wave emitted from the boundary, and aperiodic spatiotemporal dynamics. The transformation into a fixed, periodic pattern is analyzed by crossing of local nullclines at each spatial point, shifted by diffusion terms, as is analyzed by using recursive equations, to obtain the spatial pattern as an attractor. The generality of the boundary-induced pattern formation as well as its relevance to biological morphogenesis is discussed.

Spatially heterogeneous stochasticity and the adaptive diversification of dormancy.

PubMed

Rajon, E; Venner, S; Menu, F

2009-10-01

Diversified bet-hedging, a strategy that leads several individuals with the same genotype to express distinct phenotypes in a given generation, is now well established as a common evolutionary response to environmental stochasticity. Life-history traits defined as diversified bet-hedging (e.g. germination or diapause strategies) display marked differences between populations in spatial proximity. In order to find out whether such differences can be explained by local adaptations to spatially heterogeneous environmental stochasticity, we explored the evolution of bet-hedging dormancy strategies in a metapopulation using a two-patch model with patch differences in stochastic juvenile survival. We found that spatial differences in the level of environmental stochasticity, restricted dispersal, increased fragmentation and intermediate survival during dormancy all favour the adaptive diversification of bet-hedging dormancy strategies. Density dependency also plays a major role in the diversification of dormancy strategies because: (i) it may interact locally with environmental stochasticity and amplify its effects; however, (ii) it can also generate chaotic population dynamics that may impede diversification. Our work proposes new hypotheses to explain the spatial patterns of bet-hedging strategies that we hope will encourage new empirical studies of this topic.

Spatial coherence resonance and spatial pattern transition induced by the decrease of inhibitory effect in a neuronal network

NASA Astrophysics Data System (ADS)

Tao, Ye; Gu, Huaguang; Ding, Xueli

2017-10-01

Spiral waves were observed in the biological experiment on rat brain cortex with the application of carbachol and bicuculline which can block inhibitory coupling from interneurons to pyramidal neurons. To simulate the experimental spiral waves, a two-dimensional neuronal network composed of pyramidal neurons and inhibitory interneurons was built. By decreasing the percentage of active inhibitory interneurons, the random-like spatial patterns change to spiral waves and to random-like spatial patterns or nearly synchronous behaviors. The spiral waves appear at a low percentage of inhibitory interneurons, which matches the experimental condition that inhibitory couplings of the interneurons were blocked. The spiral waves exhibit a higher order or signal-to-noise ratio (SNR) characterized by spatial structure function than both random-like spatial patterns and nearly synchronous behaviors, which shows that changes of the percentage of active inhibitory interneurons can induce spatial coherence resonance-like behaviors. In addition, the relationship between the coherence degree and the spatial structures of the spiral waves is identified. The results not only present a possible and reasonable interpretation to the spiral waves observed in the biological experiment on the brain cortex with disinhibition, but also reveal that the spiral waves exhibit more ordered degree in spatial patterns.

Integrating spatial and numerical structure in mathematical patterning

NASA Astrophysics Data System (ADS)

Ni’mah, K.; Purwanto; Irawan, E. B.; Hidayanto, E.

2018-03-01

This paper reports a study monitoring the integrating spatial and numerical structure in mathematical patterning skills of 30 students grade 7th of junior high school. The purpose of this research is to clarify the processes by which learners construct new knowledge in mathematical patterning. Findings indicate that: (1) students are unable to organize the structure of spatial and numerical, (2) students were only able to organize the spatial structure, but the numerical structure is still incorrect, (3) students were only able to organize numerical structure, but its spatial structure is still incorrect, (4) students were able to organize both of the spatial and numerical structure.

Sonic Hedgehog functions through dynamic changes in temporal competence in the developing ventral telencephalon

PubMed Central

Sousa, Vitor H.; Fishell, Gord

2010-01-01

Morphogens act during development to provide graded spatial information that controls patterning and cell lineage specification in the nervous system. The role of morphogen signaling in instructing the expression of downstream effector transcription factors has been well established. However, a key requirement for morphogen signaling is the existence of functional intracellular machinery able to mediate the appropriate response in target cells. Here we suggest that dynamic changes in the temporal responses to Shh in the developing ventral telencephalon occur through alterations in progenitor competence. We suggest these developmental changes in competence are mediated by a transcriptional mechanism that intrinsically integrates information from the distinct signaling pathways that act to pattern the telencephalic neuroepithelium. PMID:20466536

Ancient homology underlies adaptive mimetic diversity across butterflies

PubMed Central

Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

2014-01-01

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

Spatial localization of EGF family ligands and receptors in the zebrafish ovarian follicle and their expression profiles during folliculogenesis.

PubMed

Tse, Anna Chung-Kwan; Ge, Wei

2010-07-01

The roles of epidermal growth factor (EGF) family in the ovary have received increasing attention recently. Despite this, the production sites of EGF family members in the ovarian follicle still remain controversial. Using zebrafish as the model, the present study investigated spatial distribution of several EGF family ligands and receptors in the follicle as well as their temporal expression profiles during folliculogenesis. RT-PCR analysis on the somatic follicle layer and oocyte revealed that all EGF family ligands examined (egf, tgfa, btc and hbegf) were mostly or exclusively expressed in the oocyte. In contrast, their common receptor (egfr) was expressed exclusively in the follicle layer. By comparison, members of activin family showed an opposite pattern of distribution. Activin subunits (inhbaa and inhbb) were both expressed exclusively in the follicle layer whereas activin receptors and follistatin were abundantly present in the oocyte. During folliculogenesis, egf, tgfa and hbegf increased their expression together with egfr in the fast secondary growth phase. The developmental profiles of EGF family during embryogenesis appeared to argue for an important role for EGF family in folliculogenesis rather than embryogenesis as maternal molecules. The present study provided clear evidence for the existence of two paracrine pathways in the follicle, the oocyte-derived EGF family ligands and follicle cell-derived activins, which may mediate oocyte-to-follicle cell and follicle cell-to-oocyte communications, respectively. The functional relationship between these two signaling systems in the follicle is suggested by the observation that all four EGFR ligands examined significantly stimulated activin subunit expression in cultured follicle cells. (c) 2009 Elsevier Inc. All rights reserved.

Temporal, but not spatial, changes in expression patterns of petal identity genes are associated with loss of papillate conical cells and the shift to bird pollination in Macaronesian Lotus (Leguminosae).

PubMed

Ojeda, D I; Jaén-Molina, R; Santos-Guerra, A; Caujape-Castells, J; Cronk, Q

2017-05-01

In the generally bee-pollinated genus Lotus a group of four species have evolved bird-pollinated flowers. The floral changes in these species include altered petal orientation, shape and texture. In Lotus these characters are associated with dorsiventral petal identity, suggesting that shifts in the expression of dorsal identity genes may be involved in the evolution of bird pollination. Of particular interest is Lotus japonicus CYCLOIDEA 2 (LjCYC2), known to determine the presence of papillate conical cells on the dorsal petal in L. japonicus. Bird-pollinated species are unusual in not having papillate conical cells on the dorsal petal. Using RT-PCR at various stages of flower development, we determined the timing of expression in all petal types for the three putative petal identity genes (CYC-like genes) in different species with contrasting floral morphology and pollination syndromes. In bird-pollinated species the dorsal identity gene, LjCYC2, is not expressed at the floral stage when papillate conical cells are normally differentiating in bee-pollinated species. In contrast, in bee-pollinated species, LjCYC2 is expressed during conical cell development. Changes in the timing of expression of the above two genes are associated with modifications in petal growth and lateralisation of the dorsal and ventral petals in the bird-pollinated species. This study indicates that changes in the timing, rather than spatial distribution, of expression likely contribute to the modifications of petal micromorphology and petal size during the transition from bee to bird pollination in Macaronesian Lotus species. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Expression of FAP, ADAM12, WISP1, and SOX11 is heterogeneous in aggressive fibromatosis and spatially relates to the histologic features of tumor activity.

PubMed

Misemer, Benjamin S; Skubitz, Amy P N; Carlos Manivel, J; Schmechel, Stephen C; Cheng, Edward Y; Henriksen, Jonathan C; Koopmeiners, Joseph S; Corless, Christopher L; Skubitz, Keith M

2014-02-01

Aggressive fibromatosis (AF) represents a group of tumors with a variable and unpredictable clinical course, characterized by a monoclonal proliferation of myofibroblastic cells. The optimal treatment for AF remains unclear. Identification and validation of genes whose expression patterns are associated with AF may elucidate biological mechanisms in AF, and aid treatment selection. This study was designed to examine the protein expression by immunohistochemistry (IHC) of four genes, ADAM12, FAP, SOX11, and WISP1, that were found in an earlier study to be uniquely overexpressed in AF compared with normal tissues. Digital image analysis was performed to evaluate inter- and intratumor heterogeneity, and correlate protein expression with histologic features, including a histopathologic assessment of tumor activity, defined by nuclear chromatin density ratio (CDR). AF tumors exhibited marked inter- and intratumor histologic heterogeneity. Pathologic assessment of tumor activity and digital assessment of average nuclear size and CDR were all significantly correlated. IHC revealed protein expression of all four genes. IHC staining for ADAM12, FAP, and WISP1 correlated with CDR and was higher, whereas SOX11 staining was lower in tumors with earlier recurrence following excision. All four proteins were expressed, and the regional variation in tumor activity within and among AF cases was demonstrated. A spatial correlation between protein expression and nuclear morphology was observed. IHC also correlated with the probability of recurrence following excision. These proteins may be involved in AF pathogenesis and the corresponding pathways could serve as potential targets of therapy. © 2013 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Spatial scaling patterns and functional redundancies in a changing boreal lake landscape

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Uden, Daniel R.; Johnson, Richard K.

2015-01-01

Global transformations extend beyond local habitats; therefore, larger-scale approaches are needed to assess community-level responses and resilience to unfolding environmental changes. Using longterm data (1996–2011), we evaluated spatial patterns and functional redundancies in the littoral invertebrate communities of 85 Swedish lakes, with the objective of assessing their potential resilience to environmental change at regional scales (that is, spatial resilience). Multivariate spatial modeling was used to differentiate groups of invertebrate species exhibiting spatial patterns in composition and abundance (that is, deterministic species) from those lacking spatial patterns (that is, stochastic species). We then determined the functional feeding attributes of the deterministic and stochastic invertebrate species, to infer resilience. Between one and three distinct spatial patterns in invertebrate composition and abundance were identified in approximately one-third of the species; the remainder were stochastic. We observed substantial differences in metrics between deterministic and stochastic species. Functional richness and diversity decreased over time in the deterministic group, suggesting a loss of resilience in regional invertebrate communities. However, taxon richness and redundancy increased monotonically in the stochastic group, indicating the capacity of regional invertebrate communities to adapt to change. Our results suggest that a refined picture of spatial resilience emerges if patterns of both the deterministic and stochastic species are accounted for. Spatially extensive monitoring may help increase our mechanistic understanding of community-level responses and resilience to regional environmental change, insights that are critical for developing management and conservation agendas in this current period of rapid environmental transformation.

Using spatial analysis to demonstrate the heterogeneity of the cardiovascular drug-prescribing pattern in Taiwan

PubMed Central

2011-01-01

Background Geographic Information Systems (GIS) combined with spatial analytical methods could be helpful in examining patterns of drug use. Little attention has been paid to geographic variation of cardiovascular prescription use in Taiwan. The main objective was to use local spatial association statistics to test whether or not the cardiovascular medication-prescribing pattern is homogenous across 352 townships in Taiwan. Methods The statistical methods used were the global measures of Moran's I and Local Indicators of Spatial Association (LISA). While Moran's I provides information on the overall spatial distribution of the data, LISA provides information on types of spatial association at the local level. LISA statistics can also be used to identify influential locations in spatial association analysis. The major classes of prescription cardiovascular drugs were taken from Taiwan's National Health Insurance Research Database (NHIRD), which has a coverage rate of over 97%. The dosage of each prescription was converted into defined daily doses to measure the consumption of each class of drugs. Data were analyzed with ArcGIS and GeoDa at the township level. Results The LISA statistics showed an unusual use of cardiovascular medications in the southern townships with high local variation. Patterns of drug use also showed more low-low spatial clusters (cold spots) than high-high spatial clusters (hot spots), and those low-low associations were clustered in the rural areas. Conclusions The cardiovascular drug prescribing patterns were heterogeneous across Taiwan. In particular, a clear pattern of north-south disparity exists. Such spatial clustering helps prioritize the target areas that require better education concerning drug use. PMID:21609462

The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers.

PubMed

Amalric, Marie; Wang, Liping; Pica, Pierre; Figueira, Santiago; Sigman, Mariano; Dehaene, Stanislas

2017-01-01

During language processing, humans form complex embedded representations from sequential inputs. Here, we ask whether a "geometrical language" with recursive embedding also underlies the human ability to encode sequences of spatial locations. We introduce a novel paradigm in which subjects are exposed to a sequence of spatial locations on an octagon, and are asked to predict future locations. The sequences vary in complexity according to a well-defined language comprising elementary primitives and recursive rules. A detailed analysis of error patterns indicates that primitives of symmetry and rotation are spontaneously detected and used by adults, preschoolers, and adult members of an indigene group in the Amazon, the Munduruku, who have a restricted numerical and geometrical lexicon and limited access to schooling. Furthermore, subjects readily combine these geometrical primitives into hierarchically organized expressions. By evaluating a large set of such combinations, we obtained a first view of the language needed to account for the representation of visuospatial sequences in humans, and conclude that they encode visuospatial sequences by minimizing the complexity of the structured expressions that capture them.

The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers

PubMed Central

Amalric, Marie; Wang, Liping; Figueira, Santiago; Sigman, Mariano; Dehaene, Stanislas

2017-01-01

During language processing, humans form complex embedded representations from sequential inputs. Here, we ask whether a “geometrical language” with recursive embedding also underlies the human ability to encode sequences of spatial locations. We introduce a novel paradigm in which subjects are exposed to a sequence of spatial locations on an octagon, and are asked to predict future locations. The sequences vary in complexity according to a well-defined language comprising elementary primitives and recursive rules. A detailed analysis of error patterns indicates that primitives of symmetry and rotation are spontaneously detected and used by adults, preschoolers, and adult members of an indigene group in the Amazon, the Munduruku, who have a restricted numerical and geometrical lexicon and limited access to schooling. Furthermore, subjects readily combine these geometrical primitives into hierarchically organized expressions. By evaluating a large set of such combinations, we obtained a first view of the language needed to account for the representation of visuospatial sequences in humans, and conclude that they encode visuospatial sequences by minimizing the complexity of the structured expressions that capture them. PMID:28125595

Evolutionary change in the structure of the regulatory region that drives tissue and temporally regulated expression of alcohol dehydrogenase gene in Drosophila funebris.

PubMed

Amador, A; Papaceit, M; Juan, E

2001-06-01

The Adh locus of Drosophilidae is organized as a single gene transcribed from two spatially and temporally regulated promoters except in species of the repleta group, which have two single promoter genes. Here we show that in Drosophila funebris the Adh gene is transcribed from a single promoter, in both larva and adult, with qualitative and quantitative species specific-differences in tissue distribution. The gene is expressed in larval fat body but in other tissues such as gastric caeca, midgut and Malpighian tubules its expression is reduced compared to most Drosophilidae species, and in adults it is almost limited to the fat body. The comparative analysis of gene expression of two strains, which differ by a duplication, indicates that the cis elements necessary for this pattern of expression in larvae are included in the region of 1.55 kb upstream of the transcription initiation site. This new organization reveals the evolution of a different regulatory strategy to express the Adh gene in the subgenus Drosophila.

Retinal Expression of the Drosophila eyes absent Gene Is Controlled by Several Cooperatively Acting Cis-regulatory Elements

PubMed Central

Neuman, Sarah D.; Bashirullah, Arash; Kumar, Justin P.

2016-01-01

The eyes absent (eya) gene of the fruit fly, Drosophila melanogaster, is a member of an evolutionarily conserved gene regulatory network that controls eye formation in all seeing animals. The loss of eya leads to the complete elimination of the compound eye while forced expression of eya in non-retinal tissues is sufficient to induce ectopic eye formation. Within the developing retina eya is expressed in a dynamic pattern and is involved in tissue specification/determination, cell proliferation, apoptosis, and cell fate choice. In this report we explore the mechanisms by which eya expression is spatially and temporally governed in the developing eye. We demonstrate that multiple cis-regulatory elements function cooperatively to control eya transcription and that spacing between a pair of enhancer elements is important for maintaining correct gene expression. Lastly, we show that the loss of eya expression in sine oculis (so) mutants is the result of massive cell death and a progressive homeotic transformation of retinal progenitor cells into head epidermis. PMID:27930646

Low-level image properties in facial expressions.

PubMed

Menzel, Claudia; Redies, Christoph; Hayn-Leichsenring, Gregor U

2018-06-04

We studied low-level image properties of face photographs and analyzed whether they change with different emotional expressions displayed by an individual. Differences in image properties were measured in three databases that depicted a total of 167 individuals. Face images were used either in their original form, cut to a standard format or superimposed with a mask. Image properties analyzed were: brightness, redness, yellowness, contrast, spectral slope, overall power and relative power in low, medium and high spatial frequencies. Results showed that image properties differed significantly between expressions within each individual image set. Further, specific facial expressions corresponded to patterns of image properties that were consistent across all three databases. In order to experimentally validate our findings, we equalized the luminance histograms and spectral slopes of three images from a given individual who showed two expressions. Participants were significantly slower in matching the expression in an equalized compared to an original image triad. Thus, existing differences in these image properties (i.e., spectral slope, brightness or contrast) facilitate emotion detection in particular sets of face images. Copyright © 2018. Published by Elsevier B.V.

