Cell adhesion and mechanics as drivers of tissue organization and differentiation: local cues for large scale organization.

PubMed

Wickström, Sara A; Niessen, Carien M

2018-06-01

Biological patterns emerge through specialization of genetically identical cells to take up distinct fates according to their position within the organism. How initial symmetry is broken to give rise to these patterns remains an intriguing open question. Several theories of patterning have been proposed, most prominently Turing's reaction-diffusion model of a slowly diffusing activator and a fast diffusing inhibitor generating periodic patterns. Although these reaction-diffusion systems can generate diverse patterns, it is becoming increasingly evident that cell shape and tension anisotropies, mediated via cell-cell and/or cell-matrix contacts, also facilitate symmetry breaking and subsequent self-organized tissue patterning. This review will highlight recent studies that implicate local changes in adhesion and/or tension as key drivers of cell rearrangements. We will also discuss recent studies on the role of cadherin and integrin adhesive receptors in mediating and responding to local tissue tension asymmetries to coordinate cell fate, position and behavior essential for tissue self-organization and maintenance. Copyright © 2018 Elsevier Ltd. All rights reserved.

Functional characterization and cellular dynamics of the CDC-42 - RAC - CDC-24 module in Neurospora crassa.

PubMed

Araujo-Palomares, Cynthia L; Richthammer, Corinna; Seiler, Stephan; Castro-Longoria, Ernestina

2011-01-01

Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.

Transcription factors define the neuroanatomical organization of the medullary reticular formation

PubMed Central

Gray, Paul A.

2013-01-01

The medullary reticular formation contains large populations of inadequately described, excitatory interneurons that have been implicated in multiple homeostatic behaviors including breathing, viserosensory processing, vascular tone, and pain. Many hindbrain nuclei show a highly stereotyped pattern of localization across vertebrates suggesting a strong underlying genetic organization. Whether this is true for neurons within the reticular regions of hindbrain is unknown. Hindbrain neurons are derived from distinct developmental progenitor domains each of which expresses distinct patterns of transcription factors (TFs). These neuronal populations have distinct characteristics such as transmitter identity, migration, and connectivity suggesting developmentally expressed TFs might identify unique subpopulations of neurons within the reticular formation. A fate-mapping strategy using perinatal expression of reporter genes within Atoh1, Dbx1, Lmx1b, and Ptf1a transgenic mice coupled with immunohistochemistry (IHC) and in situ hybridization (ISH) were used to address the developmental organization of a large subset of reticular formation glutamatergic neurons. All hindbrain lineages have relatively large populations that extend the entire length of the hindbrain. Importantly, the location of neurons within each lineage was highly constrained. Lmx1b- and Dbx1- derived populations were both present in partially overlapping stripes within the reticular formation extending from dorsal to ventral brain. Within each lineage, distinct patterns of gene expression and organization were localized to specific hindbrain regions. Rostro-caudally sub-populations differ sequentially corresponding to proposed pseudo-rhombomereic boundaries. Dorsal-ventrally, sub-populations correspond to specific migratory positions. Together these data suggests the reticular formation is organized by a highly stereotyped developmental logic. PMID:23717265

Transcription factors define the neuroanatomical organization of the medullary reticular formation.

PubMed

Gray, Paul A

2013-01-01

The medullary reticular formation contains large populations of inadequately described, excitatory interneurons that have been implicated in multiple homeostatic behaviors including breathing, viserosensory processing, vascular tone, and pain. Many hindbrain nuclei show a highly stereotyped pattern of localization across vertebrates suggesting a strong underlying genetic organization. Whether this is true for neurons within the reticular regions of hindbrain is unknown. Hindbrain neurons are derived from distinct developmental progenitor domains each of which expresses distinct patterns of transcription factors (TFs). These neuronal populations have distinct characteristics such as transmitter identity, migration, and connectivity suggesting developmentally expressed TFs might identify unique subpopulations of neurons within the reticular formation. A fate-mapping strategy using perinatal expression of reporter genes within Atoh1, Dbx1, Lmx1b, and Ptf1a transgenic mice coupled with immunohistochemistry (IHC) and in situ hybridization (ISH) were used to address the developmental organization of a large subset of reticular formation glutamatergic neurons. All hindbrain lineages have relatively large populations that extend the entire length of the hindbrain. Importantly, the location of neurons within each lineage was highly constrained. Lmx1b- and Dbx1- derived populations were both present in partially overlapping stripes within the reticular formation extending from dorsal to ventral brain. Within each lineage, distinct patterns of gene expression and organization were localized to specific hindbrain regions. Rostro-caudally sub-populations differ sequentially corresponding to proposed pseudo-rhombomereic boundaries. Dorsal-ventrally, sub-populations correspond to specific migratory positions. Together these data suggests the reticular formation is organized by a highly stereotyped developmental logic.

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.

Multistability, local pattern formation, and global collective firing in a small-world network of nonleaky integrate-and-fire neurons.

PubMed

Rothkegel, Alexander; Lehnertz, Klaus

2009-03-01

We investigate numerically the collective dynamical behavior of pulse-coupled nonleaky integrate-and-fire neurons that are arranged on a two-dimensional small-world network. To ensure ongoing activity, we impose a probability for spontaneous firing for each neuron. We study network dynamics evolving from different sets of initial conditions in dependence on coupling strength and rewiring probability. Besides a homogeneous equilibrium state for low coupling strength, we observe different local patterns including cyclic waves, spiral waves, and turbulentlike patterns, which-depending on network parameters-interfere with the global collective firing of the neurons. We attribute the various network dynamics to distinct regimes in the parameter space. For the same network parameters different network dynamics can be observed depending on the set of initial conditions only. Such a multistable behavior and the interplay between local pattern formation and global collective firing may be attributable to the spatiotemporal dynamics of biological networks.

Infinitely robust order and local order-parameter tulips in Apollonian networks with quenched disorder

NASA Astrophysics Data System (ADS)

Kaplan, C. Nadir; Hinczewski, Michael; Berker, A. Nihat

2009-06-01

For a variety of quenched random spin systems on an Apollonian network, including ferromagnetic and antiferromagnetic bond percolation and the Ising spin glass, we find the persistence of ordered phases up to infinite temperature over the entire range of disorder. We develop a renormalization-group technique that yields highly detailed information, including the exact distributions of local magnetizations and local spin-glass order parameters, which turn out to exhibit, as function of temperature, complex and distinctive tulip patterns.

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Quantitative gene expression analysis in intact single cells can be achieved using single molecule- based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple FISH sub-probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific binding of sub-probes and tissue autofluorescence, limiting its accuracy. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on blinking frequencies of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses blinking frequency patterns, emitted frommore » a transcript bound to multiple sub-probes, which are distinct from blinking patterns emitted from partial or nonspecifically bound sub-probes and autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2, and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct blinking frequency patterns, laying the foundation for reliable single-cell transcriptomics.« less

Auditory global-local processing: effects of attention and musical experience.

PubMed

Ouimet, Tia; Foster, Nicholas E V; Hyde, Krista L

2012-10-01

In vision, global (whole) features are typically processed before local (detail) features ("global precedence effect"). However, the distinction between global and local processing is less clear in the auditory domain. The aims of the present study were to investigate: (i) the effects of directed versus divided attention, and (ii) the effect musical training on auditory global-local processing in 16 adult musicians and 16 non-musicians. Participants were presented with short nine-tone melodies, each comprised of three triplet sequences (three-tone units). In a "directed attention" task, participants were asked to focus on either the global or local pitch pattern and had to determine if the pitch pattern went up or down. In a "divided attention" task, participants judged whether the target pattern (up or down) was present or absent. Overall, global structure was perceived faster and more accurately than local structure. The global precedence effect was observed regardless of whether attention was directed to a specific level or divided between levels. Musicians performed more accurately than non-musicians overall, but non-musicians showed a more pronounced global advantage. This study provides evidence for an auditory global precedence effect across attention tasks, and for differences in auditory global-local processing associated with musical experience.

LGN plays distinct roles in oral epithelial stratification, filiform papilla morphogenesis and hair follicle development

PubMed Central

Lough, Kendall J.; Patel, Jeet H.; Descovich, Carlos Patiño; Curtis, T. Anthony

2016-01-01

Oral epithelia protect against constant challenges by bacteria, viruses, toxins and injury while also contributing to the formation of ectodermal appendages such as teeth, salivary glands and lingual papillae. Despite increasing evidence that differentiation pathway genes are frequently mutated in oral cancers, comparatively little is known about the mechanisms that regulate normal oral epithelial development. Here, we characterize oral epithelial stratification and describe multiple distinct functions for the mitotic spindle orientation gene LGN (Gpsm2) in promoting differentiation and tissue patterning in the mouse oral cavity. Similar to its function in epidermis, apically localized LGN directs perpendicular divisions that promote stratification of the palatal, buccogingival and ventral tongue epithelia. Surprisingly, however, in dorsal tongue LGN is predominantly localized basally, circumferentially or bilaterally and promotes planar divisions. Loss of LGN disrupts the organization and morphogenesis of filiform papillae but appears to be dispensable for embryonic hair follicle development. Thus, LGN has crucial tissue-specific functions in patterning surface ectoderm and its appendages by controlling division orientation. PMID:27317810

Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor.

PubMed

Jorde, Per Erik; Søvik, Guldborg; Westgaard, Jon-Ivar; Albretsen, Jon; André, Carl; Hvingel, Carsten; Johansen, Torild; Sandvik, Anne Dagrun; Kingsley, Michael; Jørstad, Knut Eirik

2015-04-01

The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = -0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5-4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment. © 2015 John Wiley & Sons Ltd.

Patterning of leaf vein networks by convergent auxin transport pathways.

PubMed

Sawchuk, Megan G; Edgar, Alexander; Scarpella, Enrico

2013-01-01

The formation of leaf vein patterns has fascinated biologists for centuries. Transport of the plant signal auxin has long been implicated in vein patterning, but molecular details have remained unclear. Varied evidence suggests a central role for the plasma-membrane (PM)-localized PIN-FORMED1 (PIN1) intercellular auxin transporter of Arabidopsis thaliana in auxin-transport-dependent vein patterning. However, in contrast to the severe vein-pattern defects induced by auxin transport inhibitors, pin1 mutant leaves have only mild vein-pattern defects. These defects have been interpreted as evidence of redundancy between PIN1 and the other four PM-localized PIN proteins in vein patterning, redundancy that underlies many developmental processes. By contrast, we show here that vein patterning in the Arabidopsis leaf is controlled by two distinct and convergent auxin-transport pathways: intercellular auxin transport mediated by PM-localized PIN1 and intracellular auxin transport mediated by the evolutionarily older, endoplasmic-reticulum-localized PIN6, PIN8, and PIN5. PIN6 and PIN8 are expressed, as PIN1 and PIN5, at sites of vein formation. pin6 synthetically enhances pin1 vein-pattern defects, and pin8 quantitatively enhances pin1pin6 vein-pattern defects. Function of PIN6 is necessary, redundantly with that of PIN8, and sufficient to control auxin response levels, PIN1 expression, and vein network formation; and the vein pattern defects induced by ectopic PIN6 expression are mimicked by ectopic PIN8 expression. Finally, vein patterning functions of PIN6 and PIN8 are antagonized by PIN5 function. Our data define a new level of control of vein patterning, one with repercussions on other patterning processes in the plant, and suggest a mechanism to select cell files specialized for vascular function that predates evolution of PM-localized PIN proteins.

Spatial pattern in Antarctica: what can we learn from Antarctic bacterial isolates?

PubMed

Chong, Chun Wie; Goh, Yuh Shan; Convey, Peter; Pearce, David; Tan, Irene Kit Ping

2013-09-01

A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.

Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

DOE Data Explorer

Smith, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Bell, R. E. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Podesta, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Smith, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Fonck, R. J. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); McKee, G. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Diallo, A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Kaye, S. M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); LeBlanc, B. P. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Sabbagh, S. A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)

2015-09-01

We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfven timescales. Some ELM events are active for less than 100~microsec, but others persist for up to 1~ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility.

Variable features on Mars. VII - Dark filamentary markings on Mars

NASA Technical Reports Server (NTRS)

Veverka, J.

1976-01-01

The paper discusses the location, variability, and possible nature of well-developed patterns of dark filamentary markings in the Mariner 9 photographic records. Although not common on Mars, the markings are concentrated in at least two areas: Depressio Hellespontica and Cerberus/Trivium Charontis. In certain localities, strong winds are required to bring these markings into prominence. The dark filamentary markings seem to be true albedo features controlled by local topography, it being unlikely that they are free linear dunes. The distinctive criss-cross pattern seen in many of the pictures suggests that jointing provides the controlling topographic grid. At this stage it cannot be inferred whether the markings are erosional or depositional in character.

Maize diversity associated with social origin and environmental variation in Southern Mexico.

PubMed

Orozco-Ramírez, Q; Ross-Ibarra, J; Santacruz-Varela, A; Brush, S

2016-05-01

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale.

Maize diversity associated with social origin and environmental variation in Southern Mexico

PubMed Central

Orozco-Ramírez, Q; Ross-Ibarra, J; Santacruz-Varela, A; Brush, S

2016-01-01

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale. PMID:26905463

Spatio-temporal dynamics of processing non-symbolic number: An ERP source localization study

PubMed Central

Hyde, Daniel C.; Spelke, Elizabeth S.