Planarian yorkie/YAP functions to integrate adult stem cell proliferation, organ homeostasis and maintenance of axial patterning.

PubMed

Lin, Alexander Y T; Pearson, Bret J

2014-03-01

During adult homeostasis and regeneration, the freshwater planarian must accomplish a constant balance between cell proliferation and cell death, while also maintaining proper tissue and organ size and patterning. How these ordered processes are precisely modulated remains relatively unknown. Here we show that planarians use the downstream effector of the Hippo signaling cascade, yorkie (yki; YAP in vertebrates) to control a diverse set of pleiotropic processes in organ homeostasis, stem cell regulation, regeneration and axial patterning. We show that yki functions to maintain the homeostasis of the planarian excretory (protonephridial) system and to limit stem cell proliferation, but does not affect the differentiation process or cell death. Finally, we show that Yki acts synergistically with WNT/β-catenin signaling to repress head determination by limiting the expression domains of posterior WNT genes and that of the WNT-inhibitor notum. Together, our data show that yki is a key gene in planarians that integrates stem cell proliferation control, organ homeostasis, and the spatial patterning of tissues.

TRMM-TMI Satellite Observed Soil Moisture and Vegetation Density (1998-2005) Show Strong Connection with El Nino in Eastern Australia

NASA Technical Reports Server (NTRS)

Liu, Yi; van Dijk, Albert I.J.M.; Owe, Manfred

2007-01-01

Spatiotemporal patterns in soil moisture and vegetation water content across mainland Australia were investigated from 1998 through 2005, using TRMMITMI passive microwave observations. The Empirical Orthogonal Function technique was used to extract dominant spatial and temporal patterns in retrieved estimates of moisture content for the top 1-cm of soil (theta) and vegetation moisture content (via optical depth tau). The dominant temporal theta and tau patterns were strongly correlated to El Nino/Southern Oscillation (ENSO) in spring (3 = 0.90), and to a progressively lesser extent autumn, summer and winter. The Indian Ocean Dipole (IOD) index also explained part of the variation in spring 8 and z. Cluster analysis suggested that the regions most affected by ENS0 are mainly located in eastern Australia. The results suggest that the drought conditions experienced in eastern Australia since 2000 an clearly expressed in these satellite observations have a strong connection with ENSO patterns.

Diffractive optics for quasi-direct space-to-time pulse shaping.

PubMed

Mínguez-Vega, Gladys; Mendoza-Yero, Omel; Lancis, Jesús; Gisbert, Rafael; Andrés, Pedro

2008-10-13

The strong chromatic behavior associated with a conventional diffractive lens is fully exploited to propose a novel optical device for pulse shaping in the femtosecond regime. This device consists of two optical elements: a spatially patterned circularly symmetric mask and a kinoform diffractive lens, which are facing each other. The system performs a mapping between the spatial position of the masking function expressed in the squared radial coordinate and the temporal position in the output waveform. This space-to-time conversion occurs at the chromatic focus of the diffractive lens, and makes it possible to tailor the output central wavelength along the axial location of the output point. Inspection of the validity of our device is performed by means of computer simulations involving the generation of femtosecond optical packets.

Diagnosis of the influence of the solar cycle in the annular character of the NAM using RAM.

NASA Astrophysics Data System (ADS)

de La Torre, L.; Gimeno, L.; Tesouro, M.; Nieto, R.; Añel, J. A.; Ribera, P.; García, R.; Hernández, E.

2003-04-01

It has been suggested that the North Atlantic Oscillation is a regional expression of the so called Northern Hemisphere Annular Mode (NAM), although some evidences have been found against this hypothesis. However, recent studies conect the spatial structure of the NAM with the phase of solar cycle, being annular-like only for the periods of high solar activity. With this work we try to make a contribution to the debate by using atmospheric relative angular momentum (RAM) to diagnose the annular character of the mode. Correlations of RAM vs. temperature and geopotential height at different levels for high activity years show a more zonally extended pattern than those for low activity years. Moreover, the Atlantic pattern is always shown, even when using RAM computed by 60º longitude sectors. On the other hand, the Pacific pattern almost dissapear.

Balancing geo-privacy and spatial patterns in epidemiological studies.

PubMed

Chen, Chien-Chou; Chuang, Jen-Hsiang; Wang, Da-Wei; Wang, Chien-Min; Lin, Bo-Cheng; Chan, Ta-Chien

2017-11-08

To balance the protection of geo-privacy and the accuracy of spatial patterns, we developed a geo-spatial tool (GeoMasker) intended to mask the residential locations of patients or cases in a geographic information system (GIS). To elucidate the effects of geo-masking parameters, we applied 2010 dengue epidemic data from Taiwan testing the tool's performance in an empirical situation. The similarity of pre- and post-spatial patterns was measured by D statistics under a 95% confidence interval. In the empirical study, different magnitudes of anonymisation (estimated Kanonymity ≥10 and 100) were achieved and different degrees of agreement on the pre- and post-patterns were evaluated. The application is beneficial for public health workers and researchers when processing data with individuals' spatial information.

Pattern transitions in spatial epidemics: Mechanisms and emergent properties.

PubMed

Sun, Gui-Quan; Jusup, Marko; Jin, Zhen; Wang, Yi; Wang, Zhen

2016-12-01

Infectious diseases are a threat to human health and a hindrance to societal development. Consequently, the spread of diseases in both time and space has been widely studied, revealing the different types of spatial patterns. Transitions between patterns are an emergent property in spatial epidemics that can serve as a potential trend indicator of disease spread. Despite the usefulness of such an indicator, attempts to systematize the topic of pattern transitions have been few and far between. We present a mini-review on pattern transitions in spatial epidemics, describing the types of transitions and their underlying mechanisms. We show that pattern transitions relate to the complexity of spatial epidemics by, for example, being accompanied with phenomena such as coherence resonance and cyclic evolution. The results presented herein provide valuable insights into disease prevention and control, and may even be applicable outside epidemiology, including other branches of medical science, ecology, quantitative finance, and elsewhere. Copyright © 2016 Elsevier B.V. All rights reserved.

An exploration of spatial patterns of seasonal diarrhoeal morbidity in Thailand.

PubMed

McCormick, B J J; Alonso, W J; Miller, M A

2012-07-01

Studies of temporal and spatial patterns of diarrhoeal disease can suggest putative aetiological agents and environmental or socioeconomic drivers. Here, the seasonal patterns of monthly acute diarrhoeal morbidity in Thailand, where diarrhoeal morbidity is increasing, are explored. Climatic data (2003-2006) and Thai Ministry of Health annual reports (2003-2009) were used to construct a spatially weighted panel regression model. Seasonal patterns of diarrhoeal disease were generally bimodal with aetiological agents peaking at different times of the year. There is a strong association between daily mean temperature and precipitation and the incidence of hospitalization due to acute diarrhoea in Thailand leading to a distinct spatial pattern in the seasonal pattern of diarrhoea. Model performance varied across the country in relation to per capita GDP and population density. While climatic factors are likely to drive the general pattern of diarrhoeal disease in Thailand, the seasonality of diarrhoeal disease is dampened in affluent urban populations.

Simple Process-Based Simulators for Generating Spatial Patterns of Habitat Loss and Fragmentation: A Review and Introduction to the G-RaFFe Model

PubMed Central

Pe'er, Guy; Zurita, Gustavo A.; Schober, Lucia; Bellocq, Maria I.; Strer, Maximilian; Müller, Michael; Pütz, Sandro

2013-01-01

Landscape simulators are widely applied in landscape ecology for generating landscape patterns. These models can be divided into two categories: pattern-based models that generate spatial patterns irrespective of the processes that shape them, and process-based models that attempt to generate patterns based on the processes that shape them. The latter often tend toward complexity in an attempt to obtain high predictive precision, but are rarely used for generic or theoretical purposes. Here we show that a simple process-based simulator can generate a variety of spatial patterns including realistic ones, typifying landscapes fragmented by anthropogenic activities. The model “G-RaFFe” generates roads and fields to reproduce the processes in which forests are converted into arable lands. For a selected level of habitat cover, three factors dominate its outcomes: the number of roads (accessibility), maximum field size (accounting for land ownership patterns), and maximum field disconnection (which enables field to be detached from roads). We compared the performance of G-RaFFe to three other models: Simmap (neutral model), Qrule (fractal-based) and Dinamica EGO (with 4 model versions differing in complexity). A PCA-based analysis indicated G-RaFFe and Dinamica version 4 (most complex) to perform best in matching realistic spatial patterns, but an alternative analysis which considers model variability identified G-RaFFe and Qrule as performing best. We also found model performance to be affected by habitat cover and the actual land-uses, the latter reflecting on land ownership patterns. We suggest that simple process-based generators such as G-RaFFe can be used to generate spatial patterns as templates for theoretical analyses, as well as for gaining better understanding of the relation between spatial processes and patterns. We suggest caution in applying neutral or fractal-based approaches, since spatial patterns that typify anthropogenic landscapes are often non-fractal in nature. PMID:23724108

Simple process-based simulators for generating spatial patterns of habitat loss and fragmentation: a review and introduction to the G-RaFFe model.

PubMed

Pe'er, Guy; Zurita, Gustavo A; Schober, Lucia; Bellocq, Maria I; Strer, Maximilian; Müller, Michael; Pütz, Sandro

2013-01-01

Landscape simulators are widely applied in landscape ecology for generating landscape patterns. These models can be divided into two categories: pattern-based models that generate spatial patterns irrespective of the processes that shape them, and process-based models that attempt to generate patterns based on the processes that shape them. The latter often tend toward complexity in an attempt to obtain high predictive precision, but are rarely used for generic or theoretical purposes. Here we show that a simple process-based simulator can generate a variety of spatial patterns including realistic ones, typifying landscapes fragmented by anthropogenic activities. The model "G-RaFFe" generates roads and fields to reproduce the processes in which forests are converted into arable lands. For a selected level of habitat cover, three factors dominate its outcomes: the number of roads (accessibility), maximum field size (accounting for land ownership patterns), and maximum field disconnection (which enables field to be detached from roads). We compared the performance of G-RaFFe to three other models: Simmap (neutral model), Qrule (fractal-based) and Dinamica EGO (with 4 model versions differing in complexity). A PCA-based analysis indicated G-RaFFe and Dinamica version 4 (most complex) to perform best in matching realistic spatial patterns, but an alternative analysis which considers model variability identified G-RaFFe and Qrule as performing best. We also found model performance to be affected by habitat cover and the actual land-uses, the latter reflecting on land ownership patterns. We suggest that simple process-based generators such as G-RaFFe can be used to generate spatial patterns as templates for theoretical analyses, as well as for gaining better understanding of the relation between spatial processes and patterns. We suggest caution in applying neutral or fractal-based approaches, since spatial patterns that typify anthropogenic landscapes are often non-fractal in nature.

Doing ecohydrology backward: Inferring wetland flow and hydroperiod from landscape patterns

NASA Astrophysics Data System (ADS)

Acharya, Subodh; Kaplan, David A.; Jawitz, James W.; Cohen, Matthew J.

2017-07-01

Human alterations to hydrology have globally impacted wetland ecosystems. Preventing or reversing these impacts is a principal focus of restoration efforts. However, restoration effectiveness is often hampered by limited information on historical landscape properties and hydrologic regime. To help address this gap, we developed a novel statistical approach for inferring flows and inundation frequency (i.e., hydroperiod, HP) in wetlands where changes in spatial vegetation and geomorphic patterns have occurred due to hydrologic alteration. We developed an analytical expression for HP as a transformation of the landscape-scale stage-discharge relationship. We applied this model to the Everglades "ridge-slough" (RS) landscape, a patterned, lotic peatland in southern Florida that has been drastically degraded by compartmentalization, drainage, and flow diversions. The new method reliably estimated flow and HP for a range of RS landscape patterns. Crucially, ridge-patch anisotropy and elevation above sloughs were strong drivers of flow-HP relationships. Increasing ridge heights markedly increased flow required to achieve sufficient HP to support peat accretion. Indeed, ridge heights inferred from historical accounts would require boundary flows 3-4 times greater than today, which agrees with restoration flow estimates from more complex, spatially distributed models. While observed loss of patch anisotropy allows HP targets to be met with lower flows, such landscapes likely fail to support other ecological functions. This work helps inform restoration flows required to restore stable ridge-slough patterning and positive peat accretion in this degraded ecosystem, and, more broadly, provides tools for exploring interactions between landscape and hydrology in lotic wetlands and floodplains.

Developmental changes in face visual scanning in autism spectrum disorder as assessed by data-based analysis

PubMed Central

Amestoy, Anouck; Guillaud, Etienne; Bouvard, Manuel P.; Cazalets, Jean-René

2015-01-01

Individuals with autism spectrum disorder (ASD) present reduced visual attention to faces. However, contradictory conclusions have been drawn about the strategies involved in visual face scanning due to the various methodologies implemented in the study of facial screening. Here, we used a data-driven approach to compare children and adults with ASD subjected to the same free viewing task and to address developmental aspects of face scanning, including its temporal patterning, in healthy children, and adults. Four groups (54 subjects) were included in the study: typical adults, typically developing children, and adults and children with ASD. Eye tracking was performed on subjects viewing unfamiliar faces. Fixations were analyzed using a data-driven approach that employed spatial statistics to provide an objective, unbiased definition of the areas of interest. Typical adults expressed a spatial and temporal strategy for visual scanning that differed from the three other groups, involving a sequential fixation of the right eye (RE), left eye (LE), and mouth. Typically developing children, adults and children with autism exhibited similar fixation patterns and they always started by looking at the RE. Children (typical or with ASD) subsequently looked at the LE or the mouth. Based on the present results, the patterns of fixation for static faces that mature from childhood to adulthood in typical subjects are not found in adults with ASD. The atypical patterns found after developmental progression and experience in ASD groups appear to remain blocked in an immature state that cannot be differentiated from typical developmental child patterns of fixation. PMID:26236264

Reaction-diffusion pattern in shoot apical meristem of plants.

PubMed

Fujita, Hironori; Toyokura, Koichi; Okada, Kiyotaka; Kawaguchi, Masayoshi

2011-03-29

A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants.

Reaction-Diffusion Pattern in Shoot Apical Meristem of Plants

PubMed Central

Fujita, Hironori; Toyokura, Koichi; Okada, Kiyotaka; Kawaguchi, Masayoshi

2011-01-01

A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM) development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ) and a surrounding peripheral zone (PZ). SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS) and CLAVATA (CLV). We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants. PMID:21479227

Spatial distribution patterns of soil mite communities and their relationships with edaphic factors in a 30-year tillage cornfield in northeast China.

PubMed

Liu, Jie; Gao, Meixiang; Liu, Jinwen; Guo, Yuxi; Liu, Dong; Zhu, Xinyu; Wu, Donghui

2018-01-01

Spatial distribution is an important topic in community ecology and a key to understanding the structure and dynamics of populations and communities. However, the available information related to the spatial patterns of soil mite communities in long-term tillage agroecosystems remains insufficient. In this study, we examined the spatial patterns of soil mite communities to explain the spatial relationships between soil mite communities and soil parameters. Soil fauna were sampled three times (August, September and October 2015) at 121 locations arranged regularly within a 400 m × 400 m monitoring plot. Additionally, we estimated the physical and chemical parameters of the same sampling locations. The distribution patterns of the soil mite community and the edaphic parameters were analyzed using a range of geostatistical tools. Moran's I coefficient showed that, during each sampling period, the total abundance of the soil mite communities and the abundance of the dominant mite populations were spatially autocorrelated. The soil mite communities demonstrated clear patchy distribution patterns within the study plot. These patterns were sampling period-specific. Cross-semivariograms showed both negative and positive cross-correlations between soil mite communities and environmental factors. Mantel tests showed a significant and positive relationship between soil mite community and soil organic matter and soil pH only in August. This study demonstrated that in the cornfield, the soil mite distribution exhibited strong or moderate spatial dependence, and the mites formed patches with sizes less than one hundred meters. In addition, in this long-term tillage agroecosystem, soil factors had less influence on the observed pattern of soil mite communities. Further experiments that take into account human activity and spatial factors should be performed to study the factors that drive the spatial distribution of soil microarthropods.

Spatial Pattern of Attacks of the Invasive Woodwasp Sirex noctilio, at Landscape and Stand Scales.

PubMed

Lantschner, M Victoria; Corley, Juan C

2015-01-01

Invasive insect pests are responsible for important damage to native and plantation forests, when population outbreaks occur. Understanding the spatial pattern of attacks by forest pest populations is essential to improve our understanding of insect population dynamics and for predicting attack risk by invasives or planning pest management strategies. The woodwasp Sirex noctilio is an invasive woodwasp that has become probably the most important pest of pine plantations in the Southern Hemisphere. Our aim was to study the spatial dynamics of S. noctilio populations in Southern Argentina. Specifically we describe: (1) the spatial patterns of S. noctilio outbreaks and their relation with environmental factors at a landscape scale; and (2) characterize the spatial pattern of attacked trees at the stand scale. We surveyed the spatial distribution of S. noctilio outbreaks in three pine plantation landscapes, and we assessed potential associations with topographic variables, habitat characteristics, and distance to other outbreaks. We also looked at the spatial distribution of attacked trees in 20 stands with different levels of infestation, and assessed the relationship of attacks with stand composition and management. We found that the spatial pattern of pine stands with S. noctilio outbreaks at the landscape scale is influenced mainly by the host species present, slope aspect, and distance to other outbreaks. At a stand scale, there is strong aggregation of attacked trees in stands with intermediate infestation levels, and the degree of attacks is influenced by host species and plantation management. We conclude that the pattern of S. noctilio damage at different spatial scales is influenced by a combination of both inherent population dynamics and the underlying patterns of environmental factors. Our results have important implications for the understanding and management of invasive insect outbreaks in forest systems.