2013-01-01

Coordinated studies with adults, infants, and nonhuman animals provide evidence for two distinct systems of non-verbal number representation. The ‘parallel individuation’ system selects and retains information about 1–3 individual entities and the ‘numerical magnitude’ system establishes representations of the approximate cardinal value of a group. Recent ERP work has demonstrated that these systems reliably evoke functionally and temporally distinct patterns of brain response that correspond to established behavioral signatures. However, relatively little is known about the neural generators of these ERP signatures. To address this question, we targeted known ERP signatures of these systems, by contrasting processing of small versus large non-symbolic numbers, and used a source localization algorithm (LORETA) to identify their cortical origins. Early processing of small numbers, showing the signature effects of parallel individuation on the N1 (∼150 ms), was localized primarily to extrastriate visual regions. In contrast, qualitatively and temporally distinct processing of large numbers, showing the signatures of approximate number representation on the mid-latency P2p (∼200–250 ms), was localized primarily to right intraparietal regions. In comparison, mid-latency small number processing was localized to the right temporal-parietal junction and left-lateralized intraparietal regions. These results add spatial information to the emerging ERP literature documenting the process by which we represent number. Furthermore, these results substantiate recent claims that early attentional processes determine whether a collection of objects will be represented through parallel individuation or as an approximate numerical magnitude by providing evidence that downstream processing diverges to distinct cortical regions. PMID:21830257

Spatiotemporal dynamics of processing nonsymbolic number: an event-related potential source localization study.

PubMed

Hyde, Daniel C; Spelke, Elizabeth S

2012-09-01

Coordinated studies with adults, infants, and nonhuman animals provide evidence for two distinct systems of nonverbal number representation. The "parallel individuation" (PI) system selects and retains information about one to three individual entities and the "numerical magnitude" system establishes representations of the approximate cardinal value of a group. Recent event-related potential (ERP) work has demonstrated that these systems reliably evoke functionally and temporally distinct patterns of brain response that correspond to established behavioral signatures. However, relatively little is known about the neural generators of these ERP signatures. To address this question, we targeted known ERP signatures of these systems, by contrasting processing of small versus large nonsymbolic numbers, and used a source localization algorithm (LORETA) to identify their cortical origins. Early processing of small numbers, showing the signature effects of PI on the N1 (∼150 ms), was localized primarily to extrastriate visual regions. In contrast, qualitatively and temporally distinct processing of large numbers, showing the signatures of approximate number representation on the mid-latency P2p (∼200-250 ms), was localized primarily to right intraparietal regions. In comparison, mid-latency small number processing was localized to the right temporal-parietal junction and left-lateralized intraparietal regions. These results add spatial information to the emerging ERP literature documenting the process by which we represent number. Furthermore, these results substantiate recent claims that early attentional processes determine whether a collection of objects will be represented through PI or as an approximate numerical magnitude by providing evidence that downstream processing diverges to distinct cortical regions. Copyright © 2011 Wiley Periodicals, Inc.

Different patterns of local field potentials from limbic DBS targets in patients with major depressive and obsessive compulsive disorder

PubMed Central

Neumann, W-J; Huebl, J; Brücke, C; Gabriëls, L; Bajbouj, M; Merkl, A; Schneider, G-H; Nuttin, B; Brown, P; Kühn, AA

2016-01-01

The role of distinct limbic areas in emotion regulation has been largely inferred from neuroimaging studies. Recently, the opportunity for intracranial recordings from limbic areas has arisen in patients undergoing deep brain stimulation (DBS) for neuropsychiatric disorders including major depressive disorder (MDD) and obsessive compulsive disorder (OCD). Here we test the hypothesis that distinct temporal patterns of local field potential (LFP) activity in the human limbic system reflect disease state and symptom severity in MDD and OCD patients. To this end, we recorded LFPs via implanted DBS electrodes from the bed nucleus of stria terminalis (BNST area) in 12 patients (5 OCD, 7 MDD) and from the subgenual cingulate cortex in 7 MDD patients (CG25 area). We found a distinct pattern of oscillatory activity with significantly higher α-power in MDD compared with OCD in the BNST area (broad α-band 8–14 Hz; P<0.01) and a similar level of α-activity in the CG25 area as in the BNST area in MDD patients. The mean α-power correlated with severity of depressive symptoms as assessed by the Beck depression inventory in MDD (n = 14, r = 0.55, P = 0.042) but not with severity of obsessive compulsive symptoms in OCD. Here we show larger α-band activity in MDD patients compared with OCD recorded from intracranial DBS targets. Our results suggest that α-activity in the limbic system may be a signature of symptom severity in MDD and may serve as a potential state biomarker for closed loop DBS in MDD. PMID:24514569

Local or distributed activation? The view from biology

NASA Astrophysics Data System (ADS)

Reimers, Mark

2011-06-01

There is considerable disagreement among connectionist modellers over whether to represent distinct properties by distinct nodes of a network or whether properties should be represented by patterns of activity across all nodes. This paper draws on the literature of neuroscience to say that a more subtle way of describing how different brain regions contribute to a behaviour, in terms of individual learning and in terms of degrees of importance, may render the current debate moot: both sides of the 'localist' versus 'distributed' debate emphasise different aspects of biology.

Point process models for localization and interdependence of punctate cellular structures.

PubMed

Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

2016-07-01

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

Infantile Hemangiomas of the Lip: Patterns, Outcomes, and Implications.

PubMed

Yanes, Daniel A; Pearson, Gregory D; Witman, Patricia M

2016-09-01

Infantile hemangiomas of the lip are potentially problematic because of high visibility and risk of disfigurement and ulceration. This study examined sizes, patterns, and locations of lip hemangiomas, their prognostic value, and their implications in hemangioma pathogenesis. Records of 106 patients seen for lip hemangiomas from 2006 to 2013 at Nationwide Children's Hospital were reviewed. Localized hemangiomas were mapped to a location on the lip based on their focus. Size, location, and morphology were assessed with regard to outcome. Poor outcomes were considered to be marked anatomic deformity, scarring, functional complications, and ulceration. Of 72 untreated hemangiomas with discernible outcomes, 92% of segmental lip hemangiomas were associated with poor outcomes, as opposed to 32% of localized hemangiomas (p < 0.001). Localized lip hemangiomas originated from six distinct locations. Localized untreated hemangiomas with poor outcomes were, on average, approximately 2.36 cm(2) larger (95% confidence interval 1.47, 3.25) than those that resolved favorably (p < 0.001); 52% of upper lip untreated hemangiomas and 6% of lower lip hemangiomas had poor outcomes (p = 0.001), and 61% of untreated localized hemangiomas involving the vermilion border and 25% of those that did not had poor outcomes (p = 0.01). Hemangiomas that received early medical or surgical intervention were less likely to have poor outcomes than untreated hemangiomas (p = 0.03). Localized lip hemangiomas occur in distinct locations on the lip that are not random and appear to reflect known models of facial development. Segmental morphology is associated with poor outcomes. In localized hemangiomas, the upper lip is associated with more problematic outcomes than the lower lip. Large size and involvement of the vermilion border are also valuable prognostic indicators associated with poor outcomes. Early intervention in lip hemangiomas is associated with better outcomes. © 2016 Wiley Periodicals, Inc.

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod.

PubMed

Berg, Paul R; Star, Bastiaan; Pampoulie, Christophe; Sodeland, Marte; Barth, Julia M I; Knutsen, Halvor; Jakobsen, Kjetill S; Jentoft, Sissel

2016-03-17

Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod - historically a major marine resource - Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. These regions likely represent genomic inversions. The frequency of these distinct regions differ markedly between the ecotypes, spawning in the vicinity of each other, which contrasts with the low level of divergence in the rest of the genome. The observed patterns strongly suggest that these chromosomal rearrangements are instrumental in local adaptation and separation of Atlantic cod populations, leaving footprints of large genomic regions under selection. Our findings demonstrate the power of using genomic information in further understanding the population dynamics and defining management units in one of the world's most economically important marine resources.

Combined DNA methylation and gene expression profiling in gastrointestinal stromal tumors reveals hypomethylation of SPP1 as an independent prognostic factor.

PubMed

Haller, Florian; Zhang, Jitao David; Moskalev, Evgeny A; Braun, Alexander; Otto, Claudia; Geddert, Helene; Riazalhosseini, Yasser; Ward, Aoife; Balwierz, Aleksandra; Schaefer, Inga-Marie; Cameron, Silke; Ghadimi, B Michael; Agaimy, Abbas; Fletcher, Jonathan A; Hoheisel, Jörg; Hartmann, Arndt; Werner, Martin; Wiemann, Stefan; Sahin, Ozgür

2015-03-01

Gastrointestinal stromal tumors (GISTs) have distinct gene expression patterns according to localization, genotype and aggressiveness. DNA methylation at CpG dinucleotides is an important mechanism for regulation of gene expression. We performed targeted DNA methylation analysis of 1.505 CpG loci in 807 cancer-related genes in a cohort of 76 GISTs, combined with genome-wide mRNA expression analysis in 22 GISTs, to identify signatures associated with clinicopathological parameters and prognosis. Principal component analysis revealed distinct DNA methylation patterns associated with anatomical localization, genotype, mitotic counts and clinical follow-up. Methylation of a single CpG dinucleotide in the non-CpG island promoter of SPP1 was significantly correlated with shorter disease-free survival. Hypomethylation of this CpG was an independent prognostic parameter in a multivariate analysis compared to anatomical localization, genotype, tumor size and mitotic counts in a cohort of 141 GISTs with clinical follow-up. The epigenetic regulation of SPP1 was confirmed in vitro, and the functional impact of SPP1 protein on tumorigenesis-related signaling pathways was demonstrated. In summary, SPP1 promoter methylation is a novel and independent prognostic parameter in GISTs, and might be helpful in estimating the aggressiveness of GISTs from the intermediate-risk category. © 2014 UICC.

The spectrum of dermatoscopic patterns in blue nevi.

PubMed

Di Cesare, Antonella; Sera, Francesco; Gulia, Andrea; Coletti, Gino; Micantonio, Tamara; Fargnoli, Maria Concetta; Peris, Ketty

2012-08-01

Blue nevi are congenital or acquired, dermal dendritic melanocytic proliferations that can simulate melanocytic and nonmelanocytic lesions including melanoma, cutaneous metastasis of melanoma, Spitz/Reed nevi, and basal cell carcinoma. We sought to investigate global and local dermatoscopic patterns of blue nevi compared with melanomas and basal cell carcinomas. We retrospectively analyzed global and local features in 95 dermatoscopic images of blue nevi and in 190 melanomas and basal cell carcinomas that were selected as control lesions on the basis of similar pigmentation. Lesion pigmentation was classified as monochromatic, dichromatic, or multichromatic. A global pattern characterized by homogeneous pigmentation was observed in all of 95 (100%) blue nevi. Eighty of 95 (84.2%) blue nevi presented a homogeneous pattern consisting of one color (blue, black, or brown) or two colors (blue-brown, blue-gray, or blue-black). Fifteen of 95 (15.8%) blue nevi had a multichromatic (blue, gray, black, brown, and/or red) pigmentation. In all, 47 of 95 (49.5%) blue nevi were characterized by pigmentation in the absence of pigment network or any other local dermatoscopic features. And 48 of 95 (50.5%) blue nevi showed local dermatoscopic patterns including whitish scarlike depigmentation, dots/globules, vascular pattern, streaks, and networklike pattern. The study was retrospective and involved only Caucasian people of Italian origin. The characteristic feature of blue nevi is a homogeneous pigmentation that is blue, blue-gray, blue-brown, or blue-black. We showed that a wide spectrum of local dermatoscopic features (whitish scarlike depigmentation, dots/globules, peripheral streaks or vessels) may also be present. In such cases, clinical and dermatoscopic distinction from melanoma or nonmelanocytic lesions may be difficult or impossible, and surgical excision is necessary. Copyright © 2011 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

Observations of Local Positive Low Cloud Feedback Patterns and Their Role in Internal Variability and Climate Sensitivity

NASA Astrophysics Data System (ADS)

Yuan, Tianle; Oreopoulos, Lazaros; Platnick, Steven E.; Meyer, Kerry

2018-05-01

Modeling studies have shown that cloud feedbacks are sensitive to the spatial pattern of sea surface temperature (SST) anomalies, while cloud feedbacks themselves strongly influence the magnitude of SST anomalies. Observational counterparts to such patterned interactions are still needed. Here we show that distinct large-scale patterns of SST and low-cloud cover (LCC) emerge naturally from objective analyses of observations and demonstrate their close coupling in a positive local SST-LCC feedback loop that may be important for both internal variability and climate change. The two patterns that explain the maximum amount of covariance between SST and LCC correspond to the Interdecadal Pacific Oscillation and the Atlantic Multidecadal Oscillation, leading modes of multidecadal internal variability. Spatial patterns and time series of SST and LCC anomalies associated with both modes point to a strong positive local SST-LCC feedback. In many current climate models, our analyses suggest that SST-LCC feedback strength is too weak compared to observations. Modeled local SST-LCC feedback strength affects simulated internal variability so that stronger feedback produces more intense and more realistic patterns of internal variability. To the extent that the physics of the local positive SST-LCC feedback inferred from observed climate variability applies to future greenhouse warming, we anticipate significant amount of delayed warming because of SST-LCC feedback when anthropogenic SST warming eventually overwhelm the effects of internal variability that may mute anthropogenic warming over parts of the ocean. We postulate that many climate models may be underestimating both future warming and the magnitude of modeled internal variability because of their weak SST-LCC feedback.

LocSigDB: a database of protein localization signals

PubMed Central

Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M.; Mohammed, Akram; Guda, Chittibabu

2015-01-01

LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/ PMID:25725059

Topological Mechanics of Origami and Kirigami

NASA Astrophysics Data System (ADS)

Chen, Bryan Gin-ge; Liu, Bin; Evans, Arthur A.; Paulose, Jayson; Cohen, Itai; Vitelli, Vincenzo; Santangelo, C. D.

2016-04-01

Origami and kirigami have emerged as potential tools for the design of mechanical metamaterials whose properties such as curvature, Poisson ratio, and existence of metastable states can be tuned using purely geometric criteria. A major obstacle to exploiting this property is the scarcity of tools to identify and program the flexibility of fold patterns. We exploit a recent connection between spring networks and quantum topological states to design origami with localized folding motions at boundaries and study them both experimentally and theoretically. These folding motions exist due to an underlying topological invariant rather than a local imbalance between constraints and degrees of freedom. We give a simple example of a quasi-1D folding pattern that realizes such topological states. We also demonstrate how to generalize these topological design principles to two dimensions. A striking consequence is that a domain wall between two topologically distinct, mechanically rigid structures is deformable even when constraints locally match the degrees of freedom.

Arousal and locomotion make distinct contributions to cortical activity patterns and visual encoding

PubMed Central

Vinck, Martin; Batista-Brito, Renata; Knoblich, Ulf; Cardin, Jessica A.

2015-01-01

Spontaneous and sensory-evoked cortical activity is highly state-dependent, yet relatively little is known about transitions between distinct waking states. Patterns of activity in mouse V1 differ dramatically between quiescence and locomotion, but this difference could be explained by either motor feedback or a change in arousal levels. We recorded single cells and local field potentials from area V1 in mice head-fixed on a running wheel and monitored pupil diameter to assay arousal. Using naturally occurring and induced state transitions, we dissociated arousal and locomotion effects in V1. Arousal suppressed spontaneous firing and strongly altered the temporal patterning of population activity. Moreover, heightened arousal increased the signal-to-noise ratio of visual responses and reduced noise correlations. In contrast, increased firing in anticipation of and during movement was attributable to locomotion effects. Our findings suggest complementary roles of arousal and locomotion in promoting functional flexibility in cortical circuits. PMID:25892300

Expression of most matrix metalloproteinase family members in breast cancer represents a tumor-induced host response.

PubMed Central

Heppner, K. J.; Matrisian, L. M.; Jensen, R. A.; Rodgers, W. H.

1996-01-01

Matrix metalloproteinase (MMP) family members have been associated with advanced-stage cancer and contribute to tumor progression, invasion, and metastasis as determined by inhibitor studies. In situ hybridization was performed to analyze the expression and localization of all known MMPs in a series of human breast cancer biopsy specimens. Most MMPs were localized to tumor stroma, and all MMPs had very distinct expression patterns. Matrilysin was expressed by morphologically normal epithelial ducts within tumors and in tissue from reduction mammoplasties, and by epithelial-derived tumor cells. Many family members, including stromelysin-3, gelatinase A, MT-MMP, interstitial collagenase, and stromelysin-1 were localized to fibroblasts of tumor stroma of invasive cancers but in quite distinct, and generally widespread, patterns. Gelatinase B, collagenase-3, and metalloelastase expression were more focal; gelatinase B was primarily localized to endothelial cells, collagenase-3 to isolated tumor cells, and metalloelastase to cytokeratin-negative, macrophage-like cells. The MMP inhibitor, TIMP-1, was expressed in both stromal and tumor components in most tumors, and neither stromelysin-2 nor neutrophil collagenase were detected in any of the tumors. These results indicate that there is very tight and complex regulation in the expression of MMP family members in breast cancer that generally represents a host response to the tumor and emphasize the need to further evaluate differential functions for MMP family members in breast tumor progression. Images Figure 1 Figure 2 Figure 3 PMID:8686751

Do radiative feedbacks depend on the structure and type of climate forcing, or only on the spatial pattern of surface temperature change?

NASA Astrophysics Data System (ADS)

Haugstad, A.; Battisti, D. S.; Armour, K.

2016-12-01

Earth's climate sensitivity depends critically on the strength of radiative feedbacks linking surface warming to changes in top-of-atmosphere (TOA) radiation. Many studies use a simplistic idea of radiative feedbacks, either by treating them as global mean quantities, or by assuming they can be defined uniquely by geographic location and thus that TOA radiative response depends only on local surface warming. For example, a uniform increase in sea-surface temperature has been widely used as a surrogate for global warming (e.g., Cess et al 1990 and the CMIP 'aqua4k' simulations), with the assumption that this produces the same radiative feedbacks as those arising from a doubling of carbon dioxide - even though the spatial patterns of warming differ. However, evidence suggests that these assumptions are not valid, and local feedbacks may be integrally dependent on the structure of warming or type of climate forcing applied (Rose et al 2014). This study thus investigates the following questions: to what extent do local feedbacks depend on the structure and type of forcing applied? And, to what extent do they depend on the pattern of surface temperature change induced by that forcing? Using an idealized framework of an aquaplanet atmosphere-only model, we show that radiative feedbacks are indeed dependent on the large scale structure of warming and type of forcing applied. For example, the climate responds very differently to two forcings of equal global magnitude but applied in different global regions; the pattern of local feedbacks arising from uniform warming are not the same as that arising from polar amplified warming; and the same local feedbacks can be induced by distinct forcing patterns, provided that they produce the same pattern of surface temperature change. These findings suggest that the so-called `efficacies' of climate forcings can be understood simply in terms of how local feedbacks depend on the temperature patterns they induce.

Expression and sub-cellular localization of an epigenetic regulator, co-activator arginine methyltransferase 1 (CARM1), is associated with specific breast cancer subtypes and ethnicity

PubMed Central

2013-01-01

Background Co-Activator Arginine Methyltransferase 1(CARM1) is an Estrogen Receptor (ER) cofactor that remodels chromatin for gene regulation via methylation of Histone3. We investigated CARM1 levels and localization across breast cancer tumors in a cohort of patients of either European or African ancestry. Methods We analyzed CARM1 levels using tissue microarrays with over 800 histological samples from 549 female cancer patients from the US and Nigeria, Africa. We assessed associations between CARM1 expression localized to the nucleus and cytoplasm for 11 distinct variables, including; ER status, Progesterone Receptor status, molecular subtypes, ethnicity, HER2+ status, other clinical variables and survival. Results We found that levels of cytoplasmic CARM1 are distinct among tumor sub-types and increased levels are associated with ER-negative (ER-) status. Higher nuclear CARM1 levels are associated with HER2 receptor status. EGFR expression also correlates with localization of CARM1 into the cytoplasm. This suggests there are distinct functions of CARM1 among molecular tumor types. Our data reveals a basal-like subtype association with CARM1, possibly due to expression of Epidermal Growth Factor Receptor (EGFR). Lastly, increased cytoplasmic CARM1, relative to nuclear levels, appear to be associated with self-identified African ethnicity and this result is being further investigated using quantified genetic ancestry measures. Conclusions Although it is known to be an ER cofactor in breast cancer, CARM1 expression levels are independent of ER. CARM1 has distinct functions among molecular subtypes, as is indicative of its sub-cellular localization and it may function in subtype etiology. These sub-cellular localization patterns, indicate a novel role beyond its ER cofactor function in breast cancer. Differential localization among ethnic groups may be due to ancestry-specific polymorphisms which alter the gene product. PMID:23663560

Defect Localization Capabilities of a Global Detection Scheme: Spatial Pattern Recognition Using Full-field Vibration Test Data in Plates

NASA Technical Reports Server (NTRS)

Saleeb, A. F.; Prabhu, M.; Arnold, S. M. (Technical Monitor)

2002-01-01

Recently, a conceptually simple approach, based on the notion of defect energy in material space has been developed and extensively studied (from the theoretical and computational standpoints). The present study focuses on its evaluation from the viewpoint of damage localization capabilities in case of two-dimensional plates; i.e., spatial pattern recognition on surfaces. To this end, two different experimental modal test results are utilized; i.e., (1) conventional modal testing using (white noise) excitation and accelerometer-type sensors and (2) pattern recognition using Electronic speckle pattern interferometry (ESPI), a full field method capable of analyzing the mechanical vibration of complex structures. Unlike the conventional modal testing technique (using contacting accelerometers), these emerging ESPI technologies operate in a non-contacting mode, can be used even under hazardous conditions with minimal or no presence of noise and can simultaneously provide measurements for both translations and rotations. Results obtained have clearly demonstrated the robustness and versatility of the global NDE scheme developed. The vectorial character of the indices used, which enabled the extraction of distinct patterns for localizing damages proved very useful. In the context of the targeted pattern recognition paradigm, two algorithms were developed for the interrogation of test measurements; i.e., intensity contour maps for the damaged index, and the associated defect energy vector field plots.

Dental and phylogeographic patterns of variation in gorillas.

PubMed

Pilbrow, Varsha

2010-07-01

Gorilla patterns of variation have great relevance for studies of human evolution. In this study, molar morphometrics were used to evaluate patterns of geographic variation in gorillas. Dental specimens of 323 adult individuals, drawn from the current distribution of gorillas in equatorial Africa were divided into 14 populations. Discriminant analyses and Mahalanobis distances were used to study population structure. Results reveal that: 1) the West and East African gorillas form distinct clusters, 2) the Cross River gorillas are well separated from the rest of the western populations, 3) gorillas from the Virunga mountains and the Bwindi Forest can be differentiated from the lowland gorillas of Utu and Mwenga-Fizi, 4) the Tshiaberimu gorillas are distinct from other eastern gorillas, and the Kahuzi-Biega gorillas are affiliated with them. These findings provide support for a species distinction between Gorilla gorilla and Gorilla beringei, with subspecies G. g. diehli, G. g. gorilla, G. b. graueri, G. b. beringei, and possibly, G. b. rex-pygmaeorum. Clear correspondence between dental and other patterns of taxonomic diversity demonstrates that dental data reveal underlying genetic patterns of differentiation. Dental distances increased predictably with altitude but not with geographic distances, indicating that altitudinal segregation explains gorilla patterns of population divergence better than isolation-by-distance. The phylogeographic pattern of gorilla dental metric variation supports the idea that Plio-Pleistocene climatic fluctuations and local mountain building activity in Africa affected gorilla phylogeography. I propose that West Africa comprised the historic center of gorilla distribution and experienced drift-gene flow equilibrium, whereas Nigeria and East Africa were at the periphery, where climatic instability and altitudinal variation promoted drift and genetic differentiation. This understanding of gorilla population structure has implications for gorilla conservation, and for understanding the distribution of sympatric chimpanzees and Plio-Pleistocene hominins.

Human Corneal Limbal-Epithelial Cell Response to Varying Silk Film Geometric Topography In Vitro

PubMed Central

Lawrence, Brian D.; Pan, Zhi; Liu, Aihong; Kaplan, David L.; Rosenblatt, Mark I.

2012-01-01

Silk fibroin films are a promising class of biomaterials that have a number of advantages for use in ophthalmic applications due to their transparent nature, mechanical properties and minimal inflammatory response upon implantation. Freestanding silk films with parallel line and concentric ring topographies were generated for in vitro characterization of human corneal limbal-epithelial (HCLE) cell response upon differing geometric patterned surfaces. Results indicated that silk film topography significantly affected initial HCLE culture substrate attachment, cellular alignment, cell-to-cell contact formation, actin cytoskeleton alignment, and focal adhesion (FA) localization. Most notably, parallel line patterned surfaces displayed a 36%–54% increase on average in initial cell attachment, which corresponded to an over 2-fold increase in FA localization when compared to other silk film surfaces and controls. In addition, distinct localization of FA formation was observed along the edges for all patterned silk film topographies. In conclusion, silk film feature topography appears to help direct corneal epithelial cell response and cytoskeleton development, especially in regards to FA distribution, in vitro. PMID:22705042

Source localization of small sharp spikes: low resolution electromagnetic tomography (LORETA) reveals two distinct cortical sources.

PubMed

Zumsteg, Dominik; Andrade, Danielle M; Wennberg, Richard A

2006-06-01

We have investigated the cortical sources and electroencephalographic (EEG) characteristics of small sharp spikes (SSS) by using statistical non-parametric mapping (SNPM) of low resolution electromagnetic tomography (LORETA). We analyzed 7 SSS patterns (501 individual SSS) in 6 patients who underwent sleep EEG studies with 29 or 23 scalp electrodes. The scalp signals were averaged time-locked to the SSS peak activity and subjected to SNPM of LORETA values. All 7 SSS patterns (mean 72 individual SSS, range 11-200) revealed a very similar and highly characteristic transhemispheric oblique scalp voltage distribution comprising a first negative field maximum over ipsilateral lateral temporal areas, followed by a second negative field maximum over the contralateral subtemporal region approximately 30 ms later. SNPM-LORETA consistently localized the first component into the ipsilateral posterior insular region, and the second component into ipsilateral posterior mesial temporo-occipital structures. SSS comprise an amalgam of two sequential, distinct cortical components, showing a very uniform and peculiar EEG pattern and cortical source solutions. As such, they must be clearly distinguished from interictal epileptiform discharges in patients with epilepsy. The awareness of these peculiar EEG characteristics may increase our ability to differentiate SSS from interictal epileptiform activity. The finding of a posterior insular source might serve as an inspiration for new physiological considerations regarding these enigmatic waveforms.

Infinitely Robust Order and Local Order-Parameter Tulips in Apollonian Networks with Quenched Disorder

NASA Astrophysics Data System (ADS)

Nadir Kaplan, C.; Hinczewski, Michael; Berker, A. Nihat

2009-03-01

For a variety of quenched random spin systems on an Apollonian network, including ferromagnetic and antiferromagnetic bond percolation and the Ising spin glass, we find the persistence of ordered phases up to infinite temperature over the entire range of disorder.[1] We develop a renormalization-group technique that yields highly detailed information, including the exact distributions of local magnetizations and local spin-glass order parameters, which turn out to exhibit, as function of temperature, complex and distinctive tulip patterns. [1] C.N. Kaplan, M. Hinczewski, and A.N. Berker, arXiv:0811.3437v1 [cond-mat.dis-nn] (2008).