Describing spatial pattern in stream networks: A practical approach

USGS Publications Warehouse

Ganio, L.M.; Torgersen, C.E.; Gresswell, R.E.

2005-01-01

The shape and configuration of branched networks influence ecological patterns and processes. Recent investigations of network influences in riverine ecology stress the need to quantify spatial structure not only in a two-dimensional plane, but also in networks. An initial step in understanding data from stream networks is discerning non-random patterns along the network. On the other hand, data collected in the network may be spatially autocorrelated and thus not suitable for traditional statistical analyses. Here we provide a method that uses commercially available software to construct an empirical variogram to describe spatial pattern in the relative abundance of coastal cutthroat trout in headwater stream networks. We describe the mathematical and practical considerations involved in calculating a variogram using a non-Euclidean distance metric to incorporate the network pathway structure in the analysis of spatial variability, and use a non-parametric technique to ascertain if the pattern in the empirical variogram is non-random.

A geostatistical approach for describing spatial pattern in stream networks

USGS Publications Warehouse

Ganio, L.M.; Torgersen, C.E.; Gresswell, R.E.

2005-01-01

The shape and configuration of branched networks influence ecological patterns and processes. Recent investigations of network influences in riverine ecology stress the need to quantify spatial structure not only in a two-dimensional plane, but also in networks. An initial step in understanding data from stream networks is discerning non-random patterns along the network. On the other hand, data collected in the network may be spatially autocorrelated and thus not suitable for traditional statistical analyses. Here we provide a method that uses commercially available software to construct an empirical variogram to describe spatial pattern in the relative abundance of coastal cutthroat trout in headwater stream networks. We describe the mathematical and practical considerations involved in calculating a variogram using a non-Euclidean distance metric to incorporate the network pathway structure in the analysis of spatial variability, and use a non-parametric technique to ascertain if the pattern in the empirical variogram is non-random.

Measuring spatial patterns in floodplains: A step towards understanding the complexity of floodplain ecosystems: Chapter 6

USGS Publications Warehouse

Scown, Murray W.; Thoms, Martin C.; DeJager, Nathan R.; Gilvear, David J.; Greenwood, Malcolm T.; Thoms, Martin C.; Wood, Paul J.

2016-01-01

Floodplains can be viewed as complex adaptive systems (Levin, 1998) because they are comprised of many different biophysical components, such as morphological features, soil groups and vegetation communities as well as being sites of key biogeochemical processing (Stanford et al., 2005). Interactions and feedbacks among the biophysical components often result in additional phenomena occuring over a range of scales, often in the absence of any controlling factors (sensu Hallet, 1990). This emergence of new biophysical features and rates of processing can lead to alternative stable states which feed back into floodplain adaptive cycles (cf. Hughes, 1997; Stanford et al., 2005). Interactions between different biophysical components, feedbacks, self emergence and scale are all key properties of complex adaptive systems (Levin, 1998; Phillips, 2003; Murray et al., 2014) and therefore will influence the manner in which we study and view spatial patterns. Measuring the spatial patterns of floodplain biophysical components is a prerequisite to examining and understanding these ecosystems as complex adaptive systems. Elucidating relationships between pattern and process, which are intrinsically linked within floodplains (Ward et al., 2002), is dependent upon an understanding of spatial pattern. This knowledge can help river scientists determine the major drivers, controllers and responses of floodplain structure and function, as well as the consequences of altering those drivers and controllers (Hughes and Cass, 1997; Whited et al., 2007). Interactions and feedbacks between physical, chemical and biological components of floodplain ecosystems create and maintain a structurally diverse and dynamic template (Stanford et al., 2005). This template influences subsequent interactions between components that consequently affect system trajectories within floodplains (sensu Bak et al., 1988). Constructing and evaluating models used to predict floodplain ecosystem responses to natural and anthropogenic disturbances therefore require quantification of spatial pattern (Asselman and Middelkoop, 1995; Walling and He, 1998). Quantifying these patterns also provides insights into the spatial and temporal domains of structuring processes as well as enabling the detection of self-emergent phenomena, environmental constraints or anthropogenic interference (Turner et al., 1990; Holling, 1992; De Jager and Rohweder, 2012). Thus, quantifying spatial pattern is an important building block on which to examine floodplains as complex adaptive systems (Levin, 1998). Approaches to measuring spatial pattern in floodplains must be cognisant of scale, self-emergent phenomena, spatial organisation, and location. Fundamental problems may arise when patterns observed at a site or transect scale are scaled-up to infer processes and patterns over entire floodplain surfaces (Wiens, 2002; Thorp et al., 2008). Likewise, patterns observed over the entire spatial extent of a landscape can mask important variation and detail at finer scales (Riitters et al., 2002). Indeed, different patterns often emerge at different scales (Turner et al., 1990) because of hierarchical structuring processes (O'Neill et al., 1991). Categorising data into discrete, homogeneous and predefined spatial units at a particular scale (e.g. polygons) creates issues and errors associated with scale and subjective classification (McGarigal et al., 2009; Cushman et al., 2010). These include, loss of information within classified ‘patches’, as well as the ability to detect the emergence of new features that do not fit the original classification scheme. Many of these issues arise because floodplains are highly heterogeneous and have complex spatial organizations (Carbonneau et al., 2012; Legleiter, 2013). As a result, the scale and location at which measurements are made can influence the observed spatial patterns; and patterns may not be scale independent or applicable in different geomorp

Point pattern analysis of FIA data

Treesearch

Chris Woodall

2002-01-01

Point pattern analysis is a branch of spatial statistics that quantifies the spatial distribution of points in two-dimensional space. Point pattern analysis was conducted on stand stem-maps from FIA fixed-radius plots to explore point pattern analysis techniques and to determine the ability of pattern descriptions to describe stand attributes. Results indicate that the...

Comparative analysis of expression of two p97 homologues in Caenorhabditis elegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamauchi, Seiji; Yamanaka, Kunitoshi; Ogura, Teru

2006-06-30

Caenorhabditis elegans possesses two p97/VCP/Cdc48p homologues, named CDC-48.1 (C06A1.1) and CDC-48.2 (C41C4.8), although their expression regulation and functional diversity have not yet been studied. We therefore investigated spatial and temporal expression patterns of two p97 homologues in this study. RT-PCR and Western blot analysis showed that the amount of cdc-48.1 was about twofold of that of cdc-48.2 in adults and that two p97 homologues were induced by ER stress. The amount of cdc-48.1 mRNA did not increase in the cdc-48.2 deletion mutant and vice versa. In situ hybridization showed that two p97 homologues are mainly expressed in germ cells. Inmore » vivo expression analysis by using GFP translational fusion constructs revealed that CDC-48.1::GFP was expressed from embryos through to adult worms, while CDC-48.2::GFP was expressed mainly in embryos. These results suggest that the expression of two p97 homologues of C. elegans is differently regulated and independent of each other.« less

Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns.

PubMed

Liu, Quan-Xing; Rietkerk, Max; Herman, Peter M J; Piersma, Theunis; Fryxell, John M; van de Koppel, Johan

2016-12-01

Many ecosystems develop strikingly regular spatial patterns because of small-scale interactions between organisms, a process generally referred to as spatial self-organization. Self-organized spatial patterns are important determinants of the functioning of ecosystems, promoting the growth and survival of the involved organisms, and affecting the capacity of the organisms to cope with changing environmental conditions. The predominant explanation for self-organized pattern formation is spatial heterogeneity in establishment, growth and mortality, resulting from the self-organization processes. A number of recent studies, however, have revealed that movement of organisms can be an important driving process creating extensive spatial patterning in many ecosystems. Here, we review studies that detail movement-based pattern formation in contrasting ecological settings. Our review highlights that a common principle, where movement of organisms is density-dependent, explains observed spatial regular patterns in all of these studies. This principle, well known to physics as the Cahn-Hilliard principle of phase separation, has so-far remained unrecognized as a general mechanism for self-organized complexity in ecology. Using the examples presented in this paper, we explain how this movement principle can be discerned in ecological settings, and clarify how to test this mechanism experimentally. Our study highlights that animal movement, both in isolation and in unison with other processes, is an important mechanism for regular pattern formation in ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Inferring controls on the epidemiology of beech bark disease from spatial patterning of disease organisms

Treesearch

Jeffrey R. Garnas; David R. Houston; Mark J. Twery; Matthew P. Ayres; Celia Evans

2013-01-01

Spatial pattern in the distribution and abundance of organisms is an emergent property of collective rates of reproduction, survival and movement of individuals in a heterogeneous environment. The form, intensity and scale of spatial patterning can be used to test hypotheses regarding the relative importance of candidate processes to population dynamics. Using 84 plots...

Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis.

PubMed

Hammond, Stephanie; Wagenknecht-Wiesner, Alice; Veatch, Sarah L; Holowka, David; Baird, Barbara

2009-10-01

In mast cells, antigen-mediated cross-linking of IgE bound to its high-affinity surface receptor, FcepsilonRI, initiates a signaling cascade that culminates in degranulation and release of allergic mediators. Antigen-patterned surfaces, in which the antigen is deposited in micron-sized features on a silicon substrate, were used to examine the spatial relationship between clustered IgE-FcepsilonRI complexes and Lyn, the signal-initiating tyrosine kinase. RBL mast cells expressing wild-type Lyn-EGFP showed co-redistribution of this protein with clustered IgE receptors on antigen-patterned surfaces, whereas Lyn-EGFP containing an inhibitory point mutation in its SH2 domain did not significantly accumulate with the patterned antigen, and Lyn-EGFP with an inhibitory point mutation in its SH3 domain exhibited reduced interactions. Our results using antigen-patterned surfaces and quantitative cross-correlation image analysis reveal that both the SH2 and SH3 domains contribute to interactions between Lyn kinase and cross-linked IgE receptors in stimulated mast cells.

Uncovering Patterns of Inter-Urban Trip and Spatial Interaction from Social Media Check-In Data

PubMed Central

Liu, Yu; Sui, Zhengwei; Kang, Chaogui; Gao, Yong

2014-01-01

The article revisits spatial interaction and distance decay from the perspective of human mobility patterns and spatially-embedded networks based on an empirical data set. We extract nationwide inter-urban movements in China from a check-in data set that covers half a million individuals within 370 cities to analyze the underlying patterns of trips and spatial interactions. By fitting the gravity model, we find that the observed spatial interactions are governed by a power law distance decay effect. The obtained gravity model also closely reproduces the exponential trip displacement distribution. The movement of an individual, however, may not obey the same distance decay effect, leading to an ecological fallacy. We also construct a spatial network where the edge weights denote the interaction strengths. The communities detected from the network are spatially cohesive and roughly consistent with province boundaries. We attribute this pattern to different distance decay parameters between intra-province and inter-province trips. PMID:24465849

Uncovering patterns of inter-urban trip and spatial interaction from social media check-in data.

PubMed

Liu, Yu; Sui, Zhengwei; Kang, Chaogui; Gao, Yong

2014-01-01

The article revisits spatial interaction and distance decay from the perspective of human mobility patterns and spatially-embedded networks based on an empirical data set. We extract nationwide inter-urban movements in China from a check-in data set that covers half a million individuals within 370 cities to analyze the underlying patterns of trips and spatial interactions. By fitting the gravity model, we find that the observed spatial interactions are governed by a power law distance decay effect. The obtained gravity model also closely reproduces the exponential trip displacement distribution. The movement of an individual, however, may not obey the same distance decay effect, leading to an ecological fallacy. We also construct a spatial network where the edge weights denote the interaction strengths. The communities detected from the network are spatially cohesive and roughly consistent with province boundaries. We attribute this pattern to different distance decay parameters between intra-province and inter-province trips.

Middle-aged human apoE4 targeted-replacement mice show retention deficits on a wide range of spatial memory tasks.

PubMed

Bour, Alexandra; Grootendorst, Jeannette; Vogel, Elise; Kelche, Christian; Dodart, Jean-Cosme; Bales, Kelly; Moreau, Pierre-Henri; Sullivan, Patrick M; Mathis, Chantal

2008-11-21

Apolipoprotein (apo) E4, one of three human apoE (h-apoE) isoforms, has been identified as a major genetic risk factor for Alzheimer's disease and for cognitive deficits associated with aging. However, the biological mechanisms involving apoE in learning and memory processes are unclear. A potential isoform-dependent role of apoE in cognitive processes was studied in human apoE targeted-replacement (TR) mice. These mice express either the human apoE3 or apoE4 gene under the control of endogenous murine apoE regulatory sequences, resulting in physiological expression of h-apoE in both a temporal and spatial pattern similar to humans. Male and female apoE3-TR, apoE4-TR, apoE-knockout and C57BL/6J mice (15-18 months) were tested with spatial memory and avoidance conditioning tasks. Compared to apoE3-TR mice, spatial memory in female apoE4-TR mice was impaired based on their poor performances in; (i) the probe test of the water-maze reference memory task, (ii) the water-maze working memory task and (iii) an active avoidance Y-maze task. Retention performance on a passive avoidance task was also impaired in apoE4-TR mice, but not in other genotypes. These deficits in both spatial and avoidance memory tasks may be related to the anatomical and functional abnormalities previously reported in the hippocampus and the amygdala of apoE4-TR mice. We conclude that the apoE4-TR mice provide an excellent model for understanding the mechanisms underlying apoE4-dependent susceptibility to cognitive decline.

LocExpress: a web server for efficiently estimating expression of novel transcripts.

PubMed

Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

2016-12-22

The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

Integrating satellite actual evapotranspiration patterns into distributed model parametrization and evaluation for a mesoscale catchment

NASA Astrophysics Data System (ADS)

Demirel, M. C.; Mai, J.; Stisen, S.; Mendiguren González, G.; Koch, J.; Samaniego, L. E.

2016-12-01

Distributed hydrologic models are traditionally calibrated and evaluated against observations of streamflow. Spatially distributed remote sensing observations offer a great opportunity to enhance spatial model calibration schemes. For that it is important to identify the model parameters that can change spatial patterns before the satellite based hydrologic model calibration. Our study is based on two main pillars: first we use spatial sensitivity analysis to identify the key parameters controlling the spatial distribution of actual evapotranspiration (AET). Second, we investigate the potential benefits of incorporating spatial patterns from MODIS data to calibrate the mesoscale Hydrologic Model (mHM). This distributed model is selected as it allows for a change in the spatial distribution of key soil parameters through the calibration of pedo-transfer function parameters and includes options for using fully distributed daily Leaf Area Index (LAI) directly as input. In addition the simulated AET can be estimated at the spatial resolution suitable for comparison to the spatial patterns observed using MODIS data. We introduce a new dynamic scaling function employing remotely sensed vegetation to downscale coarse reference evapotranspiration. In total, 17 parameters of 47 mHM parameters are identified using both sequential screening and Latin hypercube one-at-a-time sampling methods. The spatial patterns are found to be sensitive to the vegetation parameters whereas streamflow dynamics are sensitive to the PTF parameters. The results of multi-objective model calibration show that calibration of mHM against observed streamflow does not reduce the spatial errors in AET while they improve only the streamflow simulations. We will further examine the results of model calibration using only multi spatial objective functions measuring the association between observed AET and simulated AET maps and another case including spatial and streamflow metrics together.

Photomodulating Gene Expression by Using Caged siRNAs with Single-Aptamer Modification.

PubMed

Zhang, Liangliang; Chen, Changmai; Fan, Xinli; Tang, Xinjing

2018-06-18

Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5' terminus of the antisense RNA strand, enhancement of the blocking effect for RNA-induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC-1) were chosen for aptamer-siRNA conjugation through a photolabile linker. This caging strategy was successfully used to photoregulate gene expression both of firefly luciferase and of green fluorescent protein (GFP) in cells. Further patterning experiments revealed that spatial regulation of GFP expression was successfully achieved by using the aptamer-modified caged siRNA and light activation. We expect that further optimized caged siRNAs featuring aptamer conjugation will be promising for practical applications to spatiotemporal photoregulation of gene expression in the future. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruebel, Oliver; Keranen, Soile V.E.; Biggin, Mark

Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila Transcription Network Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point-Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions. We address this challenge by linking PCX and Matlab via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchersmore » the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.« less

A Theoretical Approach to Analyze the Parametric Influence on Spatial Patterns of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) Populations.

PubMed

Garcia, A G; Godoy, W A C

2017-06-01

Studies of the influence of biological parameters on the spatial distribution of lepidopteran insects can provide useful information for managing agricultural pests, since the larvae of many species cause serious impacts on crops. Computational models to simulate the spatial dynamics of insect populations are increasingly used, because of their efficiency in representing insect movement. In this study, we used a cellular automata model to explore different patterns of population distribution of Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), when the values of two biological parameters that are able to influence the spatial pattern (larval viability and adult longevity) are varied. We mapped the spatial patterns observed as the parameters varied. Additionally, by using population data for S. frugiperda obtained in different hosts under laboratory conditions, we were able to describe the expected spatial patterns occurring in corn, cotton, millet, and soybean crops based on the parameters varied. The results are discussed from the perspective of insect ecology and pest management. We concluded that computational approaches can be important tools to study the relationship between the biological parameters and spatial distributions of lepidopteran insect pests.

Shaping skeletal growth by modular regulatory elements in the Bmp5 gene.

PubMed

Guenther, Catherine; Pantalena-Filho, Luiz; Kingsley, David M

2008-12-01

Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

Spatial controls of occurrence and spread of wildfires in the Missouri Ozark Highlands.