Neutrophils Express Distinct RNA Receptors in a Non-canonical Way*

PubMed Central

Berger, Michael; Hsieh, Chin-Yuan; Bakele, Martina; Marcos, Veronica; Rieber, Nikolaus; Kormann, Michael; Mays, Lauren; Hofer, Laura; Neth, Olaf; Vitkov, Ljubomir; Krautgartner, Wolf Dietrich; von Schweinitz, Dietrich; Kappler, Roland; Hector, Andreas; Weber, Alexander; Hartl, Dominik

2012-01-01

RNAs are capable of modulating immune responses by binding to specific receptors. Neutrophils represent the major fraction of circulating immune cells, but receptors and mechanisms by which neutrophils sense RNA are poorly defined. Here, we analyzed the mRNA and protein expression patterns and the subcellular localization of the RNA receptors RIG-I, MDA-5, TLR3, TLR7, and TLR8 in primary neutrophils and immortalized neutrophil-like differentiated HL-60 cells. Our results demonstrate that both neutrophils and differentiated HL-60 cells express RIG-I, MDA-5, and TLR8 at the mRNA and protein levels, whereas TLR3 and TLR7 are not expressed at the protein level. Subcellular fractionation, flow cytometry, confocal laser scanning microscopy, and immuno-transmission electron microscopy provided evidence that, besides the cytoplasm, RIG-I and MDA-5 are stored in secretory vesicles of neutrophils and showed that RIG-I and its ligand, 3p-RNA, co-localize at the cell surface without triggering neutrophil activation. In summary, this study demonstrates that neutrophils express a distinct pattern of RNA recognition receptors in a non-canonical way, which could have essential implications for future RNA-based therapeutics. PMID:22532562

Taxonomic status and morphological variation of Hydrodynastes bicinctus (Hermann, 1804) (Serpentes: Dipsadidae).

PubMed

Murta-Fonseca, Roberta A; Franco, Francisco L; Fernandes, Daniel Silva

2016-08-26

Hydrodynastes bicinctus was described with no type material or locality and it has two subspecies currently recognized that are not taxonomically well defined. We tested the validity of the two subspecies through meristic, morphometric, and color pattern characters. Two apparently distinct color patterns of H. bicinctus were noticed, one from the Cerrado open formations and the other from the Amazon rainforest. These aforementioned patterns, however, exhibited a high degree of geographic overlap and many specimens showed a blended pattern. Based on these results we propose synonymizing H. bicinctus schultzi with the nominal taxon. Furthermore, we designate a neotype for the species, present data on geographic distribution, and provide morphological descriptions of the hemipenis, cephalic glands, and skull.

Subcellular localization of the Snf1 kinase is regulated by specific β subunits and a novel glucose signaling mechanism

PubMed Central

Vincent, Olivier; Townley, Robert; Kuchin, Sergei; Carlson, Marian

2001-01-01

The Snf1/AMP-activated protein kinase family has broad roles in transcriptional, metabolic, and developmental regulation in response to stress. In Saccharomyces cerevisiae, Snf1 is required for the response to glucose limitation. Snf1 kinase complexes contain the α (catalytic) subunit Snf1, one of the three related β subunits Gal83, Sip1, or Sip2, and the γ subunit Snf4. We present evidence that the β subunits regulate the subcellular localization of the Snf1 kinase. Green fluorescent protein fusions to Gal83, Sip1, and Sip2 show different patterns of localization to the nucleus, vacuole, and/or cytoplasm. We show that Gal83 directs Snf1 to the nucleus in a glucose-regulated manner. We further identify a novel signaling pathway that controls this nuclear localization in response to glucose phosphorylation. This pathway is distinct from the glucose signaling pathway that inhibits Snf1 kinase activity and responds not only to glucose but also to galactose and sucrose. Such independent regulation of the localization and the activity of the Snf1 kinase, combined with the distinct localization of kinases containing different β subunits, affords versatility in regulating physiological responses. PMID:11331606

Local and Global Auditory Processing: Behavioral and ERP Evidence

PubMed Central

Sanders, Lisa D.; Poeppel, David

2007-01-01

Differential processing of local and global visual features is well established. Global precedence effects, differences in event-related potentials (ERPs) elicited when attention is focused on local versus global levels, and hemispheric specialization for local and global features all indicate that relative scale of detail is an important distinction in visual processing. Observing analogous differential processing of local and global auditory information would suggest that scale of detail is a general organizational principle of the brain. However, to date the research on auditory local and global processing has primarily focused on music perception or on the perceptual analysis of relatively higher and lower frequencies. The study described here suggests that temporal aspects of auditory stimuli better capture the local-global distinction. By combining short (40 ms) frequency modulated tones in series to create global auditory patterns (500 ms), we independently varied whether pitch increased or decreased over short time spans (local) and longer time spans (global). Accuracy and reaction time measures revealed better performance for global judgments and asymmetric interference that were modulated by amount of pitch change. ERPs recorded while participants listened to identical sounds and indicated the direction of pitch change at the local or global levels provided evidence for differential processing similar to that found in ERP studies employing hierarchical visual stimuli. ERP measures failed to provide evidence for lateralization of local and global auditory perception, but differences in distributions suggest preferential processing in more ventral and dorsal areas respectively. PMID:17113115

Subwavelength and directional control of flexural waves in zone-folding induced topological plates

NASA Astrophysics Data System (ADS)

Chaunsali, Rajesh; Chen, Chun-Wei; Yang, Jinkyu

2018-02-01

Inspired by the quantum spin Hall effect shown by topological insulators, we propose a plate structure that can be used to demonstrate the pseudospin Hall effect for flexural waves. The system consists of a thin plate with periodically arranged resonators mounted on its top surface. We extend a technique based on the plane-wave expansion method to identify a double Dirac cone emerging due to the zone-folding in frequency band structures. This particular design allows us to move the double Dirac cone to a lower frequency than the resonating frequency of local resonators. We then manipulate the pattern of local resonators to open subwavelength Bragg band gaps that are topologically distinct. Building on this method, we verify numerically that a waveguide at an interface between two topologically distinct resonating plate structures can be used for guiding low-frequency, spin-dependent one-way flexural waves along a desired path with bends.

Cellular automata and integrodifferential equation models for cell renewal in mosaic tissues

PubMed Central

Bloomfield, J. M.; Sherratt, J. A.; Painter, K. J.; Landini, G.

2010-01-01

Mosaic tissues are composed of two or more genetically distinct cell types. They occur naturally, and are also a useful experimental method for exploring tissue growth and maintenance. By marking the different cell types, one can study the patterns formed by proliferation, renewal and migration. Here, we present mathematical modelling suggesting that small changes in the type of interaction that cells have with their local cellular environment can lead to very different outcomes for the composition of mosaics. In cell renewal, proliferation of each cell type may depend linearly or nonlinearly on the local proportion of cells of that type, and these two possibilities produce very different patterns. We study two variations of a cellular automaton model based on simple rules for renewal. We then propose an integrodifferential equation model, and again consider two different forms of cellular interaction. The results of the continuous and cellular automata models are qualitatively the same, and we observe that changes in local environment interaction affect the dynamics for both. Furthermore, we demonstrate that the models reproduce some of the patterns seen in actual mosaic tissues. In particular, our results suggest that the differing patterns seen in organ parenchymas may be driven purely by the process of cell replacement under different interaction scenarios. PMID:20375040

Cognitive and affective theory of mind share the same local patterns of activity in posterior temporal but not medial prefrontal cortex

PubMed Central

Hofstetter, Christoph; Vuilleumier, Patrik

2014-01-01

Understanding emotions in others engages specific brain regions in temporal and medial prefrontal cortices. These activations are often attributed to more general cognitive ‘mentalizing’ functions, associated with theory of mind and also necessary to represent people’s non-emotional mental states, such as beliefs or intentions. Here, we directly investigated whether understanding emotional feelings recruit similar or specific brain systems, relative to other non-emotional mental states. We used functional magnetic resonance imaging with multivoxel pattern analysis in 46 volunteers to compare activation patterns in theory-of-mind tasks for emotions, relative to beliefs or somatic states accompanied with pain. We found a striking dissociation between the temporoparietal cortex, that exhibited a remarkable voxel-by-voxel pattern overlap between emotions and beliefs (but not pain), and the dorsomedial prefrontal cortex, that exhibited distinct (and yet nearby) patterns of activity during the judgment of beliefs and emotions in others. Pain judgment was instead associated with activity in the supramarginal gyrus, middle cingulate cortex and middle insular cortex. Our data reveal for the first time a functional dissociation within brain networks sub-serving theory of mind for different mental contents, with a common recruitment for cognitive and affective states in temporal regions, and distinct recruitment in prefrontal areas. PMID:23770622

Distinct Sequence Elements of Cyclin B1 Promote Localization to Chromatin, Centrosomes, and Kinetochores during Mitosis

PubMed Central

Bentley, Anna M.; Normand, Guillaume; Hoyt, Jonathan

2007-01-01

The mitotic cyclins promote cell division by binding and activating cyclin-dependent kinases (CDKs). Each cyclin has a unique pattern of subcellular localization that plays a vital role in regulating cell division. During mitosis, cyclin B1 is known to localize to centrosomes, microtubules, and chromatin. To determine the mechanisms of cyclin B1 localization in M phase, we imaged full-length and mutant versions of human cyclin B1-enhanced green fluorescent protein in live cells by using spinning disk confocal microscopy. In addition to centrosome, microtubule, and chromatin localization, we found that cyclin B1 also localizes to unattached kinetochores after nuclear envelope breakdown. Kinetochore recruitment of cyclin B1 required the kinetochore proteins Hec1 and Mad2, and it was stimulated by microtubule destabilization. Mutagenesis studies revealed that cyclin B1 is recruited to kinetochores through both CDK1-dependent and -independent mechanisms. In contrast, localization of cyclin B1 to chromatin and centrosomes is independent of CDK1 binding. The N-terminal domain of cyclin B1 is necessary and sufficient for chromatin association, whereas centrosome recruitment relies on sequences within the cyclin box. Our data support a role for cyclin B1 function at unattached kinetochores, and they demonstrate that separable and distinct sequence elements target cyclin B1 to kinetochores, chromatin, and centrosomes during mitosis. PMID:17881737

Sensitivity to image recurrence across eye-movement-like image transitions through local serial inhibition in the retina

PubMed Central

Krishnamoorthy, Vidhyasankar; Weick, Michael; Gollisch, Tim

2017-01-01

Standard models of stimulus encoding in the retina postulate that image presentations activate neurons according to the increase of preferred contrast inside the receptive field. During natural vision, however, images do not arrive in isolation, but follow each other rapidly, separated by sudden gaze shifts. We here report that, contrary to standard models, specific ganglion cells in mouse retina are suppressed after a rapid image transition by changes in visual patterns across the transition, but respond with a distinct spike burst when the same pattern reappears. This sensitivity to image recurrence depends on opposing effects of glycinergic and GABAergic inhibition and can be explained by a circuit of local serial inhibition. Rapid image transitions thus trigger a mode of operation that differs from the processing of simpler stimuli and allows the retina to tag particular image parts or to detect transition types that lead to recurring stimulus patterns. DOI: http://dx.doi.org/10.7554/eLife.22431.001 PMID:28230526

Laser-induced erasable patterns in a N* liquid crystal on an iron doped lithium niobate surface.

PubMed

Habibpourmoghadam, Atefeh; Lucchetti, Liana; Evans, Dean R; Reshetnyak, Victor Y; Omairat, Faissal; Schafforz, Samuel L; Lorenz, Alexander

2017-10-16

A chiral nematic (N*) liquid crystal (LC) was hybridized with a z-cut iron doped lithium niobate (Fe:LN) substrate and exposed with a focused continuous wave diode laser beam. The N* LC layer was confined with a cover glass to provide a homogeneous LC layer thickness. Two distinct kinds of test cells were investigated, one with an uncoated glass covering slip and one with an indium tin oxide (ITO) coated cover glass. Photo generated electric fields (generated in the Fe:LN) resulted in a localized defect formation and textural transitions in the N* LC. Due to field confinement, the field induced responses were more localized in samples with ITO coated cover glasses. By scanning the laser beam on programmed trajectories, formation of persistent patterns could be achieved in the N* LC layer. Polarized optical microscopy of the exposed samples revealed that these patterns consisted of adjacent circular Frank-Pryce defects. Exposure with a slightly defocused laser beam could be applied selectively to erase these patterns. Thus, a promising method is reported to generate reconfigurable patterns, photonic motives, and touch sensitive devices in a hybridized N* LC with micron accuracy.

Localized direction selective responses in the dendrites of visual interneurons of the fly

PubMed Central

2010-01-01

Background The various tasks of visual systems, including course control, collision avoidance and the detection of small objects, require at the neuronal level the dendritic integration and subsequent processing of many spatially distributed visual motion inputs. While much is known about the pooled output in these systems, as in the medial superior temporal cortex of monkeys or in the lobula plate of the insect visual system, the motion tuning of the elements that provide the input has yet received little attention. In order to visualize the motion tuning of these inputs we examined the dendritic activation patterns of neurons that are selective for the characteristic patterns of wide-field motion, the lobula-plate tangential cells (LPTCs) of the blowfly. These neurons are known to sample direction-selective motion information from large parts of the visual field and combine these signals into axonal and dendro-dendritic outputs. Results Fluorescence imaging of intracellular calcium concentration allowed us to take a direct look at the local dendritic activity and the resulting local preferred directions in LPTC dendrites during activation by wide-field motion in different directions. These 'calcium response fields' resembled a retinotopic dendritic map of local preferred directions in the receptive field, the layout of which is a distinguishing feature of different LPTCs. Conclusions Our study reveals how neurons acquire selectivity for distinct visual motion patterns by dendritic integration of the local inputs with different preferred directions. With their spatial layout of directional responses, the dendrites of the LPTCs we investigated thus served as matched filters for wide-field motion patterns. PMID:20384983

Localized population divergence of vervet monkeys (Chlorocebus spp.) in South Africa: evidence from mtDNA

PubMed Central

Turner, Trudy R.; Coetzer, Willem G.; Schmitt, Christopher A.; Lorenz, Joseph G.; Freimer, Nelson B.; Grobler, J. Paul

2015-01-01

Objectives Vervet monkeys are common in most tree-rich areas of South Africa, but their absence from grassland and semi-desert areas of the country suggest potentially restricted and mosaic local population patterns that may have relevance to local phenotype patterns and selection. A portion of the mtDNA control region was sequenced to study patterns of genetic differentiation. Materials and Methods DNA was extracted and mtDNA sequences were obtained from 101 vervet monkeys at 15 localities which represent both an extensive (widely across the distribution range) and intensive (more than one troop at most of the localities) sampling strategy. Analyses utilized Arlequin 3.1, MEGA 6, BEAST v1.5.2 and Network V3.6.1 Results The dataset contained 26 distinct haplotypes, with six populations fixed for single haplotypes. Pairwise P-distance among population pairs showed significant differentiation among most population pairs, but with non-significant differences among populations within some regions. Populations were grouped into three broad clusters in a maximum likelihood phylogenetic tree and a haplotype network. These clusters correspond to (i) north-western, northern and north-eastern parts of the distribution range as well as the northern coastal belt; (ii) central areas of the country; and (iii) southern part of the Indian Ocean coastal belt, and adjacent inland areas. Discussion Apparent patterns of genetic structure correspond to current and past distribution of suitable habitat, geographic barriers to gene flow, geographic distance and female philopatry. However, further work on nuclear markers and other genomic data is necessary to confirm these results. PMID:26265297

High variation in clonal vs. sexual reproduction in populations of the wild strawberry, Fragaria virginiana (Rosaceae)

PubMed Central

Wilk, John A.; Kramer, Andrea T.; Ashley, Mary V.