PubMed

Yang, Jian; He, Hong S; Shifley, Stephen R

2008-07-01

Understanding spatial controls on wildfires is important when designing adaptive fire management plans and optimizing fuel treatment locations on a forest landscape. Previous research about this topic focused primarily on spatial controls for fire origin locations alone. Fire spread and behavior were largely overlooked. This paper contrasts the relative importance of biotic, abiotic, and anthropogenic constraints on the spatial pattern of fire occurrence with that on burn probability (i.e., the probability that fire will spread to a particular location). Spatial point pattern analysis and landscape succession fire model (LANDIS) were used to create maps to show the contrast. We quantified spatial controls on both fire occurrence and fire spread in the Midwest Ozark Highlands region, USA. This area exhibits a typical anthropogenic surface fire regime. We found that (1) human accessibility and land ownership were primary limiting factors in shaping clustered fire origin locations; (2) vegetation and topography had a negligible influence on fire occurrence in this anthropogenic regime; (3) burn probability was higher in grassland and open woodland than in closed-canopy forest, even though fire occurrence density was less in these vegetation types; and (4) biotic and abiotic factors were secondary descriptive ingredients for determining the spatial patterns of burn probability. This study demonstrates how fire occurrence and spread interact with landscape patterns to affect the spatial distribution of wildfire risk. The application of spatial point pattern data analysis would also be valuable to researchers working on landscape forest fire models to integrate historical ignition location patterns in fire simulation.

Changes in Spatial Patterns of Caragana stenophylla along a Climatic Drought Gradient on the Inner Mongolian Plateau

PubMed Central

Xie, Li-Na; Guo, Hong-Yu; Gabler, Christopher A.; Li, Qing-Fang; Ma, Cheng-Cang

2015-01-01

Few studies have investigated the influence of water availability on plant population spatial patterns. We studied changes in the spatial patterns of Caragana stenophylla along a climatic drought gradient within the Inner Mongolian Plateau, China. We examined spatial patterns, seed density, “nurse effects” of shrubs on seedlings, transpiration rates and water use efficiency (WUE) of C. stenophylla across semi-arid, arid, and intensively arid zones. Our results showed that patches of C. stenophylla populations shifted from a random to a clumped spatial pattern towards drier environments. Seed density and seedling survival rate of C. stenophylla decreased from the semi-arid zone to the intensively arid zone. Across the three zones, there were more C. stenophylla seeds and seedlings underneath shrub canopies than outside shrub canopies; and in the intensively arid zone, there were almost no seeds or seedlings outside shrub canopies. Transpiration rates of outer-canopy leaves and WUE of both outer-canopy and inner-canopy leaves increased from the semi-arid zone to the intensively arid zone. In the intensively arid zone, transpiration rates and WUE of inner-canopy leaves were significantly lower and higher, respectively, than those of outer-canopy leaves. We conclude that, as drought stress increased, seed density decreased, seed proportions inside shrubs increased, and “nurse effects” of shrubs on seedlings became more important. These factors, combined with water-saving characteristics associated with clumped spatial patterns, are likely driving the changes in C. stenophylla spatial patterns. PMID:25785848

Spatio-temporal diffusion pattern and hotspot detection of dengue in Chachoengsao province, Thailand.

PubMed

Jeefoo, Phaisarn; Tripathi, Nitin Kumar; Souris, Marc

2011-01-01

In recent years, dengue has become a major international public health concern. In Thailand it is also an important concern as several dengue outbreaks were reported in last decade. This paper presents a GIS approach to analyze the spatial and temporal dynamics of dengue epidemics. The major objective of this study was to examine spatial diffusion patterns and hotspot identification for reported dengue cases. Geospatial diffusion pattern of the 2007 dengue outbreak was investigated. Map of daily cases was generated for the 153 days of the outbreak. Epidemiological data from Chachoengsao province, Thailand (reported dengue cases for the years 1999-2007) was used for this study. To analyze the dynamic space-time pattern of dengue outbreaks, all cases were positioned in space at a village level. After a general statistical analysis (by gender and age group), data was subsequently analyzed for temporal patterns and correlation with climatic data (especially rainfall), spatial patterns and cluster analysis, and spatio-temporal patterns of hotspots during epidemics. The results revealed spatial diffusion patterns during the years 1999-2007 representing spatially clustered patterns with significant differences by village. Villages on the urban fringe reported higher incidences. The space and time of the cases showed outbreak movement and spread patterns that could be related to entomologic and epidemiologic factors. The hotspots showed the spatial trend of dengue diffusion. This study presents useful information related to the dengue outbreak patterns in space and time and may help public health departments to plan strategies to control the spread of disease. The methodology is general for space-time analysis and can be applied for other infectious diseases as well.

Macroecological factors shape local-scale spatial patterns in agriculturalist settlements.

PubMed

Tao, Tingting; Abades, Sebastián; Teng, Shuqing; Huang, Zheng Y X; Reino, Luís; Chen, Bin J W; Zhang, Yong; Xu, Chi; Svenning, Jens-Christian

2017-11-15

Macro-scale patterns of human systems ranging from population distribution to linguistic diversity have attracted recent attention, giving rise to the suggestion that macroecological rules shape the assembly of human societies. However, in which aspects the geography of our own species is shaped by macroecological factors remains poorly understood. Here, we provide a first demonstration that macroecological factors shape strong local-scale spatial patterns in human settlement systems, through an analysis of spatial patterns in agriculturalist settlements in eastern mainland China based on high-resolution Google Earth images. We used spatial point pattern analysis to show that settlement spatial patterns are characterized by over-dispersion at fine spatial scales (0.05-1.4 km), consistent with territory segregation, and clumping at coarser spatial scales beyond the over-dispersion signals, indicating territorial clustering. Statistical modelling shows that, at macroscales, potential evapotranspiration and topographic heterogeneity have negative effects on territory size, but positive effects on territorial clustering. These relationships are in line with predictions from territory theory for hunter-gatherers as well as for many animal species. Our results help to disentangle the complex interactions between intrinsic spatial processes in agriculturalist societies and external forcing by macroecological factors. While one may speculate that humans can escape ecological constraints because of unique abilities for environmental modification and globalized resource transportation, our work highlights that universal macroecological principles still shape the geography of current human agricultural societies. © 2017 The Author(s).

Exploring the Linkage between Urban Flood Risk and Spatial Patterns in Small Urbanized Catchments of Beijing, China

PubMed Central

Yao, Lei; Chen, Liding; Wei, Wei

2017-01-01

In the context of global urbanization, urban flood risk in many cities has become a serious environmental issue, threatening the health of residents and the environment. A number of hydrological studies have linked urban flooding issues closely to the spectrum of spatial patterns of urbanization, but relatively little attention has been given to small-scale catchments within the realm of urban systems. This study aims to explore the hydrological effects of small-scaled urbanized catchments assigned with various landscape patterns. Twelve typical residential catchments in Beijing were selected as the study areas. Total Impervious Area (TIA), Directly Connected Impervious Area (DCIA), and a drainage index were used as the catchment spatial metrics. Three scenarios were designed as different spatial arrangement of catchment imperviousness. Runoff variables including total and peak runoff depth (Qt and Qp) were simulated by using Strom Water Management Model (SWMM). The relationship between catchment spatial patterns and runoff variables were determined, and the results demonstrated that, spatial patterns have inherent influences on flood risks in small urbanized catchments. Specifically: (1) imperviousness acts as an effective indicator in affecting both Qt and Qp; (2) reducing the number of rainwater inlets appropriately will benefit the catchment peak flow mitigation; (3) different spatial concentrations of impervious surfaces have inherent influences on Qp. These findings provide insights into the role of urban spatial patterns in driving rainfall-runoff processes in small urbanized catchments, which is essential for urban planning and flood management. PMID:28264521

Exploring the Linkage between Urban Flood Risk and Spatial Patterns in Small Urbanized Catchments of Beijing, China.

PubMed

Yao, Lei; Chen, Liding; Wei, Wei

2017-02-28

In the context of global urbanization, urban flood risk in many cities has become a serious environmental issue, threatening the health of residents and the environment. A number of hydrological studies have linked urban flooding issues closely to the spectrum of spatial patterns of urbanization, but relatively little attention has been given to small-scale catchments within the realm of urban systems. This study aims to explore the hydrological effects of small-scaled urbanized catchments assigned with various landscape patterns. Twelve typical residential catchments in Beijing were selected as the study areas. Total Impervious Area ( TIA ), Directly Connected Impervious Area ( DCIA ), and a drainage index were used as the catchment spatial metrics. Three scenarios were designed as different spatial arrangement of catchment imperviousness. Runoff variables including total and peak runoff depth ( Q t and Q p ) were simulated by using Strom Water Management Model (SWMM). The relationship between catchment spatial patterns and runoff variables were determined, and the results demonstrated that, spatial patterns have inherent influences on flood risks in small urbanized catchments. Specifically: (1) imperviousness acts as an effective indicator in affecting both Q t and Q p ; (2) reducing the number of rainwater inlets appropriately will benefit the catchment peak flow mitigation; (3) different spatial concentrations of impervious surfaces have inherent influences on Q p . These findings provide insights into the role of urban spatial patterns in driving rainfall-runoff processes in small urbanized catchments, which is essential for urban planning and flood management.

Genomic Organization, Phylogenetic and Expression Analysis of the B-BOX Gene Family in Tomato

PubMed Central

Chu, Zhuannan; Wang, Xin; Li, Ying; Yu, Huiyang; Li, Jinhua; Lu, Yongen; Li, Hanxia; Ouyang, Bo

2016-01-01

The B-BOX (BBX) proteins encode a class of zinc-finger transcription factors possessing one or two B-BOX domains and in some cases an additional CCT (CO, CO-like and TOC1) motif, which play important roles in regulating plant growth, development and stress response. Nevertheless, no systematic study of BBX genes has undertaken in tomato (Solanum lycopersicum). Here we present the results of a genome-wide analysis of the 29 BBX genes in this important vegetable species. Their structures, conserved domains, phylogenetic relationships, subcellular localizations, and promoter cis-regulatory elements were analyzed; their tissue expression profiles and expression patterns under various hormones and stress treatments were also investigated in detail. Tomato BBX genes can be divided into five subfamilies, and twelve of them were found to be segmentally duplicated. Real-time quantitative PCR analysis showed that most BBX genes exhibited different temporal and spatial expression patterns. The expression of most BBX genes can be induced by drought, polyethylene glycol-6000 or heat stress. Some BBX genes were induced strongly by phytohormones such as abscisic acid, gibberellic acid, or ethephon. The majority of tomato BBX proteins was predicted to be located in nuclei, and the transient expression assay using Arabidopsis mesophyll protoplasts demonstrated that all the seven BBX members tested (SlBBX5, 7, 15, 17, 20, 22, and 24) were localized in nucleus. Our analysis of tomato BBX genes on the genome scale would provide valuable information for future functional characterization of specific genes in this family. PMID:27807440

Expression of HtKNOT1, a class I KNOX gene, overlaps cell layers and development compartments of differentiating cells in stems and flowers of Helianthus tuberosus.

PubMed

Michelotti, V; Giorgetti, L; Geri, C; Cionini, G; Pugliesi, C; Fambrini, M

2007-10-01

In plant, post-embryonic development relies on the activities of indeterminate cell populations termed meristems, spatially clustered cell lineages, wherein a subset divides indeterminately. For correct growth, the plant must maintain a constant flow of cells through the meristem, where the input of dividing pluripotent cells offsets the output of differentiating cells. KNOTTED1-like homeobox (KNOX) genes are expressed in specific patterns in the plant meristems and play important roles in maintaining meristematic cell identity. We have analyzed the expression pattern of HtKNOT1, a class I KNOX gene of Helianthus tuberosus, in stems, inflorescence meristems, floral meristems and floral organs. HtKNOT1 is expressed in cambial cells, phloem cells and xylematic parenchyma within apical stem internodes, while in basal internodes HtKNOT1 expression was restricted to the presumptive initials and recently derived phloem cells. In the reproductive phase, HtKNOT1 mRNAs were detected in both the inflorescence and floral meristems as well within lateral organ primordia (i.e. floral bracts, petals, stamens and carpels). In more differentiated flowers, the expression of HtKNOT1 was restricted to developing ovules and pollen mother cells. HtKNOT1 may play a dual role being required to maintain the meristem initials as well as initiating differentiation and/or conferring new cell identity. In particular, it is possible that HtKNOT1 cooperates at floral level with additional factors that more specifically control floral organs and pollen development in H. tuberosus.

Calibration of a distributed hydrologic model using observed spatial patterns from MODIS data

NASA Astrophysics Data System (ADS)

Demirel, Mehmet C.; González, Gorka M.; Mai, Juliane; Stisen, Simon

2016-04-01

Distributed hydrologic models are typically calibrated against streamflow observations at the outlet of the basin. Along with these observations from gauging stations, satellite based estimates offer independent evaluation data such as remotely sensed actual evapotranspiration (aET) and land surface temperature. The primary objective of the study is to compare model calibrations against traditional downstream discharge measurements with calibrations against simulated spatial patterns and combinations of both types of observations. While the discharge based model calibration typically improves the temporal dynamics of the model, it seems to give rise to minimum improvement of the simulated spatial patterns. In contrast, objective functions specifically targeting the spatial pattern performance could potentially increase the spatial model performance. However, most modeling studies, including the model formulations and parameterization, are not designed to actually change the simulated spatial pattern during calibration. This study investigates the potential benefits of incorporating spatial patterns from MODIS data to calibrate the mesoscale hydrologic model (mHM). This model is selected as it allows for a change in the spatial distribution of key soil parameters through the optimization of pedo-transfer function parameters and includes options for using fully distributed daily Leaf Area Index (LAI) values directly as input. In addition the simulated aET can be estimated at a spatial resolution suitable for comparison to the spatial patterns observed with MODIS data. To increase our control on spatial calibration we introduced three additional parameters to the model. These new parameters are part of an empirical equation to the calculate crop coefficient (Kc) from daily LAI maps and used to update potential evapotranspiration (PET) as model inputs. This is done instead of correcting/updating PET with just a uniform (or aspect driven) factor used in the mHM model (version 5.3). We selected the 20 most important parameters out of 53 mHM parameters based on a comprehensive sensitivity analysis (Cuntz et al., 2015). We calibrated 1km-daily mHM for the Skjern basin in Denmark using the Shuffled Complex Evolution (SCE) algorithm and inputs at different spatial scales i.e. meteorological data at 10km and morphological data at 250 meters. We used correlation coefficients between observed monthly (summer months only) MODIS data calculated from cloud free days over the calibration period from 2001 to 2008 and simulated aET from mHM over the same period. Similarly other metrics, e.g mapcurves and fraction skill-score, are also included in our objective function to assess the co-location of the grid-cells. The preliminary results show that multi-objective calibration of mHM against observed streamflow and spatial patterns together does not significantly reduce the spatial errors in aET while it improves the streamflow simulations. This is a strong signal for further investigation of the multi parameter regionalization affecting spatial aET patterns and weighting the spatial metrics in the objective function relative to the streamflow metrics.

Optimization of landscape pattern [Chapter 8

Treesearch

John Hof; Curtis Flather

2007-01-01

A fundamental assumption in landscape ecology is that spatial patterns have significant influences on the flows of materials, energy, and information while processes create, modify, and maintain spatial patterns. Thus, it is of paramount importance in both theory and practice to address the questions of landscape pattern optimization ... For example, can landscape...

Expression of insulin-like growth factor I receptors at mRNA and protein levels during metamorphosis of Japanese flounder (Paralichthys olivaceus).

PubMed

Zhang, Junling; Shi, Zhiyi; Cheng, Qi; Chen, Xiaowu

2011-08-01

Insulin-like growth factor I (IGF-I) is an important regulator of fish growth and development, and its biological actions are initiated by binding to IGF-I receptor (IGF-IR). Our previous study has revealed that IGF-I could play an important role during metamorphosis of Japanese flounder, Paralichthys olivaceus. The analysis of IGF-IR expression thus helps further elucidate the IGF-I regulation of metamorphic processes. In this study, the spatial-temporal expression of two distinct IGF-IR mRNAs was investigated by real-time RT-PCR. The spatial distribution of two IGF-IR mRNAs in adult tissues is largely overlapped, but they exhibit distinct temporal expression patterns during larval development. A remarkable decrease in IGF-IR-2 mRNA was detected during metamorphosis. In contrast, a significant increase in IGF-IR-1 mRNA was determined from pre-metamorphosis to metamorphic completion. These indicate that they may play different function roles during the flounder metamorphosis. The levels and localization of IGF-IR proteins during larval development were further studied by Western blotting and immunohistochemistry. Immunoreactive IGF-IRs were detected throughout larval development, and the IGF-IR proteins displayed a relatively abundant expression during metamorphosis. Moreover, the IGF-IR proteins appeared in key tissues, such as thickened skin beneath the migrating eye, developing intestine, gills and kidney during metamorphosis. These results further suggest that the IGF-I system may be involved in metamorphic development of Japanese flounder. Copyright © 2011 Elsevier Inc. All rights reserved.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Introduction of the human AVPR1A gene substantially alters brain receptor expression patterns and enhances aspects of social behavior in transgenic mice.