2009-01-01

Background and Aims Many plants reproduce both clonally and sexually, and the balance between the two modes of reproduction will vary among populations. Clonal reproduction was characterized in three populations of the wild strawberry, Fragaria virginiana, to determine the extent that reproductive mode varied locally between sites. The study sites were fragmented woodlands in Cook County, Illinois, USA. Methods A total of 95 strawberry ramets were sampled from the three sites via transects. Ramets were mapped and genotyped at five variable microsatellite loci. The variability at these five loci was sufficient to assign plants to clones with high confidence, and the spatial pattern of genets was mapped at each site. Key Results A total of 27 distinct multilocus genotypes were identified. Of these, 18 genotypes were detected only once, with the remaining nine detected in multiple ramets. The largest clone was identified in 16 ramets. No genets were shared between sites, and each site exhibited markedly different clonal and sexual recruitment patterns, ranging from two non-overlapping and widespread genets to 19 distinct genets. Only one flowering genet was female; the remainder were hermaphrodites. Conclusions Local population history or fine-scale ecological differences can result in dramatically different reproductive patterns at small spatial scales. This finding may be fairly widespread among clonal plant species, and studies that aim to characterize reproductive modes in species capable of asexual reproduction need to evaluate reproductive modes in multiple populations and sites. PMID:19797422

Culture in great apes: using intricate complexity in feeding skills to trace the evolutionary origin of human technical prowess.

PubMed

Byrne, Richard W

2007-04-29

Geographical cataloguing of traits, as used in human ethnography, has led to the description of 'culture' in some non-human great apes. Culture, in these terms, is detected as a pattern of local ignorance resulting from environmental constraints on knowledge transmission. However, in many cases, the geographical variations may alternatively be explained by ecology. Social transmission of information can reliably be identified in many other animal species, by experiment or distinctive patterns in distribution; but the excitement of detecting culture in great apes derives from the possibility of understanding the evolution of cumulative technological culture in humans. Given this interest, I argue that great ape research should concentrate on technically complex behaviour patterns that are ubiquitous within a local population; in these cases, a wholly non-social ontogeny is highly unlikely. From this perspective, cultural transmission has an important role in the elaborate feeding skills of all species of great ape, in conveying the 'gist' or organization of skills. In contrast, social learning is unlikely to be responsible for local stylistic differences, which are apt to reflect sensitive adaptations to ecology.

Multivariate Brain Prediction of Heart Rate and Skin Conductance Responses to Social Threat.

PubMed

Eisenbarth, Hedwig; Chang, Luke J; Wager, Tor D

2016-11-23

Psychosocial stressors induce autonomic nervous system (ANS) responses in multiple body systems that are linked to health risks. Much work has focused on the common effects of stress, but ANS responses in different body systems are dissociable and may result from distinct patterns of cortical-subcortical interactions. Here, we used machine learning to develop multivariate patterns of fMRI activity predictive of heart rate (HR) and skin conductance level (SCL) responses during social threat in humans (N = 18). Overall, brain patterns predicted both HR and SCL in cross-validated analyses successfully (r HR = 0.54, r SCL = 0.58, both p < 0.0001). These patterns partly reflected central stress mechanisms common to both responses because each pattern predicted the other signal to some degree (r HR→SCL = 0.21 and r SCL→HR = 0.22, both p < 0.01), but they were largely physiological response specific. Both patterns included positive predictive weights in dorsal anterior cingulate and cerebellum and negative weights in ventromedial PFC and local pattern similarity analyses within these regions suggested that they encode common central stress mechanisms. However, the predictive maps and searchlight analysis suggested that the patterns predictive of HR and SCL were substantially different across most of the brain, including significant differences in ventromedial PFC, insula, lateral PFC, pre-SMA, and dmPFC. Overall, the results indicate that specific patterns of cerebral activity track threat-induced autonomic responses in specific body systems. Physiological measures of threat are not interchangeable, but rather reflect specific interactions among brain systems. We show that threat-induced increases in heart rate and skin conductance share some common representations in the brain, located mainly in the vmPFC, temporal and parahippocampal cortices, thalamus, and brainstem. However, despite these similarities, the brain patterns that predict these two autonomic responses are largely distinct. This evidence for largely output-measure-specific regulation of autonomic responses argues against a common system hypothesis and provides evidence that different autonomic measures reflect distinct, measurable patterns of cortical-subcortical interactions. Copyright © 2016 the authors 0270-6474/16/3611987-12$15.00/0.

In the right place at the right time: visualizing and understanding mRNA localization

PubMed Central

Buxbaum, Adina R.; Haimovich, Gal

2015-01-01

The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization. PMID:25549890

Common Warming Pattern Emerges Irrespective of Forcing Location

NASA Astrophysics Data System (ADS)

Kang, Sarah M.; Park, Kiwoong; Jin, Fei-Fei; Stuecker, Malte F.

2017-10-01

The Earth's climate is changing due to the existence of multiple radiative forcing agents. It is under question whether different forcing agents perturb the global climate in a distinct way. Previous studies have demonstrated the existence of similar climate response patterns in response to aerosol and greenhouse gas (GHG) forcings. In this study, the sensitivity of tropospheric temperature response patterns to surface heating distributions is assessed by forcing an atmospheric general circulation model coupled to an aquaplanet slab ocean with a wide range of possible forcing patterns. We show that a common climate pattern emerges in response to localized forcing at different locations. This pattern, characterized by enhanced warming in the tropical upper troposphere and the polar lower troposphere, resembles the historical trends from observations and models as well as the future projections. Atmospheric dynamics in combination with thermodynamic air-sea coupling are primarily responsible for shaping this pattern. Identifying this common pattern strengthens our confidence in the projected response to GHG and aerosols in complex climate models.

Retrospective Analysis of Radiological Recurrence Patterns in Glioblastoma, Their Prognostic Value And Association to Postoperative Infarct Volume.

PubMed

Bette, Stefanie; Barz, Melanie; Huber, Thomas; Straube, Christoph; Schmidt-Graf, Friederike; Combs, Stephanie E; Delbridge, Claire; Gerhardt, Julia; Zimmer, Claus; Meyer, Bernhard; Kirschke, Jan S; Boeckh-Behrens, Tobias; Wiestler, Benedikt; Gempt, Jens

2018-03-14

Recent studies suggested that postoperative hypoxia might trigger invasive tumor growth, resulting in diffuse/multifocal recurrence patterns. Aim of this study was to analyze distinct recurrence patterns and their association to postoperative infarct volume and outcome. 526 consecutive glioblastoma patients were analyzed, of which 129 met our inclusion criteria: initial tumor diagnosis, surgery, postoperative diffusion-weighted imaging and tumor recurrence during follow-up. Distinct patterns of contrast-enhancement at initial diagnosis and at first tumor recurrence (multifocal growth/progression, contact to dura/ventricle, ependymal spread, local/distant recurrence) were recorded by two blinded neuroradiologists. The association of radiological patterns to survival and postoperative infarct volume was analyzed by uni-/multivariate survival analyses and binary logistic regression analysis. With increasing postoperative infarct volume, patients were significantly more likely to develop multifocal recurrence, recurrence with contact to ventricle and contact to dura. Patients with multifocal recurrence (Hazard Ratio (HR) 1.99, P = 0.010) had significantly shorter OS, patients with recurrent tumor with contact to ventricle (HR 1.85, P = 0.036), ependymal spread (HR 2.97, P = 0.004) and distant recurrence (HR 1.75, P = 0.019) significantly shorter post-progression survival in multivariate analyses including well-established prognostic factors like age, Karnofsky Performance Score (KPS), therapy, extent of resection and patterns of primary tumors. Postoperative infarct volume might initiate hypoxia-mediated aggressive tumor growth resulting in multifocal and diffuse recurrence patterns and impaired survival.

Nanopore sensing of individual transcription factors bound to DNA

PubMed Central

Squires, Allison; Atas, Evrim; Meller, Amit

2015-01-01

Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes. PMID:26109509

Nanopore sensing of individual transcription factors bound to DNA

NASA Astrophysics Data System (ADS)

Squires, Allison; Atas, Evrim; Meller, Amit

2015-06-01

Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.

Protein functional features are reflected in the patterns of mRNA translation speed.

PubMed

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Seasonal movement, residency, and migratory patterns of Wilson's Snipe (Gallinago delicata)

USGS Publications Warehouse

Cline, Brittany B.; Haig, Susan M.

2011-01-01

Cross-seasonal studies of avian movement establish links between geographically distinct wintering, breeding, and migratory stopover locations, or assess site fidelity and movement between distinct phases of the annual cycle. Far fewer studies have investigated individual movement patterns within and among seasons over an annual cycle. Within western Oregon's Willamette Valley throughout 2007, we quantified intra- and interseasonal movement patterns, fidelity (regional and local), and migratory patterns of 37 radiomarked Wilson's Snipe (Gallinago delicata) to elucidate residency in a region of breeding- and wintering-range overlap. Telemetry revealed complex regional population structure, including winter residents (74%), winter transients (14%), summer residents (9%), and one year-round resident breeder (3%). Results indicated a lack of connectivity between winter and summer capture populations, some evidence of partial migration, and between-season fidelity to the region (winter-resident return; subsequent fall). Across seasons, the extent of movements and use of multiple wetland sites suggested that Wilson's Snipe were capable of exploratory movements but more regularly perceived local and fine-scale segments of the landscape as connected. Movements differed significantly by season and residency; individuals exhibited contracted movements during late winter and more expansive movements during precipitation-limited periods (late spring, summer, fall). Mean home-range size was 3.5 ± 0.93 km2 (100% minimum convex polygon [MCP]) and 1.6 ± 0.42 km2 (95% fixed kernel) and did not vary by sex; however, home range varied markedly by season (range of 100% MCPs: 1.04–7.56 km2). The results highlight the need to consider seasonal and interspecific differences in shorebird life histories and space-use requirements when developing regional wetland conservation plans.

Flexible or leaky attention in creative people? Distinct patterns of attention for different types of creative thinking.

PubMed

Zabelina, Darya; Saporta, Arielle; Beeman, Mark

2016-04-01

Creativity has been putatively linked to distinct forms of attention, but which aspects of creativity and which components of attention remains unclear. Two experiments examined how divergent thinking and creative achievement relate to visual attention. In both experiments, participants identified target letters (S or H) within hierarchical stimuli (global letters made of local letters), after being cued to either the local or global level. In Experiment 1, participants identified the targets more quickly following valid cues (80% of trials) than following invalid cues. However, this smaller validity effect was associated with higher divergent thinking, suggesting that divergent thinking was related to quicker overcoming of invalid cues, and thus to flexible attention. Creative achievement was unrelated to the validity effect. Experiment 2 examined whether divergent thinking (or creative achievement) is related to "leaky attention," so that when cued to one level of a stimulus, some information is still processed, or leaks in, from the non-cued level. In this case, the cued stimulus level always contained a target, and the non-cued level was congruent, neutral, or incongruent with the target. Divergent thinking did not relate to stimulus congruency. In contrast, high creative achievement was related to quicker responses to the congruent than to the incongruent stimuli, suggesting that real-world creative achievement is indeed associated with leaky attention, whereas standard laboratory tests of divergent thinking are not. Together, these results elucidate distinct patterns of attention for different measures of creativity. Specifically, creative achievers may have leaky attention, as suggested by previous literature, whereas divergent thinkers have selective yet flexible attention.

Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumn-spawners confined to early postglacial arrival

PubMed Central

Delling, Bo; Palm, Stefan; Palkopoulou, Eleftheria; Prestegaard, Tore

2014-01-01

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized. PMID:25540695

Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumn-spawners confined to early postglacial arrival.

PubMed

Delling, Bo; Palm, Stefan; Palkopoulou, Eleftheria; Prestegaard, Tore

2014-11-01

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.

The heterotrimeric motor protein kinesin-II localizes to the midpiece and flagellum of sea urchin and sand dollar sperm.