PubMed

Charles, Rhonda; Sakurai, Takeshi; Takahashi, Nagahide; Elder, Gregory A; Gama Sosa, Miguel A; Young, Larry J; Buxbaum, Joseph D

2014-08-01

Central arginine vasopressin receptor 1A (AVPR1A) modulates a wide range of behaviors, including stress management and territorial aggression, as well as social bonding and recognition. Inter- and intra-species variations in the expression pattern of AVPR1A in the brain and downstream differential behavioral phenotypes have been attributed to differences in the non-coding regions of the AVPR1A gene, including polymorphic elements within upstream regulatory areas. Gene association studies have suggested a link between AVPR1A polymorphisms and autism, and AVPR1A has emerged as a potential pharmacological target for treatment of social cognitive impairments and mood and anxiety disorders. To further investigate the genetic mechanism giving rise to species differences in AVPR1A expression patterns and associated social behaviors, and to create a preclinical mouse model useful for screening drugs targeting AVPR1A, we engineered and extensively characterized bacterial artificial chromosome (BAC) transgenic mice harboring the entire human AVPR1A locus with the surrounding regulatory elements. Compared with wild-type animals, the humanized mice displayed a more widely distributed ligand-AVPR1A binding pattern, which overlapped with that of primates. Furthermore, humanized AVPR1A mice displayed increased reciprocal social interactions compared with wild-type animals, but no differences in social approach and preference for social novelty were observed. Aspects of learning and memory, specifically novel object recognition and spatial relocation recognition, were unaffected. The biological alterations in humanized AVPR1A mice resulted in the rescue of the prepulse inhibition impairments that were observed in knockout mice, indicating conserved functionality. Although further behavioral paradigms and additional cohorts need to be examined in humanized AVPR1A mice, the results demonstrate that species-specific variations in the genomic content of regulatory regions surrounding the AVPR1A locus are responsible for differential receptor protein expression patterns across species and that they are likely to contribute to species-specific behavioral variation. The humanized AVPR1A mouse is a potential preclinical model for further understanding the regulation of receptor gene expression and the impact of variation in receptor expression on behaviors, and should be useful for screening drugs targeting human AVPR1A, taking advantage of the expression of human AVPR1A in human-relevant brain regions. © 2014. Published by The Company of Biologists Ltd.

Environmental drivers and spatial dependency in wildfire ignition patterns of northwestern Patagonia.

PubMed

Mundo, Ignacio A; Wiegand, Thorsten; Kanagaraj, Rajapandian; Kitzberger, Thomas

2013-07-15

Fire management requires an understanding of the spatial characteristics of fire ignition patterns and how anthropogenic and natural factors influence ignition patterns across space. In this study we take advantage of a recent fire ignition database (855 points) to conduct a comprehensive analysis of the spatial pattern of fire ignitions in the western area of Neuquén province (57,649 km(2)), Argentina, for the 1992-2008 period. The objectives of our study were to better understand the spatial pattern and the environmental drivers of the fire ignitions, with the ultimate aim of supporting fire management. We conducted our analyses on three different levels: statistical "habitat" modelling of fire ignition (natural, anthropogenic, and all causes) based on an information theoretic approach to test several competing hypotheses on environmental drivers (i.e. topographic, climatic, anthropogenic, land cover, and their combinations); spatial point pattern analysis to quantify additional spatial autocorrelation in the ignition patterns; and quantification of potential spatial associations between fires of different causes relative to towns using a novel implementation of the independence null model. Anthropogenic fire ignitions were best predicted by the most complex habitat model including all groups of variables, whereas natural ignitions were best predicted by topographic, climatic and land-cover variables. The spatial pattern of all ignitions showed considerable clustering at intermediate distances (<40 km) not captured by the probability of fire ignitions predicted by the habitat model. There was a strong (linear) and highly significant increase in the density of fire ignitions with decreasing distance to towns (<5 km), but fire ignitions of natural and anthropogenic causes were statistically independent. A two-dimensional habitat model that quantifies differences between ignition probabilities of natural and anthropogenic causes allows fire managers to delineate target areas for consideration of major preventive treatments, strategic placement of fuel treatments, and forecasting of fire ignition. The techniques presented here can be widely applied to situations where a spatial point pattern is jointly influenced by extrinsic environmental factors and intrinsic point interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Scaling Issues Between Plot and Satellite Radiobrightness Observations of Arctic Tundra

NASA Technical Reports Server (NTRS)

Kim, Edward J.; England, Anthony W.; Judge, Jasmeet; Zukor, Dorothy J. (Technical Monitor)

2000-01-01

Data from generation of satellite microwave radiometer will allow the detection of seasonal to decadal changes in the arctic hydrology cycle as expressed in temporal and spatial patterns of moisture stored in soil and snow This nw capability will require calibrated Land Surface Process/Radiobrightness (LSP/R) model for the principal terrains found in the circumpolar Arctic. These LSP/R models can than be used in weak constraint. Dimensional Data Assimilation (DDA)of the daily satellite observation to estimate temperature and moisture profiles within the permafrost in active layer.

Spatial pattern and ecological process in the coffee agroforestry system.

PubMed

Perfecto, Ivette; Vandermeer, John

2008-04-01

The coffee agroforestry system provides an ideal platform for the study of spatial ecology. The uniform pattern of the coffee plants and shade trees allows for the study of pattern generation through intrinsic biological forces rather than extrinsic habitat patchiness. Detailed studies, focusing on a key mutualism between an ant (Azteca instabilis) and a scale insect (Coccus viridis), conducted in a 45-ha plot in a coffee agroforestry system have provided insights into (1) the quantitative evaluation of spatial pattern of the scale insect Coccus viridis on coffee bushes, (2) the mechanisms for the generation of patterns through the combination of local satellite ant nest formation and regional control from natural enemies, and (3) the consequences of the spatial pattern for the stability of predator-prey (host-parasitoid) systems, for a key coccinelid beetle preying on the scale insects and a phorid fly parasitoid parasitizing the ant.

Grid cell hexagonal patterns formed by fast self-organized learning within entorhinal cortex.

PubMed

Mhatre, Himanshu; Gorchetchnikov, Anatoli; Grossberg, Stephen

2012-02-01

Grid cells in the dorsal segment of the medial entorhinal cortex (dMEC) show remarkable hexagonal activity patterns, at multiple spatial scales, during spatial navigation. It has previously been shown how a self-organizing map can convert firing patterns across entorhinal grid cells into hippocampal place cells that are capable of representing much larger spatial scales. Can grid cell firing fields also arise during navigation through learning within a self-organizing map? This article describes a simple and general mathematical property of the trigonometry of spatial navigation which favors hexagonal patterns. The article also develops a neural model that can learn to exploit this trigonometric relationship. This GRIDSmap self-organizing map model converts path integration signals into hexagonal grid cell patterns of multiple scales. GRIDSmap creates only grid cell firing patterns with the observed hexagonal structure, predicts how these hexagonal patterns can be learned from experience, and can process biologically plausible neural input and output signals during navigation. These results support an emerging unified computational framework based on a hierarchy of self-organizing maps for explaining how entorhinal-hippocampal interactions support spatial navigation. Copyright © 2010 Wiley Periodicals, Inc.

Modification of hippocampal markers of synaptic plasticity by memantine in animal models of acute and repeated restraint stress: implications for memory and behavior.

PubMed

Amin, Shaimaa Nasr; El-Aidi, Ahmed Amro; Ali, Mohamed Mostafa; Attia, Yasser Mahmoud; Rashed, Laila Ahmed

2015-06-01

Stress is any condition that impairs the balance of the organism physiologically or psychologically. The response to stress involves several neurohormonal consequences. Glutamate is the primary excitatory neurotransmitter in the central nervous system, and its release is increased by stress that predisposes to excitotoxicity in the brain. Memantine is an uncompetitive N-methyl D-aspartate glutamatergic receptors antagonist and has shown beneficial effect on cognitive function especially in Alzheimer's disease. The aim of the work was to investigate memantine effect on memory and behavior in animal models of acute and repeated restraint stress with the evaluation of serum markers of stress and the expression of hippocampal markers of synaptic plasticity. Forty-two male rats were divided into seven groups (six rats/group): control, acute restraint stress, acute restraint stress with Memantine, repeated restraint stress, repeated restraint stress with Memantine and Memantine groups (two subgroups as positive control). Spatial working memory and behavior were assessed by performance in Y-maze. We evaluated serum cortisol, tumor necrotic factor, interleukin-6 and hippocampal expression of brain-derived neurotrophic factor, synaptophysin and calcium-/calmodulin-dependent protein kinase II. Our results revealed that Memantine improved spatial working memory in repeated stress, decreased serum level of stress markers and modified the hippocampal synaptic plasticity markers in both patterns of stress exposure; in ARS, Memantine upregulated the expression of synaptophysin and brain-derived neurotrophic factor and downregulated the expression of calcium-/calmodulin-dependent protein kinase II, and in repeated restraint stress, it upregulated the expression of synaptophysin and downregulated calcium-/calmodulin-dependent protein kinase II expression.

Differential Arc expression in the hippocampus and striatum during the transition from attentive to automatic navigation on a plus maze

PubMed Central

Gardner, Robert S.; Suarez, Daniel F.; Robinson-Burton, Nadira K.; Rudnicky, Christopher J.; Gulati, Asish; Ascoli, Giorgio A.; Dumas, Theodore C.

2016-01-01

The strategies utilized to effectively perform a given task change with practice and experience. During a spatial navigation task, with relatively little training, performance is typically attentive enabling an individual to locate the position of a goal by relying on spatial landmarks. These (place) strategies require an intact hippocampus. With task repetition, performance becomes automatic; the same goal is reached using a fixed response or sequence of actions. These (response) strategies require an intact striatum. The current work aims to understand the activation patterns across these neural structures during this experience-dependent strategy transition. This was accomplished by region-specific measurement of activity-dependent immediate early gene expression among rats trained to different degrees on a dual-solution task (i.e., a task that can be solved using either place or response navigation). As expected, rats increased their reliance on response navigation with extended task experience. In addition, dorsal hippocampal expression of the immediate early gene Arc was considerably reduced in rats that used a response strategy late in training (as compared with hippocampal expression in rats that used a place strategy early in training). In line with these data, vicarious trial and error, a behavior linked to hippocampal function, also decreased with task repetition. Although Arc mRNA expression in dorsal medial or lateral striatum alone did not correlate with training stage, the ratio of expression in the medial striatum to that in the lateral striatum was relatively high among rats that used a place strategy early in training as compared with the ratio among over-trained response rats. Altogether, these results identify specific changes in the activation of dissociated neural systems that may underlie the experience-dependent emergence of response-based automatic navigation. PMID:26976088

Expression of RYamide in the nervous and endocrine system of Bombyx mori.

PubMed

Roller, Ladislav; Čižmár, Daniel; Bednár, Branislav; Žitňan, Dušan

2016-06-01

RYamides are neuropeptides encoded by a gene whose precise expression and function have not yet been determined. We identified the RYamide gene transcript (fmgV1g15f, SilkBase database) and predicted two candidates for G-protein coupled RYamide receptors (A19-BAG68418 and A22-BAG68421) in the silkworm Bombyx mori. We cloned the RYamide transcript and described its spatial expression using in situ hybridisation. In the larval central nervous system (CNS) expression of RYamide was restricted to 12-14 small neurons in the brain and two posterior neurons in the terminal abdominal ganglion. During metamorphosis their number decreased to eight protocerebral neurons in the adults. Multiple staining, using various insect neuropeptide antibodies, revealed that neurons expressing RYamide are different from other peptidergic cells in the CNS. We also found RYamide expression in the enteroendocrine cells (EC) of the anterior midgut of larvae, pupae and adults. Two minor subpopulations of these EC were also immunoreactive to antibodies against tachykinin and myosupressin. This expression pattern suggests RYamides may play a role in the regulation of feeding and digestion. Copyright © 2016 Elsevier Inc. All rights reserved.

The SPAtial EFficiency metric (SPAEF): multiple-component evaluation of spatial patterns for optimization of hydrological models

NASA Astrophysics Data System (ADS)

Koch, Julian; Cüneyd Demirel, Mehmet; Stisen, Simon

2018-05-01

The process of model evaluation is not only an integral part of model development and calibration but also of paramount importance when communicating modelling results to the scientific community and stakeholders. The modelling community has a large and well-tested toolbox of metrics to evaluate temporal model performance. In contrast, spatial performance evaluation does not correspond to the grand availability of spatial observations readily available and to the sophisticate model codes simulating the spatial variability of complex hydrological processes. This study makes a contribution towards advancing spatial-pattern-oriented model calibration by rigorously testing a multiple-component performance metric. The promoted SPAtial EFficiency (SPAEF) metric reflects three equally weighted components: correlation, coefficient of variation and histogram overlap. This multiple-component approach is found to be advantageous in order to achieve the complex task of comparing spatial patterns. SPAEF, its three components individually and two alternative spatial performance metrics, i.e. connectivity analysis and fractions skill score, are applied in a spatial-pattern-oriented model calibration of a catchment model in Denmark. Results suggest the importance of multiple-component metrics because stand-alone metrics tend to fail to provide holistic pattern information. The three SPAEF components are found to be independent, which allows them to complement each other in a meaningful way. In order to optimally exploit spatial observations made available by remote sensing platforms, this study suggests applying bias insensitive metrics which further allow for a comparison of variables which are related but may differ in unit. This study applies SPAEF in the hydrological context using the mesoscale Hydrologic Model (mHM; version 5.8), but we see great potential across disciplines related to spatially distributed earth system modelling.

Single beam write and/or replay of spatial heterodyne holograms

DOEpatents

Thomas, Clarence E.; Hanson, Gregory R.

2007-11-20

A method of writing a spatially heterodyne hologram having spatially heterodyne fringes includes: passing a single write beam through a spatial light modulator that digitally modulates said single write beam; and focusing the single write beam at a focal plane of a lens to impose a holographic diffraction grating pattern on the photorefractive crystal, the holographic diffraction grating pattern including the spatially heterodyne hologram having spatially heterodyne fringes, wherein only said single write beam is incident on said photorefractive crystal without a reference beam. A method of replaying a spatially heterodyne hologram having spatially heterodyne fringes at a replay angle includes: illuminating a photorefractive crystal having a holographic diffraction grating with a beam from a laser at an illumination angle, the holographic diffraction grating pattern including the spatially heterodyne hologram having spatially heterodyne fringes, wherein a difference between said illumination angle and said replay angle defines a diffraction angle .alpha. that is a function of a plane wave mathematically added to original object wave phase and amplitude data of said spatially heterodyne hologram having spatially heterodyne fringes.

Spatial patterns and climate drivers of carbon fluxes in terrestrial ecosystems of China.

PubMed

Yu, Gui-Rui; Zhu, Xian-Jin; Fu, Yu-Ling; He, Hong-Lin; Wang, Qiu-Feng; Wen, Xue-Fa; Li, Xuan-Ran; Zhang, Lei-Ming; Zhang, Li; Su, Wen; Li, Sheng-Gong; Sun, Xiao-Min; Zhang, Yi-Ping; Zhang, Jun-Hui; Yan, Jun-Hua; Wang, Hui-Min; Zhou, Guang-Sheng; Jia, Bing-Rui; Xiang, Wen-Hua; Li, Ying-Nian; Zhao, Liang; Wang, Yan-Fen; Shi, Pei-Li; Chen, Shi-Ping; Xin, Xiao-Ping; Zhao, Feng-Hua; Wang, Yu-Ying; Tong, Cheng-Li

2013-03-01

Understanding the dynamics and underlying mechanism of carbon exchange between terrestrial ecosystems and the atmosphere is one of the key issues in global change research. In this study, we quantified the carbon fluxes in different terrestrial ecosystems in China, and analyzed their spatial variation and environmental drivers based on the long-term observation data of ChinaFLUX sites and the published data from other flux sites in China. The results indicate that gross ecosystem productivity (GEP), ecosystem respiration (ER), and net ecosystem productivity (NEP) of terrestrial ecosystems in China showed a significantly latitudinal pattern, declining linearly with the increase of latitude. However, GEP, ER, and NEP did not present a clear longitudinal pattern. The carbon sink functional areas of terrestrial ecosystems in China were mainly located in the subtropical and temperate forests, coastal wetlands in eastern China, the temperate meadow steppe in the northeast China, and the alpine meadow in eastern edge of Qinghai-Tibetan Plateau. The forest ecosystems had stronger carbon sink than grassland ecosystems. The spatial patterns of GEP and ER in China were mainly determined by mean annual precipitation (MAP) and mean annual temperature (MAT), whereas the spatial variation in NEP was largely explained by MAT. The combined effects of MAT and MAP explained 79%, 62%, and 66% of the spatial variations in GEP, ER, and NEP, respectively. The GEP, ER, and NEP in different ecosystems in China exhibited 'positive coupling correlation' in their spatial patterns. Both ER and NEP were significantly correlated with GEP, with 68% of the per-unit GEP contributed to ER and 29% to NEP. MAT and MAP affected the spatial patterns of ER and NEP mainly by their direct effects on the spatial pattern of GEP. © 2012 Blackwell Publishing Ltd.

Integrating the statistical analysis of spatial data in ecology

Treesearch

A. M. Liebhold; J. Gurevitch

2002-01-01

In many areas of ecology there is an increasing emphasis on spatial relationships. Often ecologists are interested in new ways of analyzing data with the objective of quantifying spatial patterns, and in designing surveys and experiments in light of the recognition that there may be underlying spatial pattern in biotic responses. In doing so, ecologists have adopted a...

Spatial ecology of the aquatic garter snake, Thamnophis atratus, in a free-flowing stream environment

Treesearch

H. H. Welsh; C. A. Wheeler; A. J. Lind

2010-01-01

Spatial patterns of animals have important implications for population dynamics and can reveal other key aspects of a species' ecology. Movements and the resulting spatial arrangements have fitness and genetic consequences for both individuals and populations. We studied the spatial and dispersal patterns of the Oregon Gartersnake, Thamnophis atratus...

Spatial scaling of non-native fish richness across the United States

Treesearch

Qinfeng Guo; Julian D. Olden

2014-01-01

A major goal and challenge of invasion ecology is to describe and interpret spatial and temporal patterns of species invasions. Here, we examined fish invasion patterns at four spatially structured and hierarchically nested scales across the contiguous United States (i.e., from large to small: region, basin, watershed, and sub-watershed). All spatial relationships in...

Pattern-Based Inverse Modeling for Characterization of Subsurface Flow Models with Complex Geologic Heterogeneity

NASA Astrophysics Data System (ADS)

Golmohammadi, A.; Jafarpour, B.; M Khaninezhad, M. R.