PubMed

Henson, J H; Cole, D G; Roesener, C D; Capuano, S; Mendola, R J; Scholey, J M

1997-01-01

We have utilized immunoblotting and light microscopic immunofluorescent staining methods to examine the expression and localization of sea urchin kinesin-II, a heterotrimeric plus end-directed microtubule motor protein (previously referred to as KRP(85/95)), in sea urchin and sand dollar sperm. We demonstrate the presence of the 85 K and 115 K subunits of kinesin-II in sperm and localize these proteins to the sperm flagella and midpiece. The kinesin-II localization pattern is punctate and discontinuous, and in the flagella it is quite distinct from the continuous labeling present in sperm labeled with anti-flagellar dynein. The kinesin-II staining is largely insensitive to prefixation detergent extraction, suggesting that it is not associated with membranous elements in the sperm. In the midpiece the kinesin-II staining is similar to the pattern present in sperm labeled with an anti-centrosomal antibody. To our knowledge, this is the first localization of kinesin-like proteins in mature sperm and corroborates the recent identification and localization of kinesin-like proteins in the flagella and basal body of the unicellular green alga Chlamydomonas. We hypothesize that kinesin-II in the sperm may play functional roles in intraflagellar transport and/or the formation of flagella during spermatogenesis.

Linking Pattern Formation and Alternative Stable States: Ecohydrologic Thresholds and Critical Transitions in the Everglades Peatlands

NASA Astrophysics Data System (ADS)

Heffernan, J. B.; Ross, M. S.; Sah, J. P.; Isherwood, E.; Cohen, M. J.

2015-12-01

Spatial patterning occurs in a variety of ecosystems, and is important for the functional properties of landscapes; for testing spatial models of ecological processes; and as an indicator of landscape condition and resilience. Theory suggests that regular patterns arise from coupled local- and landscape-scale feedbacks that can also create multiple stable landscape states. In the Florida Everglades, hydrologic modification has degraded much of the historically-extensive ridge-slough landscape, a patterned peatland mosaic with distinct, flow-parallel patches. However, in the Everglades and in general, the hypothesis that patterned landscapes have homogeneous alternative states has little direct empirical support. Here we use microtopographic and vegetative heterogeneity, and their relation to hydrologic conditions, to infer the existence of multiple landscape equilibria and identify the hydrologic thresholds for critical transitions between these states. Dual relationships between elevation variance and water depth, and bi-modal distributions of both elevation variance and plant community distinctness, are consistent with generic predictions of multiple states, and covariation between these measures suggests that microtopography is the leading indicator of landscape degradation. Furthermore, a simple ecohydrologic multiple-state model correctly predicts the hydrologic thresholds for persistence of distinct ridges and sloughs. Predicted ridge-slough elevation differences and their relation to water depth are much greater than observed in the contemporary Everglades, but correspond closely with historical observations of pre-drainage conditions. These multiple lines of evidence represent the broadest and most direct support for the link between regular spatial pattern and landscape-scale alternative states in any ecosystem, and suggest that other patterned landscapes could undergo sudden collapse in response to changing environmental conditions. Hydrologic thresholds and leading indicators of critical transitions should guide management of the Everglades ridge-slough landscape, whose preservation is a central goal of one of the world's largest ecosystem restoration efforts.

Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions

DOE PAGES

Techtmann, Stephen M.; Fitzgerald, Kathleen S.; Stelling, Savannah C.; ...

2016-05-09

Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here in this study we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraea was investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from themore » Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. Finally, there appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates.« less

Patterns of Post-Glacial Genetic Differentiation in Marginal Populations of a Marine Microalga

PubMed Central

Tahvanainen, Pia; Alpermann, Tilman J.; Figueroa, Rosa Isabel; John, Uwe; Hakanen, Päivi; Nagai, Satoshi; Blomster, Jaanika; Kremp, Anke

2012-01-01

This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F ST) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms. PMID:23300940

Patterns of post-glacial genetic differentiation in marginal populations of a marine microalga.

PubMed

Tahvanainen, Pia; Alpermann, Tilman J; Figueroa, Rosa Isabel; John, Uwe; Hakanen, Päivi; Nagai, Satoshi; Blomster, Jaanika; Kremp, Anke

2012-01-01

This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F(ST)) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.

Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis.

PubMed

De Rybel, Bert; Adibi, Milad; Breda, Alice S; Wendrich, Jos R; Smit, Margot E; Novák, Ondřej; Yamaguchi, Nobutoshi; Yoshida, Saiko; Van Isterdael, Gert; Palovaara, Joakim; Nijsse, Bart; Boekschoten, Mark V; Hooiveld, Guido; Beeckman, Tom; Wagner, Doris; Ljung, Karin; Fleck, Christian; Weijers, Dolf

2014-08-08

Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue. Copyright © 2014, American Association for the Advancement of Science.

Re-visioning local biologies: HIV-2 and the pattern of differential valuation in biomedical research.

PubMed

Gilbert, Hannah

2013-01-01

The discovery of HIV-2, a distinctly West African variant of HIV, is often portrayed as the result of a straightforward, if serendipitous, error. This article reframes the history of how HIV-2 came to be a knowable scientific identity. Relying on narratives from an African laboratory and clinic, it suggests that the rise and fall of HIV-2 as a viable research entity is indicative of a differential visibility and valuation of both human bodies and viruses. Understanding how HIV-2 emerged as a local biology reveals the complex set of relations that contemporary African scientists face in navigating local moral economies and the mercurial politics of the contemporary global health industry.

Cellular Trafficking of Phospholamban and Formation of Functional Sarcoplasmic Reticulum During Myocyte DIfferentiation

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

Stenoien, David L.; Knyushko, Tatyana V.; Londono, Monica P.

2007-06-01

The sarco/endoplasmic reticulum Ca-ATPase (SERCA) family members are transmembrane proteins that play an essential role in regulating intracellular calcium levels. Phospholamban (PLB), a 52 amino acid phosphoprotein, regulates SERCA activity in adult heart and skeletal muscle. Using the C2C12 myocyte cell line, we find endogenous PLB constitutively expressed in both myoblasts and myotubes, whereas SERCA expression coincides with activation of the differentiation program. PLB has a punctuate distribution in myoblasts changing to a reticular distribution in myotubes where it colocalizes with SERCAs. To examine the distribution and dynamics of PLB and SERCA, we expressed fluorescent fusion proteins (GFP, CFP, andmore » YFP) of PLB and SERCA in myoblasts. Coexpressed PLB and SERCA localize to distinct cellular compartments in myoblasts but begin to colocalize as cells differentiate. Fluorescence Recovery After Photobleaching (FRAP) studies show different recovery patterns for each protein in myoblasts confirming their localization to distinct compartments. To extend these studies, we created stable cell lines expressing O6-alkylguanine-DNA alkyltransferase (AGT) fusions with PLB or SERCA to track their localization as myocytes differentiate. These experiments demonstrate that PLB localizes to punctate vesicles in myoblasts and adopts a reticular distribution that coincides with SERCA distribution after differentiation. Colocalization experiments indicate that a subset of PLB in myoblasts colocalizes with endosomes, Golgi, and the plasma membrane however PLB also localizes to other, as yet unidentified vesicles. Our results indicate that differentiation plays a critical role in regulating PLB distribution to ensure its colocalization within the same cellular compartment as SERCA in differentiated cells. The presence and altered distribution of PLB in undifferentiated myoblasts raises the possibility that this protein has additional functions distinct from SERCA regulation.« less

Linking actin networks and cell membrane via a reaction-diffusion-elastic description of nonlinear filopodia initiation.

PubMed

Ben Isaac, Eyal; Manor, Uri; Kachar, Bechara; Yochelis, Arik; Gov, Nir S

2013-08-01

Reaction-diffusion models have been used to describe pattern formation on the cellular scale, and traditionally do not include feedback between cellular shape changes and biochemical reactions. We introduce here a distinct reaction-diffusion-elasticity approach: The reaction-diffusion part describes bistability between two actin orientations, coupled to the elastic energy of the cell membrane deformations. This coupling supports spatially localized patterns, even when such solutions do not exist in the uncoupled self-inhibited reaction-diffusion system. We apply this concept to describe the nonlinear (threshold driven) initiation mechanism of actin-based cellular protrusions and provide support by several experimental observations.

Entanglement complexity in quantum many-body dynamics, thermalization, and localization

NASA Astrophysics Data System (ADS)

Yang, Zhi-Cheng; Hamma, Alioscia; Giampaolo, Salvatore M.; Mucciolo, Eduardo R.; Chamon, Claudio

2017-07-01

Entanglement is usually quantified by von Neumann entropy, but its properties are much more complex than what can be expressed with a single number. We show that the three distinct dynamical phases known as thermalization, Anderson localization, and many-body localization are marked by different patterns of the spectrum of the reduced density matrix for a state evolved after a quantum quench. While the entanglement spectrum displays Poisson statistics for the case of Anderson localization, it displays universal Wigner-Dyson statistics for both the cases of many-body localization and thermalization, albeit the universal distribution is asymptotically reached within very different time scales in these two cases. We further show that the complexity of entanglement, revealed by the possibility of disentangling the state through a Metropolis-like algorithm, is signaled by whether the entanglement spectrum level spacing is Poisson or Wigner-Dyson distributed.

The structural configuration of U.S. hospital medical staffs.

PubMed

Shortell, S M; Evashwick, C

1981-04-01

Using data from the 1973 American Hospital Association national survey of hospital medical staff organization, six factors of medical staff organization structure are examined in relation to each other and to hospital ownership, size, teaching status, geographic region and size of Standard Metropolitan Statistical Area (SMSA). The six factors include 1) Resource Capability; 2) Generalist Physician Contractual Orientation; 3) Communication and Control; 4) Local Staff Orientation; 5) Physician Participation in Decision Making; and 6) Hospital-Based Contractual Orientation. Several relatively distinct patterns emerged related to hospital ownership, size, teaching activity and region of the country, as well as interrelationships among the factors themselves. Differences between smaller and larger hospitals clearly emerged as well as a distinctive pattern for for-profit hospitals. All of the factors are subject to manipulation through administrative and/or public policy interventions and the findings suggest dimensions for future investigation of important policy issues related to the medical staff's role in cost containment, utilization, quality assurance and technology adoption.

Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly.

PubMed

Lemoine, Nathan P; Shue, Jessica; Verrico, Brittany; Erickson, David; Kress, W John; Parker, John D

2015-10-01

Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species.

Measurement of Thunderstorm Cloud-Top Parameters Using High-Frequency Satellite Imagery

DTIC Science & Technology

1978-01-01

short wave was present well to the south of this system approximately 2000 ka west of Baja California. Two distinct flow patterns were present, one...view can be observed in near real time whereas radar observations, although excellent for local purposes, involve substantial errors when composited...on a large scale. The time delay in such large scale compositing is critical when attempting to monitor convective cloud systems for a potential

Distinct neural patterns enable grasp types decoding in monkey dorsal premotor cortex.

PubMed

Hao, Yaoyao; Zhang, Qiaosheng; Controzzi, Marco; Cipriani, Christian; Li, Yue; Li, Juncheng; Zhang, Shaomin; Wang, Yiwen; Chen, Weidong; Chiara Carrozza, Maria; Zheng, Xiaoxiang

2014-12-01

Recent studies have shown that dorsal premotor cortex (PMd), a cortical area in the dorsomedial grasp pathway, is involved in grasp movements. However, the neural ensemble firing property of PMd during grasp movements and the extent to which it can be used for grasp decoding are still unclear. To address these issues, we used multielectrode arrays to record both spike and local field potential (LFP) signals in PMd in macaque monkeys performing reaching and grasping of one of four differently shaped objects. Single and population neuronal activity showed distinct patterns during execution of different grip types. Cluster analysis of neural ensemble signals indicated that the grasp related patterns emerged soon (200-300 ms) after the go cue signal, and faded away during the hold period. The timing and duration of the patterns varied depending on the behaviors of individual monkey. Application of support vector machine model to stable activity patterns revealed classification accuracies of 94% and 89% for each of the two monkeys, indicating a robust, decodable grasp pattern encoded in the PMd. Grasp decoding using LFPs, especially the high-frequency bands, also produced high decoding accuracies. This study is the first to specify the neuronal population encoding of grasp during the time course of grasp. We demonstrate high grasp decoding performance in PMd. These findings, combined with previous evidence for reach related modulation studies, suggest that PMd may play an important role in generation and maintenance of grasp action and may be a suitable locus for brain-machine interface applications.

Continuous light exposure causes cumulative stress that affects the localization oscillation dynamics of the transcription factor Msn2p.

PubMed

Bodvard, Kristofer; Wrangborg, David; Tapani, Sofia; Logg, Katarina; Sliwa, Piotr; Blomberg, Anders; Kvarnström, Mats; Käll, Mikael

2011-02-01

Light exposure is a potentially powerful stress factor during in vivo optical microscopy studies. In yeast, the general transcription factor Msn2p translocates from the cytoplasm to the nucleus in response to illumination. However, previous time-lapse fluorescence microscopy studies of Msn2p have utilized a variety of discrete exposure settings, which makes it difficult to correlate stress levels and illumination parameters. We here investigate how continuous illumination with blue light, corresponding to GFP excitation wavelengths, affects the localization pattern of Msn2p-GFP in budding yeast. The localization pattern was analyzed using a novel approach that combines wavelet decomposition and change point analysis. It was found that the Msn2p nucleocytoplasmic localization trajectories for individual cells exhibit up to three distinct and successive states; i) Msn2p localizes to the cytoplasm; ii) Msn2p rapidly shuttles between the cytoplasm and the nucleus; iii) Msn2p localizes to the nucleus. Many cells pass through all states consecutively at high light intensities, while at lower light intensities most cells only reach states i) or ii). This behaviour strongly indicates that continuous light exposure gradually increases the stress level over time, presumably through continuous accumulation of toxic photoproducts, thereby forcing the cell through a bistable region corresponding to nucleocytoplasmic oscillations. We also show that the localization patterns are dependent on protein kinase A (PKA) activity, i.e. yeast cells with constantly low PKA activity showed a stronger stress response. In particular, the nucleocytoplasmic oscillation frequency was found to be significantly higher for cells with low PKA activity for all light intensities. 2010 Elsevier B.V. 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

Subtropical Interactions: Comparing Galling Insect and Host Plant Diversity in Southern Brazil and Florida.

PubMed

D S Mendonça, M; Stiling, P

2017-11-22

Gall-inducing insects seem to have a diversity pattern distinct from the usual latitudinal decrease in species, with more species occurring in xeric environments instead. Many questions regarding galler diversity over geographical scales remain unanswered: for example, little is known about beta diversity, and the role super host plants play in local/regional richness. Our aim was to compare galling insect and host plant diversity in different biogeographical regions, but under similar environmental conditions. We sampled short stature coastal woodlands on sandy soils of the Atlantic coast in both USA (Florida) and Brazil (Rio Grande do Sul, RS), between 25° and 30° latitude. Little-used 200-m long trails were searched during 90 min for galls; there were four trails in USA and five in Brazil. Gall functional traits (galled plant organ, gall shape and colour) proportions were not different between Florida and RS. Local galling and host plant species richness also did not differ, and neither did regional galling diversity. The beta diversity pattern, however, was distinct: sites in Florida have more similar galling faunas than sites in RS. Common diversity patterns indicate common environmental biotic (plant diversity, vegetation structure) and abiotic (climate, soil) factors might be contributing to these similar responses. As Brazilian sites are in the Atlantic forest hotspot, a high galling insect beta diversity might be caused by a higher heterogeneity at larger scales-sample-based rarefaction curves were ascending for Brazil, but not for USA. Myrtaceans were super hosts in Brazil, but not in Florida, where oaks take up this role.

Recharacterization of Rhinophis dorsimaculatus Deraniyagala, 1941 (Serpentes: Uropeltidae), including description of new material.

PubMed

Gower, David J; Wickramasinghe, L J Mendis

2016-08-29

The Sri Lankan uropeltid (shieldtail) snake Rhinophis dorsimaculatus Deraniyagala, 1941 was described originally from two specimens that were subsequently lost. The small amount of previously published data and lack of published colour photographs made this one of South Asia's most poorly known snake species, and this resulted in at least one instance of taxonomic misidentification. An additional 10 specimens from a historical collection from the vicinity of the type locality recently came to light. This material is reviewed and documented and the species recharacterized. An additional locality for the species is reported. The newly reported material helps to corroborate the taxonomic validity and distinctiveness of Rhinophis dorsimaculatus. The species is readily distinguished from congeners by having 227 or more ventral scales; a large, dorsally carinate rostral shield; posterior margins of paired anals that are largely separated by the posteriormost ventral scale; and a distinctive colour pattern with bilaterally asymmetrical dark blotches within a broad, pale middorsal stripe and regularly punctate flanks.

Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm.

PubMed

Liu, Wenzheng; Russel, Jakob; Burmølle, Mette; Sørensen, Søren J; Madsen, Jonas S

2018-04-18

Microorganisms frequently coexist in complex multispecies communities, where they distribute non-randomly, reflective of the social interactions that occur. It is therefore important to understand how social interactions and local spatial organization influences multispecies biofilm succession. Here the localization of species pairs was analyzed in three dimensions in a reproducible four-species biofilm model, to study the impact of spatial positioning of individual species on the temporal development of the community. We found, that as the biofilms developed, species pairs exhibited distinct intermixing patterns unique to the four-member biofilms. Higher biomass and more intermixing were found in four-species biofilms compared to biofilms with fewer species. Intriguingly, in local regions within the four member biofilms where Microbacterium oxydans was scant, both biomass and intermixing of all species were lowered, compared to regions where M. oxydans was present at typical densities. Our data suggest that Xanthomonas retroflexus and M. oxydans, both low abundant biofilm-members, intermixed continuously during the development of the four-species biofilm, hereby facilitating their own establishment. In turn, this seems to have promoted distinct spatial organization of Stenotrophomonas rhizophila and Paenibacillus amylolyticus enabling enhanced growth of all four species. Here local intermixing of bacteria advanced the temporal development of a multi-species biofilm.

Morphologic and molecular evaluation of Chlamydia trachomatis growth in human endocervix reveals distinct growth patterns

PubMed Central

Lewis, Maria E.; Belland, Robert J.; AbdelRahman, Yasser M.; Beatty, Wandy L.; Aiyar, Ashok A.; Zea, Arnold H.; Greene, Sheila J.; Marrero, Luis; Buckner, Lyndsey R.; Tate, David J.; McGowin, Chris L.; Kozlowski, Pamela A.; O'Brien, Michelle; Lillis, Rebecca A.; Martin, David H.; Quayle, Alison J.

2014-01-01

In vitro models of Chlamydia trachomatis growth have long been studied to predict growth in vivo. Alternative or persistent growth modes in vitro have been shown to occur under the influence of numerous stressors but have not been studied in vivo. Here, we report the development of methods for sampling human infections from the endocervix in a manner that permits a multifaceted analysis of the bacteria, host and the endocervical environment. Our approach permits evaluating total bacterial load, transcriptional patterns, morphology by immunofluorescence and electron microscopy, and levels of cytokines and nutrients in the infection microenvironment. By applying this approach to two pilot patients with disparate infections, we have determined that their contrasting growth patterns correlate with strikingly distinct transcriptional biomarkers, and are associated with differences in local levels of IFNγ. Our multifaceted approach will be useful to dissect infections in the human host and be useful in identifying patients at risk for chronic disease. Importantly, the molecular and morphological analyses described here indicate that persistent growth forms can be isolated from the human endocervix when the infection microenvironment resembles the in vitro model of IFNγ-induced persistence. PMID:24959423

Integrating retrogenesis theory to Alzheimer's disease pathology: insight from DTI-TBSS investigation of the white matter microstructural integrity.

PubMed

Alves, Gilberto Sousa; Oertel Knöchel, Viola; Knöchel, Christian; Carvalho, André Férrer; Pantel, Johannes; Engelhardt, Eliasz; Laks, Jerson

2015-01-01

Microstructural abnormalities in white matter (WM) are often reported in Alzheimer's disease (AD) and may reflect primary or secondary circuitry degeneration (i.e., due to cortical atrophy). The interpretation of diffusion tensor imaging (DTI) eigenvectors, known as multiple indices, may provide new insights into the main pathological models supporting primary or secondary patterns of WM disruption in AD, the retrogenesis, and Wallerian degeneration models, respectively. The aim of this review is to analyze the current literature on the contribution of DTI multiple indices to the understanding of AD neuropathology, taking the retrogenesis model as a reference for discussion. A systematic review using MEDLINE, EMBASE, and PUBMED was performed. Evidence suggests that AD evolves through distinct patterns of WM disruption, in which retrogenesis or, alternatively, the Wallerian degeneration may prevail. Distinct patterns of WM atrophy may be influenced by complex interactions which comprise disease status and progression, fiber localization, concurrent risk factors (i.e., vascular disease, gender), and cognitive reserve. The use of DTI multiple indices in addition to other standard multimodal methods in dementia research may help to determine the contribution of retrogenesis hypothesis to the understanding of neuropathological hallmarks that lead to AD.

Rods and cones contain antigenically distinctive S-antigens.

PubMed

Nork, T M; Mangini, N J; Millecchia, L L

1993-09-01

S-antigen (48 kDa protein or arrestin) is known to be present in rod photoreceptors. Its localization in cones is less clear with several conflicting reports among various species examined. This study employed three different anti-S-antigen antibodies (a48K, a polyclonal antiserum and two monoclonal antibodies, MAb A9-C6 and MAb 5c6.47) and examined their localization in rods and cones of human and cat retinas. To identify the respective cone types, an enzyme histochemical technique for carbonic anhydrase (CA) was employed to distinguish blue cones (CA-negative) from red or green cones (CA-positive). S-antigen localization was then examined by immunocytochemical staining of adjacent sections. In human retinas, a similar labeling pattern was seen with both a48K and MAb A9-C6, i.e., the rods and blue-sensitive cones were strongly positive, whereas the red- or green-sensitive cones showed little immunoreactivity. All human photoreceptors showed reactivity to MAb 5c6.47. In the cat retina, only CA-positive cones could be found. As in the human retina, both rods and cones of the cat were positive for MAb 5c6.47. A difference from the labeling pattern in human retina was noted for the other S-antigen antibodies; a48K labeled rods and all of the cones, whereas MAb A9-C6 reacted strongly with the rods but showed no cone staining. These results suggest that both rods and cones contain S-antigen but that they are antigenically distinctive.

Finger Vein Segmentation from Infrared Images Based on a Modified Separable Mumford Shah Model and Local Entropy Thresholding

PubMed Central

Dermatas, Evangelos

2015-01-01

A novel method for finger vein pattern extraction from infrared images is presented. This method involves four steps: preprocessing which performs local normalization of the image intensity, image enhancement, image segmentation, and finally postprocessing for image cleaning. In the image enhancement step, an image which will be both smooth and similar to the original is sought. The enhanced image is obtained by minimizing the objective function of a modified separable Mumford Shah Model. Since, this minimization procedure is computationally intensive for large images, a local application of the Mumford Shah Model in small window neighborhoods is proposed. The finger veins are located in concave nonsmooth regions and, so, in order to distinct them from the other tissue parts, all the differences between the smooth neighborhoods, obtained by the local application of the model, and the corresponding windows of the original image are added. After that, veins in the enhanced image have been sufficiently emphasized. Thus, after image enhancement, an accurate segmentation can be obtained readily by a local entropy thresholding method. Finally, the resulted binary image may suffer from some misclassifications and, so, a postprocessing step is performed in order to extract a robust finger vein pattern. PMID:26120357

Wood cell-wall structure requires local 2D-microtubule disassembly by a novel plasma membrane-anchored protein.

PubMed

Oda, Yoshihisa; Iida, Yuki; Kondo, Yuki; Fukuda, Hiroo

2010-07-13

Plant cells have evolved cortical microtubules, in a two-dimensional space beneath the plasma membrane, that regulate patterning of cellulose deposition. Although recent studies have revealed that several microtubule-associated proteins facilitate self-organization of transverse cortical microtubules, it is still unknown how diverse patterns of cortical microtubules are organized in different xylem cells, which are the major components of wood. Using our newly established in vitro xylem cell differentiation system, we found that a novel microtubule end-tracking protein, microtubule depletion domain 1 (MIDD1), was anchored to distinct plasma membrane domains and promoted local microtubule disassembly, resulting in pits on xylem cell walls. The introduction of RNA interference for MIDD1 resulted in the failure of local microtubule depletion and the formation of secondary walls without pits. Conversely, the overexpression of MIDD1 reduced microtubule density. MIDD1 has two coiled-coil domains for the binding to microtubules and for the anchorage to plasma membrane domains, respectively. Combination of the two coils caused end tracking of microtubules during shrinkage and suppressed their rescue events. Our results indicate that MIDD1 integrates spatial information in the plasma membrane with cortical microtubule dynamics for determining xylem cell wall pattern. Copyright 2010 Elsevier Ltd. All rights reserved.

Machine-learned analysis of quantitative sensory testing responses to noxious cold stimulation in healthy subjects.

PubMed

Weyer-Menkhoff, I; Thrun, M C; Lötsch, J

2018-05-01

Pain in response to noxious cold has a complex molecular background probably involving several types of sensors. A recent observation has been the multimodal distribution of human cold pain thresholds. This study aimed at analysing reproducibility and stability of this observation and further exploration of data patterns supporting a complex background. Pain thresholds to noxious cold stimuli (range 32-0 °C, tonic: temperature decrease -1 °C/s, phasic: temperature decrease -8 °C/s) were acquired in 148 healthy volunteers. The probability density distribution was analysed using machine-learning derived methods implemented as Gaussian mixture modeling (GMM), emergent self-organizing maps and self-organizing swarms of data agents. The probability density function of pain responses was trimodal (mean thresholds at 25.9, 18.4 and 8.0 °C for tonic and 24.5, 18.1 and 7.5 °C for phasic stimuli). Subjects' association with Gaussian modes was consistent between both types of stimuli (weighted Cohen's κ = 0.91). Patterns emerging in self-organizing neuronal maps and swarms could be associated with different trends towards decreasing cold pain sensitivity in different Gaussian modes. On self-organizing maps, the third Gaussian mode emerged as particularly distinct. Thresholds at, roughly, 25 and 18 °C agree with known working temperatures of TRPM8 and TRPA1 ion channels, respectively, and hint at relative local dominance of either channel in respective subjects. Data patterns suggest involvement of further distinct mechanisms in cold pain perception at lower temperatures. Findings support data science approaches to identify biologically plausible hints at complex molecular mechanisms underlying human pain phenotypes. Sensitivity to pain is heterogeneous. Data-driven computational research approaches allow the identification of subgroups of subjects with a distinct pattern of sensitivity to cold stimuli. The subgroups are reproducible with different types of noxious cold stimuli. Subgroups show pattern that hints at distinct and inter-individually different types of the underlying molecular background. © 2018 European Pain Federation - EFIC®.

Nitrogen economics of root foraging: Transitive closure of the nitrate–cytokinin relay and distinct systemic signaling for N supply vs. demand

PubMed Central

Ruffel, Sandrine; Krouk, Gabriel; Ristova, Daniela; Shasha, Dennis; Birnbaum, Kenneth D.; Coruzzi, Gloria M.