2017-12-01

Calibration of heterogeneous subsurface flow models leads to ill-posed nonlinear inverse problems, where too many unknown parameters are estimated from limited response measurements. When the underlying parameters form complex (non-Gaussian) structured spatial connectivity patterns, classical variogram-based geostatistical techniques cannot describe the underlying connectivity patterns. Modern pattern-based geostatistical methods that incorporate higher-order spatial statistics are more suitable for describing such complex spatial patterns. Moreover, when the underlying unknown parameters are discrete (geologic facies distribution), conventional model calibration techniques that are designed for continuous parameters cannot be applied directly. In this paper, we introduce a novel pattern-based model calibration method to reconstruct discrete and spatially complex facies distributions from dynamic flow response data. To reproduce complex connectivity patterns during model calibration, we impose a feasibility constraint to ensure that the solution follows the expected higher-order spatial statistics. For model calibration, we adopt a regularized least-squares formulation, involving data mismatch, pattern connectivity, and feasibility constraint terms. Using an alternating directions optimization algorithm, the regularized objective function is divided into a continuous model calibration problem, followed by mapping the solution onto the feasible set. The feasibility constraint to honor the expected spatial statistics is implemented using a supervised machine learning algorithm. The two steps of the model calibration formulation are repeated until the convergence criterion is met. Several numerical examples are used to evaluate the performance of the developed method.

Age-specific contacts and travel patterns in the spatial spread of 2009 H1N1 influenza pandemic

PubMed Central

2013-01-01

Background Confirmed H1N1 cases during late spring and summer 2009 in various countries showed a substantial age shift between importations and local transmission cases, with adults mainly responsible for seeding unaffected regions and children most frequently driving community outbreaks. Methods We introduce a multi-host stochastic metapopulation model with two age classes to analytically investigate the role of a heterogeneously mixing population and its associated non-homogeneous travel behaviors on the risk of a major epidemic. We inform the model with demographic data, contact data and travel statistics of Europe and Mexico, and calibrate it to the 2009 H1N1 pandemic early outbreak. We allow for variations of the model parameters to explore the conditions of invasion under different scenarios. Results We derive the expression for the potential of global invasion of the epidemic that depends on the transmissibility of the pathogen, the transportation network and mobility features, the demographic profile and the mixing pattern. Higher assortativity in the contact pattern greatly increases the probability of spatial containment of the epidemic, this effect being contrasted by an increase in the social activity of adults vs. children. Heterogeneous features of the mobility network characterizing its topology and traffic flows strongly favor the invasion of the pathogen at the spatial level, as also a larger fraction of children traveling. Variations in the demographic profile and mixing habits across countries lead to heterogeneous outbreak situations. Model results are compatible with the H1N1 spatial transmission dynamics observed. Conclusions This work illustrates the importance of considering age-dependent mixing profiles and mobility features coupled together to study the conditions for the spatial invasion of an emerging influenza pandemic. Its results allow the immediate assessment of the risk of a major epidemic for a specific scenario upon availability of data, and the evaluation of the potential effectiveness of public health interventions targeting specific age groups, their interactions and mobility behaviors. The approach provides a general modeling framework that can be used for other types of partitions of the host population and applied to different settings. PMID:23587010

Spatial patterns of ecohydrologic properties on a hillslope-alluvial fan transect, central New Mexico

USGS Publications Warehouse

Bedford, D.R.; Small, E.E.

2008-01-01

Spatial patterns of soil properties are linked to patchy vegetation in arid and semi-arid landscapes. The patterns of soil properties are generally assumed to be linked to the ecohydrological functioning of patchy dryland vegetation ecosystems. We studied the effects of vegetation canopy, its spatial pattern, and landforms on soil properties affecting overland flow and infiltration in shrublands at the Sevilleta National Wildlife Refuge/LTER in central New Mexico, USA. We studied the patterns of microtopography and saturated conductivity (Ksat), and generally found it to be affected by vegetation canopy and pattern, as well as landform type. On gently sloping alluvial fans, both microtopography and Ksat are high under vegetation canopy and decay with distance from plant center. On steeper hillslope landforms, only microtopography was significantly higher under vegetation canopy, while there was no significant difference in Ksat between vegetation and interspaces. Using geostatistics, we found that the spatial pattern of soil properties was determined by the spatial pattern of vegetation. Most importantly, the effects of vegetation were present in the unvegetated interspaces 2-4 times the extent of vegetation canopy, on the order of 2-3??m. Our results have implications for the understanding the ecohydrologic function of semi-arid ecosystems as well as the parameterization of hydrologic models. ?? 2007 Elsevier B.V. All rights reserved.

Expression of the mRNAs encoding the limbic system-associated membrane protein (LAMP): II. Fetal rat brain.

PubMed

Pimenta, A F; Reinoso, B S; Levitt, P

1996-11-11

The limbic system-associated membrane protein (LAMP) is a 64-68 kDa neuronal surface glycoprotein expressed in cortical and subcortical regions of the limbic system of the adult and developing rat central nervous system (CNS). LAMP is a member of the immunoglobulin superfamily of cell adhesion molecules with three Ig domains and is highly conserved between rat and human. In this study, the temporal and spatial pattern of lamp gene expression during fetal rat development was analyzed by using Northern blot analysis and in situ hybridization. In Northern blot analysis, two lamp mRNA transcripts, 1.6 kb and 8.0 kb, identical in size to those present in the adult rat nervous system, were detected in developing neural tissue. In situ hybridization analysis showed close correlation, though not identity, between the expression of lamp mRNAs and the distribution of LAMP in limbic regions of the developing rat CNS, indicative of a more complex regulation of gene expression than was previously thought to be the case. The expression of lamp mRNAs is first detected on about embryonic day (E) 13. The hybridization signal is not seen in the proliferative ventricular zone at any level of the neuraxis, indicating that lamp is expressed in postmitotic neurons. In the cerebral cortex, lamp mRNAs are expressed in limbic cortical regions, such as the perirhinal cortex, prefrontal cortex, and cingulate cortex. In the hippocampus, the hybridization signal is observed in Ammon's horn by E18. The neostriatum, amygdaloid complex, and most hypothalamic areas express lamp mRNAs from early stages (E13-E14) in a pattern consistent with the onset of neurogenesis. The emerging patterns of lamp expression at the outset are similar to those seen in adult hypothalamus and dorsal thalamus. Although the hybridization signal is observed in some nonlimbic areas, including midbrain and hindbrain structures, intense labeling is evident in more classic limbic regions. The high levels of expression of lamp in limbic regions, beginning in early developmental stages, combined with the results of previous functional in vitro and in vivo studies, support a role for LAMP as a recognition molecule involved in the formation of limbic connections.

Effects of Heterogeniety on Spatial Pattern Analysis of Wild Pistachio Trees in Zagros Woodlands, Iran

NASA Astrophysics Data System (ADS)

Erfanifard, Y.; Rezayan, F.

2014-10-01

Vegetation heterogeneity biases second-order summary statistics, e.g., Ripley's K-function, applied for spatial pattern analysis in ecology. Second-order investigation based on Ripley's K-function and related statistics (i.e., L- and pair correlation function g) is widely used in ecology to develop hypothesis on underlying processes by characterizing spatial patterns of vegetation. The aim of this study was to demonstrate effects of underlying heterogeneity of wild pistachio (Pistacia atlantica Desf.) trees on the second-order summary statistics of point pattern analysis in a part of Zagros woodlands, Iran. The spatial distribution of 431 wild pistachio trees was accurately mapped in a 40 ha stand in the Wild Pistachio & Almond Research Site, Fars province, Iran. Three commonly used second-order summary statistics (i.e., K-, L-, and g-functions) were applied to analyse their spatial pattern. The two-sample Kolmogorov-Smirnov goodness-of-fit test showed that the observed pattern significantly followed an inhomogeneous Poisson process null model in the study region. The results also showed that heterogeneous pattern of wild pistachio trees biased the homogeneous form of K-, L-, and g-functions, demonstrating a stronger aggregation of the trees at the scales of 0-50 m than actually existed and an aggregation at scales of 150-200 m, while regularly distributed. Consequently, we showed that heterogeneity of point patterns may bias the results of homogeneous second-order summary statistics and we also suggested applying inhomogeneous summary statistics with related null models for spatial pattern analysis of heterogeneous vegetations.

Terrain feature recognition for synthetic aperture radar (SAR) imagery employing spatial attributes of targets

NASA Astrophysics Data System (ADS)

Iisaka, Joji; Sakurai-Amano, Takako

1994-08-01

This paper describes an integrated approach to terrain feature detection and several methods to estimate spatial information from SAR (synthetic aperture radar) imagery. Spatial information of image features as well as spatial association are key elements in terrain feature detection. After applying a small feature preserving despeckling operation, spatial information such as edginess, texture (smoothness), region-likeliness and line-likeness of objects, target sizes, and target shapes were estimated. Then a trapezoid shape fuzzy membership function was assigned to each spatial feature attribute. Fuzzy classification logic was employed to detect terrain features. Terrain features such as urban areas, mountain ridges, lakes and other water bodies as well as vegetated areas were successfully identified from a sub-image of a JERS-1 SAR image. In the course of shape analysis, a quantitative method was developed to classify spatial patterns by expanding a spatial pattern through the use of a series of pattern primitives.

Sites and Regulation of Polyamine Catabolism in the Tobacco Plant. Correlations with Cell Division/Expansion, Cell Cycle Progression, and Vascular Development1

PubMed Central

Paschalidis, Konstantinos A.; Roubelakis-Angelakis, Kalliopi A.

2005-01-01

We previously gave a picture of the homeostatic characteristics of polyamine (PA) biosynthesis and conjugation in tobacco (Nicotiana tabacum) plant organs during development. In this work, we present the sites and regulation of PA catabolism related to cell division/expansion, cell cycle progression, and vascular development in the tobacco plant. Diamine oxidase (DAO), PA oxidase (PAO), peroxidases (POXs), and putrescine N-methyltransferase expressions follow temporally and spatially discrete patterns in shoot apical cells, leaves (apical, peripheral, and central regions), acropetal and basipetal petiole regions, internodes, and young and old roots in developing plants. DAO and PAO produce hydrogen peroxide, a plant signal molecule and substrate for POXs. Gene expression and immunohistochemistry analyses reveal that amine oxidases in developing tobacco tissues precede and overlap with nascent nuclear DNA and also with POXs and lignification. In mature and old tissues, flow cytometry indicates that amine oxidase and POX activities, as well as pao gene and PAO protein levels, coincide with G2 nuclear phase and endoreduplication. In young versus the older roots, amine oxidases and POX expression decrease with parallel inhibition of G2 advance and endoreduplication, whereas putrescine N-methyltransferase dramatically increases. In both hypergeous and hypogeous tissues, DAO and PAO expression occurs in cells destined to undergo lignification, suggesting a different in situ localization. DNA synthesis early in development and the advance in cell cycle/endocycle are temporally and spatially related to PA catabolism and vascular development. PMID:16040649

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.

PubMed

Plouhinec, Jean-Louis; Medina-Ruiz, Sofía; Borday, Caroline; Bernard, Elsa; Vert, Jean-Philippe; Eisen, Michael B; Harland, Richard M; Monsoro-Burq, Anne H

2017-10-01

During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates

PubMed Central

Borday, Caroline; Bernard, Elsa; Vert, Jean-Philippe; Eisen, Michael B.; Harland, Richard M.

2017-01-01

During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research. PMID:29049289

Anteroposterior Patterning of Gene Expression in the Human Infant Sclera: Chondrogenic Potential and Wnt Signaling.

PubMed

Seko, Yuko; Azuma, Noriyuki; Yokoi, Tadashi; Kami, Daisuke; Ishii, Ryuga; Nishina, Sachiko; Toyoda, Masashi; Shimokawa, Hitoyata; Umezawa, Akihiro

2017-01-01

Purpose/Aim: We sought to identify the anteroposterior spatial gene expression hierarchy in the human sclera to develop a hypothesis for axial elongation and deformity of the eyeball. We analyzed the global gene expression of human scleral cells derived from distinct parts of the human infant sclera obtained from surgically enucleated eyes with retinoblastoma, using Affymetrix GeneChip oligonucleotide arrays, and compared, in particular, gene expression levels between the anterior and posterior parts of the sclera. The ages of three donors were 10M, 4M, and 1Y9M. K-means clustering analysis of gene expression revealed that expression levels of cartilage-associated genes such as COLXIA and ACAN increased from the anterior to the posterior part of the sclera. Microarray analyses and RT-PCR data showed that the expression levels of MGP, COLXIA, BMP4, and RARB were significantly higher in the posterior than in the anterior sclera of two independent infant eyes. Conversely, expression levels of WNT2, DKK2, GREM1, and HOXB2 were significantly higher in the anterior sclera. Among several Wnt-family genes examined, WNT2B was found to be expressed at a significantly higher level in the posterior sclera, and the reverse order was observed for WNT2. The results of luciferase reporter assays suggested that a GSK-3β inhibitor stimulated Wnt/β-catenin signaling particularly strongly in the posterior sclera. The expression pattern of RARB, a myopia-related gene, was similar in three independent eyes. Chondrogenic potential was higher and Wnt/β-catenin signaling was more potently activated by a GSK-3β inhibitor in the posterior than in the anterior part of the human infant sclera. Although the differences in the gene expression profiles between the anterior and posterior sclera might be involved only in normal growth processes, this anteroposterior hierarchy in the sclera might contribute to disorders involving abnormal elongation and deformity of the eyeball, including myopia.

Bisphenol A disrupts the temporal pattern of histofunctional changes in the female reproductive tract of Caiman latirostris.

PubMed

Galoppo, Germán H; Canesini, Guillermina; Tavalieri, Yamil E; Stoker, Cora; Kass, Laura; Luque, Enrique H; Muñoz-de-Toro, Mónica

2017-12-01

Recently, we have described the ontogeny of histofunctional differentiation changes in the oviduct of Caiman latirostris. The expression of estrogen receptor alpha and progesterone receptor shows that the caiman oviduct could be a target of the action of xenoestrogens such as the widely environmentally present Bisphenol A (BPA), early in life. The aims of this study were: to complement oviduct characterization by establishing the ontogenetic changes in androgen receptor (AR) expression and assessing the effects of early postnatal exposure to 17-β-estradiol (E2) or BPA on the histofunctional features of the oviduct. AR was expressed in all the stages studied. The spatial pattern of AR immunostaining changed from neonatal to juvenile caimans. In the luminal epithelium, changes were at the subcellular level, from cytoplasmic to nuclear. In the subepithelium, although both cytoplasmic and nuclear AR expression was observed, changes were mainly at tissue level, from the subepithelial compartment to the outer muscular layer. The oviduct was highly sensitive to E2 and BPA at the early postnatal developmental stage. E2- and BPA-exposed caimans showed increased luminal epithelial height and higher proliferative activity. Changes in histomorphological features (measured by a scoring system), steroid hormone receptors, collagen remodeling and muscle-associated proteins suggest a precocious oviduct histofunctional differentiation in E2- and BPA-exposed caimans. The modification of the temporal pattern of oviductal biomarkers suggests that organizational changes could impair C. latirostris reproductive health later in life. The alterations in the caiman female reproductive tract exposed to BPA highlight the importance of preserving aquatic environments from plastic pollution. Copyright © 2017 Elsevier Inc. All rights reserved.

Local sources of retinoic acid coincide with retinoid-mediated transgene activity during embryonic development.

PubMed Central

Colbert, M C; Linney, E; LaMantia, A S

1993-01-01

We have assessed whether retinoic acid (RA) comes from local sources or is available widely to activate gene expression in embryos. We used an RA-responsive indicator cell line, L-C2A5, to localize RA sources. In these cells, an RA-sensitive promoter/lacZ reporter construct used previously by us to produce indicator transgenic mice is induced globally by RA in medium or locally by RA released at physiological concentrations (1 nM) from AG-1X2 resin beads. Furthermore, the cells are differentially responsive to the 9-cis and all-trans isomers of RA at low concentrations. Indicator transgenic mice with the same promoter/reporter construct were used to identify regions of RA-mediated gene activation. There are distinct domains of lacZ expression in the cervical and lumbar spinal cords of embryonic indicator mice. This pattern might reflect localized RA sources or restricted spatial and temporal expression of RA receptors, binding proteins, or other factors. To resolve this issue we compared the pattern of transgene activation in indicator cell monolayers cocultured with normal embryonic spinal cords with that in transgenic spinal cords. The explants induced reporter gene expression in L-C2A5 monolayers in a pattern identical to that in transgenic mice: alar regions of the cervical and lumbar cord were positive whereas those in the thoracic and sacral regions were not. We conclude that restricted sources of RA in the developing spinal cord mediate the local activation of RA-inducible genes. Thus, region-specific gene activation in embryos can be mediated by precisely localized sources of inductive molecules like RA. Images Fig. 1 Fig. 2 Fig. 3 PMID:8341670

Spatial Organization In Europe of Decadal and Interdecadal Fluctuations In Annual Rainfall

NASA Astrophysics Data System (ADS)

Lucero, O. A.; Rodriguez, N. C.

In this research the spatial patterns of decadal and bidecadal fluctuations in annual rainfall in Europe are identified. Filtering of time series of anomaly of annual rainfall is carried out using the Morlet wavelet technique. Reconstruction is achieved by sum- ming the contributions from bands of wavelet timescales; the decadal band and the bidecadal band are composed of contributions from the band of (10- to 17-year] and (17- to 27- year] timescales respectively. Results indicate that 1) the spatial organi- zation of decadal and bidecadal components of annual rainfall are standing wave-like organized patterns. Three standing decadal fluctuations zonally aligned formed the spatial pattern from 1900 until 1931; thereafter the pattern changed into a NW-SE orientation. The decadal band shows an average 12-year period. 2) The spatial orga- nization of bidecadal component was composed of three standing fluctuations since 1903 to 1986. After 1987 two standing bidecadal fluctuations were located on Europe. The orientation of bidecadal fluctuations changed during the period under study. Until 1913 the spatial pattern of the bidecadal component was zonally aligned. Since 1913 until 1986 the three bidecadal fluctuations composing the spatial pattern were aligned SW U NE; starting 1987 the spatial pattern is composed of two standing fluctuations zonally aligned. The bidecadal spatial pattern shows an average period of 20- to 22- year length. 3) At decadal and bidecadal timescales, the first principal component of the spatial field of anomaly of annual rainfall and the NAO index are connected. The upper positive third (lower negative third) of values of first principal component are indicative of extensive area with positive (negative) anomaly of annual rainfall. 4) At decadal timescale the relative phase between the first PC and the NAO index changes through the period under study; these changes define three regimes: 1) Dur- ing the regime covering the period 1900 (start of period under study) to about 1945, at the time of peak values of decadal NAO-index it takes place a transition between extremes (a neutral state) of the decadal rainfall spatial pattern (first PC takes small absolute values). Besides, for positive (negative) peak value of NAO index the spatial pattern of annual rainfall is evolving toward an area of predominantly positive (nega- tive) anomaly. 2) The second regime starts about 1946 and reaches up to early 1980s. At the time of negative (positive) peak of decadal NAO there is a prevailing spatial pattern of positive (negative) anomaly of decadal rainfall. 3) The third regime starts 1 about late 1970s and reaches to the end of the period under study (in 1996). There is a change of relative phase within this period in late 1980s. In this regime a spatial pattern of prevailing positive or negative anomaly of decadal rainfall takes place dur- ing values of decadal NAO close to zero. 5) At bidecadal timescale the relative phase between the first PC and the NAO index remains almost constant through the period under study. The first PC of the transformed bidecadal component of annual rainfall anomaly attains its positive (negative) peak about three years before the bidecadal component of NAO reaches its negative (positive) peak. 2

Mapping PTGERs to the Ovulatory Follicle: Regional Responses to the Ovulatory PGE2 Signal1

PubMed Central

Kim, Soon Ok; Duffy, Diane M.

2016-01-01

Prostaglandin E2 (PGE2) is a key intrafollicular mediator of ovulation in many, if not all, mammalian species. PGE2 acts at follicular cells via four distinct PGE2 receptors (PTGERs). Within the ovulatory follicle, each cell type (e.g., oocyte, cumulus granulosa cell, mural granulosa cell, theca cell, endothelial cell) expresses a different subset of the four PTGERs. Expression of a subset of PTGERs has consequences for the generation of intracellular signals and ultimately the unique functions of follicular cells that respond to PGE2. Just as the ovulatory LH surge regulates PGE2 synthesis, the LH surge also regulates expression of the four PTGERs. The pattern of expression of the four PTGERs among follicular cells before and after the LH surge forms a spatial and temporal map of PGE2 responses. Differential PTGER expression, coupled with activation of cell-specific intracellular signals, may explain how a single paracrine mediator can have pleotropic actions within the ovulatory follicle. Understanding the role of each PTGER in ovulation may point to previously unappreciated opportunities to both promote and prevent fertility. PMID:27307073

A microarray analysis of retinal transcripts that are controlled by image contrast in mice.

PubMed

Brand, Christine; Schaeffel, Frank; Feldkaemper, Marita Pauline

2007-06-18

The development of myopia is controlled by still largely unknown retinal signals. The aim of this study was to investigate the changes in retinal mRNA expression after different periods of visual deprivation in mice, while controlling for retinal illuminance. Each group consisted of three male C57BL/6 mice. Treatment periods were 30 min, 4 h, and 6+6 h. High spatial frequencies were filtered from the retinal image by frosted diffusers over one eye while the fellow eyes were covered by clear neutral density (ND) filters that exhibited similar light attenuating properties (0.1 log units) as the diffusers. For the final 30 min of the respective treatment period mice were individually placed in a clear Perspex cylinder that was positioned in the center of a rotating (60 degrees) large drum. The inside of the drum was covered with a 0.1 cyc/degree vertical square wave grating. This visual environment was chosen to standardize illuminances and contrasts seen by the mice. Labeled cRNA was prepared and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Alterations in mRNA expression levels of candidate genes with potential biological relevance were confirmed by semi-quantitative real-time reverse transcription polymerase chain reaction (RT-PCR). In all groups, Egr-1 mRNA expression was reduced in diffuser-treated eyes. Furthermore, the degradation of the spatial frequency spectrum also changed the cFos mRNA level, with reduced expression after 4 h of diffuser treatment. Other interesting candidates were Akt2, which was up-regulated after 30 min of deprivation and Mapk8ip3, a neuron specific JNK binding and scaffolding protein that was temporally regulated in the diffuser-treated eyes only. The microarray analysis demonstrated a pattern of differential transcriptional changes, even though differences in the retinal images were restricted to spatial features. The candidate genes may provide further insight into the biochemical short-term changes following retinal image degradation in mice. Because deprivation of spatial vision leads to increased eye growth and myopia in both animals and humans, it is believed some of the identified genes play a role in myopia development.

Seed-deposition and recruitment patterns of Clusia species in a disturbed tropical montane forest in Bolivia

NASA Astrophysics Data System (ADS)

Saavedra, Francisco; Hensen, Isabell; Apaza Quevedo, Amira; Neuschulz, Eike Lena; Schleuning, Matthias

2017-11-01

Spatial patterns of seed dispersal and recruitment of fleshy-fruited plants in tropical forests are supposed to be driven by the activity of animal seed dispersers, but the spatial patterns of seed dispersal, seedlings and saplings have rarely been analyzed simultaneously. We studied seed deposition and recruitment patterns of three Clusia species in a tropical montane forest of the Bolivian Andes and tested whether these patterns changed between habitat types (forest edge vs. forest interior), distance to the fruiting tree and consecutive recruitment stages of the seedlings. We recorded the number of seeds deposited in seed traps to assess the local seed-deposition pattern and the abundance and distribution of seedlings and saplings to evaluate the spatial pattern of recruitment. More seeds were removed and deposited at the forest edge than in the interior. The number of deposited seeds decreased with distance from the fruiting tree and was spatially clustered in both habitat types. The density of 1-yr-old seedlings and saplings was higher at forest edges, whereas the density of 2-yr-old seedlings was similar in both habitat types. While seedlings were almost randomly distributed, seeds and saplings were spatially clustered in both habitat types. Our findings demonstrate systematic changes in spatial patterns of recruits across the plant regeneration cycle and suggest that the differential effects of biotic and abiotic factors determine plant recruitment at the edges and in the interior of tropical montane forests. These differences in the spatial distribution of individuals across recruitment stages may have strong effects on plant community dynamics and influence plant species coexistence in disturbed tropical forests.

Spatial patterns in vegetation fires in the Indian region.

PubMed

Vadrevu, Krishna Prasad; Badarinath, K V S; Anuradha, Eaturu

2008-12-01

In this study, we used fire count datasets derived from Along Track Scanning Radiometer (ATSR) satellite to characterize spatial patterns in fire occurrences across highly diverse geographical, vegetation and topographic gradients in the Indian region. For characterizing the spatial patterns of fire occurrences, observed fire point patterns were tested against the hypothesis of a complete spatial random (CSR) pattern using three different techniques, the quadrat analysis, nearest neighbor analysis and Ripley's K function. Hierarchical nearest neighboring technique was used to depict the 'hotspots' of fire incidents. Of the different states, highest fire counts were recorded in Madhya Pradesh (14.77%) followed by Gujarat (10.86%), Maharastra (9.92%), Mizoram (7.66%), Jharkhand (6.41%), etc. With respect to the vegetation categories, highest number of fires were recorded in agricultural regions (40.26%) followed by tropical moist deciduous vegetation (12.72), dry deciduous vegetation (11.40%), abandoned slash and burn secondary forests (9.04%), tropical montane forests (8.07%) followed by others. Analysis of fire counts based on elevation and slope range suggested that maximum number of fires occurred in low and medium elevation types and in very low to low-slope categories. Results from three different spatial techniques for spatial pattern suggested clustered pattern in fire events compared to CSR. Most importantly, results from Ripley's K statistic suggested that fire events are highly clustered at a lag-distance of 125 miles. Hierarchical nearest neighboring clustering technique identified significant clusters of fire 'hotspots' in different states in northeast and central India. The implications of these results in fire management and mitigation were discussed. Also, this study highlights the potential of spatial point pattern statistics in environmental monitoring and assessment studies with special reference to fire events in the Indian region.

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome

PubMed Central

Ariel, Federico; Latrasse, David; Mariappan, Kiruthiga Gayathri; Kim, Soon-Kap; Crespi, Martin; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

2016-01-01

Precise expression patterns of genes in time and space are essential for proper development of multicellular organisms. Dynamic chromatin conformation and spatial organization of the genome constitute a major step in this regulation to modulate developmental outputs. Polycomb repressive complexes (PRCs) mediate stable or flexible gene repression in response to internal and environmental cues. In Arabidopsis thaliana, LHP1 co-localizes with H3K27me3 epigenetic marks throughout the genome and interacts with PRC1 and PRC2 members as well as with a long noncoding RNA. Here, we show that LHP1 is responsible for the spreading of H3K27me3 towards the 3’ end of the gene body. We also identified a subset of LHP1-activated genes and demonstrated that LHP1 shapes local chromatin topology in order to control transcriptional co-regulation. Our work reveals a general role of LHP1 from local to higher conformation levels of chromatin configuration to determine its accessibility to define gene expression patterns. PMID:27410265

Fgf Signaling is Required for Photoreceptor Maintenance in the Adult Zebrafish Retina

PubMed Central

Hochmann, Sarah; Kaslin, Jan; Hans, Stefan; Weber, Anke; Machate, Anja; Geffarth, Michaela; Funk, Richard H. W.; Brand, Michael

2012-01-01

Fibroblast growth factors (Fgf) are secreted signaling molecules that have mitogenic, patterning, neurotrophic and angiogenic properties. Their importance during embryonic development in patterning and morphogenesis of the vertebrate eye is well known, but less is known about the role of Fgfs in the adult vertebrate retina. To address Fgf function in adult retina, we determined the spatial distribution of components of the Fgf signaling pathway in the adult zebrafish retina. We detected differential expression of Fgf receptors, ligands and downstream Fgf targets within specific retinal layers. Furthermore, we blocked Fgf signaling in the retina, by expressing a dominant negative variant of Fgf receptor 1 conditionally in transgenic animals. After blocking Fgf signaling we observe a fast and progressive photoreceptor degeneration and disorganization of retinal tissue, coupled with cell death in the outer nuclear layer. Following the degeneration of photoreceptors, a profound regeneration response is triggered that starts with proliferation in the inner nuclear layer. Ultimately, rod and cone photoreceptors are regenerated completely. Our study reveals the requirement of Fgf signaling to maintain photoreceptors and for proliferation during regeneration in the adult zebrafish retina. PMID:22291943

Development of an electro-responsive platform for the controlled transfection of mammalian cells

NASA Astrophysics Data System (ADS)

Hook, Andrew L.; Thissen, Helmut W.; Hayes, Jason P.; Voelcker, Nicolas H.

2005-02-01

The recent development of living microarrays as novel tools for the analysis of gene expression in an in-situ environment promises to unravel gene function within living organisms. In order to significantly enhance microarray performance, we are working towards electro-responsive DNA transfection chips. This study focuses on the control of DNA adsorption and desorption by appropriate surface modification of highly doped p++ silicon. Silicon was modified by plasma polymerisation of allylamine (ALAPP), a non-toxic surface that sustains cell growth. Subsequent high surface density grafting of poly(ethylene oxide) formed a layer resistant to biomolecule adsorption and cell attachment. Spatially controlled excimer laser ablation of the surface produced micron resolution patterns of re-exposed plasma polymer whilst the rest of the surface remained non-fouling. We observed electro-stimulated preferential adsorption of DNA to the ALAPP surface and subsequent desorption by the application of a negative bias. Cell culture experiments with HEK 293 cells demonstrated efficient and controlled transfection of cells using the expression of green fluorescent protein as a reporter. Thus, these chemically patterned surfaces are promising platforms for use as living microarrays.

Organization of nuclear architecture during adipocyte differentiation

PubMed Central

Charó, Nancy L.; Rodríguez Ceschan, María I.; Galigniana, Natalia M.; Toneatto, Judith; Piwien-Pilipuk, Graciela

2016-01-01

ABSTRACT Obesity is a serious health problem worldwide since it is a major risk factor for chronic diseases such as type II diabetes. Obesity is the result of hyperplasia (associated with increased adipogenesis) and hypertrophy (associated with decreased adipogenesis) of the adipose tissue. Therefore, understanding the molecular mechanisms underlying the process of adipocyte differentiation is relevant to delineate new therapeutic strategies for treatment of obesity. As in all differentiation processes, temporal patterns of transcription are exquisitely controlled, allowing the acquisition and maintenance of the adipocyte phenotype. The genome is spatially organized; therefore decoding local features of the chromatin language alone does not suffice to understand how cell type-specific gene expression patterns are generated. Elucidating how nuclear architecture is built during the process of adipogenesis is thus an indispensable step to gain insight in how gene expression is regulated to achieve the adipocyte phenotype. Here we will summarize the recent advances in our understanding of the organization of nuclear architecture as progenitor cells differentiate in adipocytes, and the questions that still remained to be answered. PMID:27416359

Predictor variable resolution governs modeled soil types

USDA-ARS?s Scientific Manuscript database

Soil mapping identifies different soil types by compressing a unique suite of spatial patterns and processes across multiple spatial scales. It can be quite difficult to quantify spatial patterns of soil properties with remotely sensed predictor variables. More specifically, matching the right scale...

Quantifying spatial patterns of tree groups and gaps in mixed-conifer forests: reference conditions and long-term changes following fire suppression and logging

Treesearch

Jamie M. Lydersen; Malcolm P. North; Eric E. Knapp; Brandon M. Collins

2013-01-01

Fire suppression and past logging have dramatically altered forest conditions in many areas, but changes to within-stand tree spatial patterns over time are not as well understood. The few studies available suggest that variability in tree spatial patterns is an important structural feature of forests with intact frequent fire regimes that should be incorporated in...

Recurrence Methods for the Identification of Morphogenetic Patterns

PubMed Central

Facchini, Angelo; Mocenni, Chiara

2013-01-01

This paper addresses the problem of identifying the parameters involved in the formation of spatial patterns in nonlinear two dimensional systems. To this aim, we perform numerical experiments on a prototypical model generating morphogenetic Turing patterns, by changing both the spatial frequency and shape of the patterns. The features of the patterns and their relationship with the model parameters are characterized by means of the Generalized Recurrence Quantification measures. We show that the recurrence measures Determinism and Recurrence Entropy, as well as the distribution of the line lengths, allow for a full characterization of the patterns in terms of power law decay with respect to the parameters involved in the determination of their spatial frequency and shape. A comparison with the standard two dimensional Fourier transform is performed and the results show a better performance of the recurrence indicators in identifying a reliable connection with the spatial frequency of the patterns. Finally, in order to evaluate the robustness of the estimation of the power low decay, extensive simulations have been performed by adding different levels of noise to the patterns. PMID:24066062

[Spatial analysis of mortality from cardiovascular diseases in Madrid City, Spain].

PubMed

Gómez-Barroso, Diana; Prieto-Flores, María-Eugenia; Mellado San Gabino, Ana; Moreno Jiménez, Antonio

2015-01-01

Cardiovascular disease is the leading cause of death worldwide, but its spatial distribution is not homogeneous. The objective of this study is to analyze the spatial pattern of mortality from these diseases for men and women, in the populated urban area (AUP) of the municipality of Madrid, and to identify spatial aggregations. An ecological study was carried out by census tract, for men and women in 2010. Standardized Mortality Ratio (SMR), Relative Risk Smoothing (RRS) and Posterior Probability (PP) were calculated to consider the spatial pattern of the disease. To identify spatial clusters the Moran index (Moran I) and the Local Index of Spatial Autocorrelation (LISA) were used. The results were mapped. SMR higher than 1.1 was observed mainly in central areas among men and in peripheral areas among women. The PP that RRS was higher than 1 surpassed 0.8 in the center and in the periphery, in both men and women. Moran's I was 0.04 for men and 0.03 for women (p <0.05 in both cases). Sex differences were observed in the spatial distribution of mortality cases. RME RRS and PP maps showed a heterogeneous pattern in men, whereas in women a clearer pattern was detected, with a relatively higher risk in peripheral areas of the AUP. The LISA method showed similar patterns to those previously observed.

Differential DNA methylation may contribute to temporal and spatial regulation of gene expression and the development of mycelia and conidia in entomopathogenic fungus Metarhizium robertsii.

PubMed

Li, Wanzhen; Wang, Yulong; Zhu, Jianyu; Wang, Zhangxun; Tang, Guiliang; Huang, Bo

2017-03-01

Conidia and mycelia are two important developmental stages in the asexual life cycle of entomopathogenic fungus Metarhizium. Despite the crucial role that DNA methylation plays in many biological processes, its role in regulation of gene expression and development in fungi is not yet fully understood. We performed genome-wide analysis of DNA methylation patterns of an M. robertsii strain with single base pair resolution. Specifically, we examined for changes in methylation patterns between the conidia and mycelia stages. The results showed that approximately 0.38 % of cytosines are methylated in conidia, which is lower than the DNA methylation level (0.42 %) in mycelia. We found that DNA methylation undergoes genome-wide reprogramming during fungal development in M. robertsii. 132 differentially methylated regions (DMRs), which were mostly distributed in gene regions, were identified. KEGG analysis revealed that the DMR-associated genes belong to metabolic pathways. Intriguingly, in contrast to most other eukaryotes, promoter activities in M. robertsii seemed differentially modulated by DNA methylation levels. We found that transcription tended to be enhanced in genes with moderate promoter methylation, while gene expression was decreased in genes with high or low promoter methylation. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

PubMed Central

Hawley, Alyse K.; Brewer, Heather M.; Norbeck, Angela D.; Paša-Tolić, Ljiljana; Hallam, Steven J.

2014-01-01

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand. PMID:25053816

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

PubMed

Hawley, Alyse K; Brewer, Heather M; Norbeck, Angela D; Paša-Tolić, Ljiljana; Hallam, Steven J

2014-08-05

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand.

Environmental sex determination mechanisms in reptiles.

PubMed

Merchant-Larios, H; Díaz-Hernández, V

2013-01-01

Temperature-dependent sex determination (TSD) was first discovered in reptiles. Since then, a great diversity of sex-determining responses to temperature has been reported. Higher temperatures can produce either males or females, and the temperature ranges and lengths of exposure that influence TSD are remarkably variable among species. In addition, transitory gene regulatory networks leading to gonadal TSD have evolved. Although most genes involved in gonadal development are conserved in vertebrates, including TSD species, temporal and spatial gene expression patterns vary among species. Despite variation in TSD pattern and gene expression heterochrony, the structural framework, the medullary cords, and cortex of the bipotential gonad have been strongly conserved. Aromatase (CYP19), which regulates gonadal estrogen levels, is proposed to be the main target of a putative thermosensitive factor for TSD. However, manipulation of estrogen levels rarely mimics the precise timing of temperature effects on expression of gonadal genes, as occurs with TSD. Estrogen levels may influence sex determination or gonad differentiation depending on the species. Furthermore, the process leading to sex determination under the influence of temperature poses problems that are not encountered by species with genetic sex determination. Yolk steroids of maternal origin and steroids produced by the embryonic nervous system should also be considered as sources of hormones that may play a role in TSD. Copyright © 2012 S. Karger AG, Basel.

Patterns and scaling properties of surface soil moisture in an agricultural landscape: An ecohydrological modeling study

NASA Astrophysics Data System (ADS)

Korres, W.; Reichenau, T. G.; Schneider, K.

2013-08-01

Soil moisture is a key variable in hydrology, meteorology and agriculture. Soil moisture, and surface soil moisture in particular, is highly variable in space and time. Its spatial and temporal patterns in agricultural landscapes are affected by multiple natural (precipitation, soil, topography, etc.) and agro-economic (soil management, fertilization, etc.) factors, making it difficult to identify unequivocal cause and effect relationships between soil moisture and its driving variables. The goal of this study is to characterize and analyze the spatial and temporal patterns of surface soil moisture (top 20 cm) in an intensively used agricultural landscape (1100 km2 northern part of the Rur catchment, Western Germany) and to determine the dominant factors and underlying processes controlling these patterns. A second goal is to analyze the scaling behavior of surface soil moisture patterns in order to investigate how spatial scale affects spatial patterns. To achieve these goals, a dynamically coupled, process-based and spatially distributed ecohydrological model was used to analyze the key processes as well as their interactions and feedbacks. The model was validated for two growing seasons for the three main crops in the investigation area: Winter wheat, sugar beet, and maize. This yielded RMSE values for surface soil moisture between 1.8 and 7.8 vol.% and average RMSE values for all three crops of 0.27 kg m-2 for total aboveground biomass and 0.93 for green LAI. Large deviations of measured and modeled soil moisture can be explained by a change of the infiltration properties towards the end of the growing season, especially in maize fields. The validated model was used to generate daily surface soil moisture maps, serving as a basis for an autocorrelation analysis of spatial patterns and scale. Outside of the growing season, surface soil moisture patterns at all spatial scales depend mainly upon soil properties. Within the main growing season, larger scale patterns that are induced by soil properties are superimposed by the small scale land use pattern and the resulting small scale variability of evapotranspiration. However, this influence decreases at larger spatial scales. Most precipitation events cause temporarily higher surface soil moisture autocorrelation lengths at all spatial scales for a short time even beyond the autocorrelation lengths induced by soil properties. The relation of daily spatial variance to the spatial scale of the analysis fits a power law scaling function, with negative values of the scaling exponent, indicating a decrease in spatial variability with increasing spatial resolution. High evapotranspiration rates cause an increase in the small scale soil moisture variability, thus leading to large negative values of the scaling exponent. Utilizing a multiple regression analysis, we found that 53% of the variance of the scaling exponent can be explained by a combination of an independent LAI parameter and the antecedent precipitation.

Species richness effects on ecosystem multifunctionality depend on evenness, composition and spatial pattern

USGS Publications Warehouse

Maestre, F.T.; Castillo-Monroy, A. P.; Bowker, M.A.; Ochoa-Hueso, R.

2012-01-01

1. Recent studies have suggested that the simultaneous maintenance of multiple ecosystem functions (multifunctionality) is positively supported by species richness. However, little is known regarding the relative importance of other community attributes (e.g. spatial pattern, species evenness) as drivers of multifunctionality. 2. We conducted two microcosm experiments using model biological soil crust communities dominated by lichens to: (i) evaluate the joint effects and relative importance of changes in species composition, spatial pattern (clumped and random distribution of lichens), evenness (maximal and low evenness) and richness (from two to eight species) on soil functions related to nutrient cycling (β-glucosidase, urease and acid phosphatase enzymes, in situ N availability, total N, organic C, and N fixation), and (ii) assess how these community attributes affect multifunctionality. 3. Species richness, composition and spatial pattern affected multiple ecosystem functions (e.g. organic C, total N, N availability, β-glucosidase activity), albeit the magnitude and direction of their effects varied with the particular function, experiment and soil depth considered. Changes in species composition had effects on organic C, total N and the activity of β-glucosidase. Significant species richness × evenness and spatial pattern × evenness interactions were found when analysing functions such as organic C, total N and the activity of phosphatase. 4. The probability of sustaining multiple ecosystem functions increased with species richness, but this effect was largely modulated by attributes such as species evenness, composition and spatial pattern. Overall, we found that model communities with high species richness, random spatial pattern and low evenness increased multifunctionality. 5. Synthesis. Our results illustrate how different community attributes have a diverse impact on ecosystem functions related to nutrient cycling, and provide new experimental evidence illustrating the importance of the spatial pattern of organisms on ecosystem functioning. They also indicate that species richness is not the only biotic driver of multifunctionality, and that particular combinations of community attributes may be required to maximize it.

Tempo-spatial analysis of Fennoscandian intraplate seismicity

NASA Astrophysics Data System (ADS)

Roberts, Roland; Lund, Björn

2017-04-01

Coupled spatial-temporal patterns of the occurrence of earthquakes in Fennoscandia are analysed using non-parametric methods. The occurrence of larger events is unambiguously and very strongly temporally clustered, with major implications for the assessment of seismic hazard in areas such as Fennoscandia. In addition, there is a clear pattern of geographical migration of activity. Data from the Swedish National Seismic Network and a collated international catalogue are analysed. Results show consistent patterns on different spatial and temporal scales. We are currently investigating these patterns in order to assess the statistical significance of the tempo-spatial patterns, and to what extent these may be consistent with stress transfer mechanism such as coulomb stress and pore fluid migration. Indications are that some further mechanism is necessary in order to explain the data, perhaps related to post-glacial uplift, which is up to 1cm/year.

Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies.

PubMed

Nuñez, Isaac N; Matute, Tamara F; Del Valle, Ilenne D; Kan, Anton; Choksi, Atri; Endy, Drew; Haseloff, Jim; Rudge, Timothy J; Federici, Fernan

2017-02-17

Morphogenetic engineering is an emerging field that explores the design and implementation of self-organized patterns, morphologies, and architectures in systems composed of multiple agents such as cells and swarm robots. Synthetic biology, on the other hand, aims to develop tools and formalisms that increase reproducibility, tractability, and efficiency in the engineering of biological systems. We seek to apply synthetic biology approaches to the engineering of morphologies in multicellular systems. Here, we describe the engineering of two mechanisms, symmetry-breaking and domain-specific cell regulation, as elementary functions for the prototyping of morphogenetic instructions in bacterial colonies. The former represents an artificial patterning mechanism based on plasmid segregation while the latter plays the role of artificial cell differentiation by spatial colocalization of ubiquitous and segregated components. This separation of patterning from actuation facilitates the design-build-test-improve engineering cycle. We created computational modules for CellModeller representing these basic functions and used it to guide the design process and explore the design space in silico. We applied these tools to encode spatially structured functions such as metabolic complementation, RNAPT7 gene expression, and CRISPRi/Cas9 regulation. Finally, as a proof of concept, we used CRISPRi/Cas technology to regulate cell growth by controlling methionine synthesis. These mechanisms start from single cells enabling the study of morphogenetic principles and the engineering of novel population scale structures from the bottom up.

Attempting to physically explain space-time correlation of extremes

NASA Astrophysics Data System (ADS)

Bernardara, Pietro; Gailhard, Joel

2010-05-01

Spatial and temporal clustering of hydro-meteorological extreme events is scientific evidence. Moreover, the statistical parameters characterizing their local frequencies of occurrence show clear spatial patterns. Thus, in order to robustly assess the hydro-meteorological hazard, statistical models need to be able to take into account spatial and temporal dependencies. Statistical models considering long term correlation for quantifying and qualifying temporal and spatial dependencies are available, such as multifractal approach. Furthermore, the development of regional frequency analysis techniques allows estimating the frequency of occurrence of extreme events taking into account spatial patterns on the extreme quantiles behaviour. However, in order to understand the origin of spatio-temporal clustering, an attempt to find physical explanation should be done. Here, some statistical evidences of spatio-temporal correlation and spatial patterns of extreme behaviour are given on a large database of more than 400 rainfall and discharge series in France. In particular, the spatial distribution of multifractal and Generalized Pareto distribution parameters shows evident correlation patterns in the behaviour of frequency of occurrence of extremes. It is then shown that the identification of atmospheric circulation pattern (weather types) can physically explain the temporal clustering of extreme rainfall events (seasonality) and the spatial pattern of the frequency of occurrence. Moreover, coupling this information with the hydrological modelization of a watershed (as in the Schadex approach) an explanation of spatio-temporal distribution of extreme discharge can also be provided. We finally show that a hydro-meteorological approach (as the Schadex approach) can explain and take into account space and time dependencies of hydro-meteorological extreme events.

Spatial patterns of distribution and abundance of Harrisia portoricensis, an endangered Caribbean cactus

Treesearch

J. Rojas-Sandoval; E. J. Melendez-Ackerman; NO-VALUE

2013-01-01

Aims The spatial distribution of biotic and abiotic factors may play a dominant role in determining the distribution and abundance of plants in arid and semiarid environments. In this study, we evaluated how spatial patterns of microhabitat variables and the degree of spatial dependence of these variables influence the distribution and abundance of the endangered...

Solution strategies as possible explanations of individual and sex differences in a dynamic spatial task.

PubMed

Peña, Daniel; Contreras, María José; Shih, Pei Chun; Santacreu, José

2008-05-01

When individuals perform spatial tasks, individual differences emerge in accuracy and speed as well as in the response patterns used to cope with the task. The purpose of this study is to identify, through empirical criteria, the different response patterns or strategies used by individuals when performing the dynamic spatial task presented in the Spatial Orientation Dynamic Test-Revised (SODT-R). Results show that participants can be classified according to their response patterns. Three different ways of solving a task are described, and their relation to (a) performance factors (response latency, response frequency, and invested time) and (b) ability tests (analytical reasoning, verbal reasoning, and spatial estimation) are investigated. Sex differences in response patterns and performance are also analyzed. It is found that the frequency with which men and women employ each one of the strategies described here, is different and statistically significant. Thus, employed strategy plays an important role when interpreting sex differences on dynamic spatial tasks.

Pixelated camouflage patterns from the perspective of hyperspectral imaging

NASA Astrophysics Data System (ADS)

Racek, František; Jobánek, Adam; Baláž, Teodor; Krejčí, Jaroslav

2016-10-01

Pixelated camouflage patterns fulfill the role of both principles the matching and the disrupting that are exploited for blending the target into the background. It means that pixelated pattern should respect natural background in spectral and spatial characteristics embodied in micro and macro patterns. The HS imaging plays the similar, however the reverse role in the field of reconnaissance systems. The HS camera fundamentally records and extracts both the spectral and spatial information belonging to the recorded scenery. Therefore, the article deals with problems of hyperspectral (HS) imaging and subsequent processing of HS images of pixelated camouflage patterns which are among others characterized by their specific spatial frequency heterogeneity.

The Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation

PubMed Central

Teske, Andreas; de Beer, Dirk; McKay, Luke J.; Tivey, Margaret K.; Biddle, Jennifer F.; Hoer, Daniel; Lloyd, Karen G.; Lever, Mark A.; Røy, Hans; Albert, Daniel B.; Mendlovitz, Howard P.; MacGregor, Barbara J.

2016-01-01

The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region. PMID:26925032

Rhabdom evolution in butterflies: insights from the uniquely tiered and heterogeneous ommatidia of the Glacial Apollo butterfly, Parnassius glacialis.

PubMed

Matsushita, Atsuko; Awata, Hiroko; Wakakuwa, Motohiro; Takemura, Shin-ya; Arikawa, Kentaro

2012-09-07

The eye of the Glacial Apollo butterfly, Parnassius glacialis, a 'living fossil' species of the family Papilionidae, contains three types of spectrally heterogeneous ommatidia. Electron microscopy reveals that the Apollo rhabdom is tiered. The distal tier is composed exclusively of photoreceptors expressing opsins of ultraviolet or blue-absorbing visual pigments, and the proximal tier consists of photoreceptors expressing opsins of green or red-absorbing visual pigments. This organization is unique because the distal tier of other known butterflies contains two green-sensitive photoreceptors, which probably function in improving spatial and/or motion vision. Interspecific comparison suggests that the Apollo rhabdom retains an ancestral tiered pattern with some modification to enhance its colour vision towards the long-wavelength region of the spectrum.

Aryl hydrocarbon receptor (AHR) in the cnidarian Nematostella vectensis: comparative expression, protein interactions, and ligand binding.

PubMed

Reitzel, Adam M; Passamaneck, Yale J; Karchner, Sibel I; Franks, Diana G; Martindale, Mark Q; Tarrant, Ann M; Hahn, Mark E

2014-02-01

The aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has diverse roles in development, physiology, and environmental sensing in bilaterian animals. Studying the expression of conserved genes and function of proteins in outgroups to protostomes and deuterostomes assists in understanding the antiquity of gene function and deciphering lineage-specific differences in these bilaterian clades. We describe the developmental expression of AHR from the sea anemone Nematostella vectensis and compare its expression with three other members of the bHLH-PAS family (AHR nuclear translocator (ARNT), Cycle, and a proto-Single-Minded/Trachealess). NvAHR expression was highest early in the larval stage with spatial expression in the basal portion of the ectoderm that became increasingly restricted to the oral pole with concentrated expression in tentacles of the juvenile polyp. The other bHLH-PAS genes showed a divergent expression pattern in later larval stages and polyps, in which gene expression was concentrated in the aboral end, with broader expression in the endoderm later in development. In co-immunoprecipitation assays, we found no evidence for heterodimerization of AHR with ARNT, contrary to the conservation of this specific interaction in all bilaterians studied to date. Similar to results with other invertebrate AHRs but in contrast to vertebrate AHRs, NvAHR failed to bind two prototypical xenobiotic AHR ligands (2,3,7,8-tetrachlorodibenzo-p-dioxin, β-naphthoflavone). Together, our data suggest that AHR's original function in Eumetazoa likely involved developmental patterning, potentially of neural tissue. The role of heterodimerization in the function of AHR may have arisen after the cnidarian-bilaterian ancestor. The absence of xenobiotic binding to NvAHR further supports a hypothesis for a derived role of this protein in chemical sensing within the chordates.

Aryl hydrocarbon receptor (AHR) in the cnidarian Nematostella vectensis: comparative expression, protein interactions, and ligand binding

PubMed Central

Reitzel, Adam M.; Passamaneck, Yale J.; Karchner, Sibel I.; Franks, Diana G.; Martindale, Mark Q.; Tarrant, Ann M.; Hahn, Mark E.

2014-01-01

The aryl hydrocarbon receptor (AHR) is a member of the basic-helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has diverse roles in development, physiology, and environmental sensing in bilaterian animals. Studying the expression of conserved genes and function of proteins in outgroups to protostomes and deuterostomes assists in understanding the antiquity of gene function and deciphering lineage-specific differences in these bilaterian clades. We describe the developmental expression of AHR from the sea anemone Nematostella vectensis and compare its expression with three other members of the bHLH-PAS family (AHR nuclear translocator (ARNT), Cycle, and a proto-Single-Minded/Trachaeless). NvAHR expression was highest early in the larval stage with spatial expression in the basal portion of the ectoderm that became increasingly restricted to the oral pole with concentrated expression in tentacles of the juvenile polyp. The other bHLH-PAS genes showed a divergent expression pattern in later larval stages and polyps, in which gene expression was concentrated in the aboral end, with broader expression in the endoderm later in development. In co-immunoprecipitation assays, we found no evidence for heterodimerization of AHR with ARNT, contrary to the conservation of this specific interaction in all bilaterians studied to date. Similar to results with other invertebrate AHRs but in contrast to vertebrate AHRs, NvAHR failed to bind two prototypical xenobiotic AHR ligands (TCDD, BNF). Together, our data suggest that AHR's original function in Eumetazoa likely involved developmental patterning, potentially of neural tissue. The role of heterodimerization in the function of AHR may have arisen after the cnidarian-bilaterian ancestor. The absence of xenobiotic binding to NvAHR further supports a hypothesis for a derived role of this protein in chemical sensing within the chordates. PMID:24292160