2011-01-01

As sessile organisms, root plasticity enables plants to forage for and acquire nutrients in a fluctuating underground environment. Here, we use genetic and genomic approaches in a “split-root” framework—in which physically isolated root systems of the same plant are challenged with different nitrogen (N) environments—to investigate how systemic signaling affects genome-wide reprogramming and root development. The integration of transcriptome and root phenotypes enables us to identify distinct mechanisms underlying “N economy” (i.e., N supply and demand) of plants as a system. Under nitrate-limited conditions, plant roots adopt an “active-foraging strategy”, characterized by lateral root outgrowth and a shared pattern of transcriptome reprogramming, in response to either local or distal nitrate deprivation. By contrast, in nitrate-replete conditions, plant roots adopt a “dormant strategy”, characterized by a repression of lateral root outgrowth and a shared pattern of transcriptome reprogramming, in response to either local or distal nitrate supply. Sentinel genes responding to systemic N signaling identified by genome-wide comparisons of heterogeneous vs. homogeneous split-root N treatments were used to probe systemic N responses in Arabidopsis mutants impaired in nitrate reduction and hormone synthesis and also in decapitated plants. This combined analysis identified genetically distinct systemic signaling underlying plant N economy: (i) N supply, corresponding to a long-distance systemic signaling triggered by nitrate sensing; and (ii) N demand, experimental support for the transitive closure of a previously inferred nitrate–cytokinin shoot–root relay system that reports the nitrate demand of the whole plant, promoting a compensatory root growth in nitrate-rich patches of heterogeneous soil. PMID:22025711

Spatial X-ray fluorescence micro-imaging of minerals in grain tissues of wheat and related genotypes.

PubMed

Singh, Sudhir P; Vogel-Mikuš, Katarina; Vavpetič, Primož; Jeromel, Luka; Pelicon, Primož; Kumar, Jitendra; Tuli, Rakesh

2014-08-01

Wheat and its related genotypes show distinct distribution patterns for mineral nutrients in maternal and filial tissues in grains. X-ray-based imaging techniques are very informative to identify genotypes with contrasting tissue-specific localization of different elements. This can help in the selection of suitable genotypes for nutritional improvement of food grain crops. Understanding mineral localization in cereal grains is important for their nutritional improvement. Spatial distribution of mineral nutrients (Mg, P, S, K, Ca, Fe, Zn, Mn and Cu) was investigated between and within the maternal and filial tissues in grains of two wheat cultivars (Triticum aestivum Cv. WH291 and WL711), a landrace (T. aestivum L. IITR26) and a related wild species Aegilops kotschyi, using micro-proton-induced X-ray emission (µ-PIXE) and micro-X-ray fluorescence (µ-XRF). Aleurone and scutellum were major storage tissues for macro (P, K, Ca and Mg) as well as micro (Fe, Zn, Cu and Mn) nutrients. Distinct elemental distribution patterns were observed in each of the four genotypes. A. kotschyi, the wild relative of wheat and the landrace, T. aestivum L. IITR26, accumulated more Zn and Fe in scutellum and aleurone than the cultivated wheat varieties, WH291 and WL711. The landrace IITR26, accumulated far more S in grains, Mn in scutellum, aleurone and embryo region, Ca and Cu in aleurone and scutellum, and Mg, K and P in scutellum than the other genotypes. Unlike wheat, lower Mn and higher Fe, Cu and Zn concentrations were noticed in the pigment strand of A. kotschyi. Multivariate statistical analysis, performed on mineral distribution in major grain tissues (aleurone, scutellum, endosperm and embryo region) resolved the four genotypes into distinct clusters.

Femtosecond laser patterning, synthesis, defect formation, and structural modification of atomic layered materials

DOE PAGES

Yoo, Jae-Hyuck; Kim, Eunpa; Hwang, David J.

2016-12-06

This article summarizes recent research on laser-based processing of twodimensional (2D) atomic layered materials, including graphene and transition metal dichalcogenides (TMDCs). Ultrafast lasers offer unique processing routes that take advantage of distinct interaction mechanisms with 2D materials to enable extremely localized energy deposition. Experiments have shown that ablative direct patterning of graphene by ultrafast lasers can achieve resolutions of tens of nanometers, as well as single-step pattern transfer. Ultrafast lasers also induce non-thermal excitation mechanisms that are useful for the thinning of TMDCs to tune the 2D material bandgap. Laser-assisted site-specific doping was recently demonstrated where ultrafast laser radiation undermore » ambient air environment could be used for the direct writing of high-quality graphene patterns on insulating substrates. This article concludes with an outlook towards developing further advanced laser processing with scalability, in situ monitoring strategies and potential applications.« less

Phase diagram of congested traffic flow: An empirical study

PubMed

Lee; Lee; Kim

2000-10-01

We analyze traffic data from a highway section containing one effective on-ramp. Based on two criteria, local velocity variation patterns and expansion (or nonexpansion) of congested regions, three distinct congested traffic states are identified. These states appear at different levels of the upstream flux and the on-ramp flux, thereby generating a phase digram of the congested traffic flow. Observed traffic states are compared with recent theoretical analyses and both agreeing and disagreeing features are found.

Identification of a Polymorphic Gene, BCL2A1, Encoding Two Novel Hematopoietic Lineage-specific Minor Histocompatibility Antigens

PubMed Central

Akatsuka, Yoshiki; Nishida, Tetsuya; Kondo, Eisei; Miyazaki, Mikinori; Taji, Hirohumi; Iida, Hiroatsu; Tsujimura, Kunio; Yazaki, Makoto; Naoe, Tomoki; Morishima, Yasuo; Kodera, Yoshihisa; Kuzushima, Kiyotaka; Takahashi, Toshitada

2003-01-01

We report the identification of two novel minor histocompatibility antigens (mHAgs), encoded by two separate single nucleotide polymorphisms on a single gene, BCL2A1, and restricted by human histocompatibility leukocyte antigen (HLA)-A*2402 (the most common HLA-A allele in Japanese) and B*4403, respectively. Two cytotoxic T lymphocyte (CTL) clones specific for these mHAgs were first isolated from two distinct recipients after hematopoietic cell transplantation. Both clones lyse only normal and malignant cells within the hematopoietic lineage. To localize the gene encoding the mHAgs, two-point linkage analysis was performed on the CTL lytic patterns of restricting HLA-transfected B lymphoblastoid cell lines obtained from Centre d'Etude du Polymorphisme Humain. Both CTL clones showed a completely identical lytic pattern for 4 pedigrees and the gene was localized within a 3.6-cM interval of 15q24.3–25.1 region that encodes at least 46 genes. Of those, only BCL2A1 has been reported to be expressed in hematopoietic cells and possess three nonsynonymous nucleotide changes. Minigene transfection and epitope reconstitution assays with synthetic peptides identified both HLA-A*2402– and B*4403-restricted mHAg epitopes to be encoded by distinct polymorphisms within BCL2A1. PMID:12771180

Patterns of Alcohol Policy Enforcement Activities among Local Law Enforcement Agencies: A Latent Class Analysis

PubMed Central

Erickson, Darin J.; Rutledge, Patricia C.; Lenk, Kathleen M.; Nelson, Toben F.; Jones-Webb, Rhonda; Toomey, Traci L.

2015-01-01

Aims We assessed levels and patterns of alcohol policy enforcement activities among U.S. local law enforcement agencies. Design/Setting/Participants We conducted a cross-sectional survey of a representative sample of 1,631 local law enforcement agencies across the 50 states. Measures/Methods We assessed 29 alcohol policy enforcement activities within each of five enforcement domains—underage alcohol possession/consumption, underage alcohol provision, underage alcohol sales, impaired driving, and overservice of alcohol—and conducted a series of latent class analyses to identify unique classes or patterns of enforcement activity for each domain. Findings We identified three to four unique enforcement activity classes for each of the enforcement domains. In four of the domains, we identified a Uniformly Low class (i.e., little or no enforcement) and a Uniformly High enforcement activity class (i.e., relatively high levels of enforcement), with one or two middle classes where some but not all activities were conducted. The underage provision domain had a Uniformly Low class but not a Uniformly High class. The Uniformly Low class was the most prevalent class in three domains: underage provision (58%), underage sales (61%), and overservice (79%). In contrast, less than a quarter of agencies were in Uniformly High classes. Conclusions We identified qualitatively distinct patterns of enforcement activity, with a large proportion of agencies in classes characterized by little or no enforcement and fewer agencies in high enforcement classes. An important next step is to determine if these patterns are associated with rates of alcohol use and alcohol-related injury and mortality. PMID:26877822

Mitochondria-specific photoactivation to monitor local sphingosine metabolism and function

PubMed Central

Feng, Suihan; Harayama, Takeshi; Montessuit, Sylvie; David, Fabrice PA; Winssinger, Nicolas; Martinou, Jean-Claude

2018-01-01

Photoactivation ('uncaging’) is a powerful approach for releasing bioactive small-molecules in living cells. Current uncaging methods are limited by the random distribution of caged molecules within cells. We have developed a mitochondria-specific photoactivation method, which permitted us to release free sphingosine inside mitochondria and thereafter monitor local sphingosine metabolism by lipidomics. Our results indicate that sphingosine was quickly phosphorylated into sphingosine 1-phosphate (S1P) driven by sphingosine kinases. In time-course studies, the mitochondria-specific uncaged sphingosine demonstrated distinct metabolic patterns compared to globally-released sphingosine, and did not induce calcium spikes. Our data provide direct evidence that sphingolipid metabolism and signaling are highly dependent on the subcellular location and opens up new possibilities to study the effects of lipid localization on signaling and metabolic fate. PMID:29376826

Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

PubMed Central

Bertazzoni, Umberto; Turci, Marco; Avesani, Francesca; Di Gennaro, Gianfranco; Bidoia, Carlo; Romanelli, Maria Grazia

2011-01-01

Human T-lymphotropic viruses type 1 (HTLV-1) and type 2 (HTLV-2) present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity. PMID:21994745

Local pharmacological effects of tungstate on the color-pattern determination of butterfly wings: a possible relationship between the eyespot and parafocal element.

PubMed

Dhungel, Bidur; Otaki, Joji M

2009-11-01

Butterfly wing color patterns can be changed by the application of a temperature shock or pharmacological agents such as tungstate, producing a distinctive type of elemental modification called the TS (temperature shock) type. Heterochronic uncoupling between the signaling and reception steps during the color-pattern determination process has been proposed as a mechanism for TS-type changes. As an extension of this hypothesis, both the parafocal element (PFE) and the eyespot in the same wing compartment are considered to be determined by morphogenic signal(s) emitted from the same eyespot focus. However, these models need to be examined with additional experimental data. Furthermore, there is controversy as to whether the action of tungstate on wing color patterns is direct or Indirect. Using a species of nymphalid butterfly (Junonia orithya), we have devised a simple method for the local application of pharmacological agents directly on developing wings of pupae. Local tungstate application resulted in reduced eyespots and circular dislocated PFEs in the eyespot-less compartments only on the treated wing, demonstrating that tungstate directly induces color-pattern changes on wings. We further examined the eyespot-PFE relationship in normal and cold-shocked Individuals, showing that an eyespot can be superimposed on a PFE and vice versa, probably depending on the timing of their fate determination. Taken together, we propose a two-morphogen model for the normal color-pattern determination, in which the morphogenic signals for the eyespot and PFE are different from each other despite their Identical origin. This two-morphogen model is compatible with the heterochronic uncoupling model for TS-type changes.

The segmentation of Thangka damaged regions based on the local distinction

NASA Astrophysics Data System (ADS)

Xuehui, Bi; Huaming, Liu; Xiuyou, Wang; Weilan, Wang; Yashuai, Yang

2017-01-01

Damaged regions must be segmented before digital repairing Thangka cultural relics. A new segmentation algorithm based on local distinction is proposed for segmenting damaged regions, taking into account some of the damaged area with a transition zone feature, as well as the difference between the damaged regions and their surrounding regions, combining local gray value, local complexity and local definition-complexity (LDC). Firstly, calculate the local complexity and normalized; secondly, calculate the local definition-complexity and normalized; thirdly, calculate the local distinction; finally, set the threshold to segment local distinction image, remove the over segmentation, and get the final segmentation result. The experimental results show that our algorithm is effective, and it can segment the damaged frescoes and natural image etc.

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

PubMed Central

2013-01-01

Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species. PMID:23311925

Identification of discrete functional subregions of the human periaqueductal gray

PubMed Central

Satpute, Ajay B.; Wager, Tor D.; Cohen-Adad, Julien; Bianciardi, Marta; Choi, Ji-Kyung; Buhle, Jason T.; Wald, Lawrence L.; Barrett, Lisa Feldman

2013-01-01

The midbrain periaqueductal gray (PAG) region is organized into distinct subregions that coordinate survival-related responses during threat and stress [Bandler R, Keay KA, Floyd N, Price J (2000) Brain Res 53 (1):95–104]. To examine PAG function in humans, researchers have relied primarily on functional MRI (fMRI), but technological and methodological limitations have prevented researchers from localizing responses to different PAG subregions. We used high-field strength (7-T) fMRI techniques to image the PAG at high resolution (0.75 mm isotropic), which was critical for dissociating the PAG from the greater signal variability in the aqueduct. Activation while participants were exposed to emotionally aversive images segregated into subregions of the PAG along both dorsal/ventral and rostral/caudal axes. In the rostral PAG, activity was localized to lateral and dorsomedial subregions. In caudal PAG, activity was localized to the ventrolateral region. This shifting pattern of activity from dorsal to ventral PAG along the rostrocaudal axis mirrors structural and functional neurobiological observations in nonhuman animals. Activity in lateral and ventrolateral subregions also grouped with distinct emotional experiences (e.g., anger and sadness) in a factor analysis, suggesting that each subregion participates in distinct functional circuitry. This study establishes the use of high-field strength fMRI as a promising technique for revealing the functional architecture of the PAG. The techniques developed here also may be extended to investigate the functional roles of other brainstem nuclei. PMID:24082116

Super Memory Bros.: going from mirror patterns to concordant patterns via similarity enhancements.

PubMed

Ozubko, Jason D; Joordens, Steve

2008-12-01

When memory is contrasted for stimuli belonging to distinct stimulus classes, one of two patterns is observed: a mirror pattern, in which one stimulus gives rise to higher hits but lower false alarms (e.g., the frequency-based mirror effect) or a concordant pattern, in which one stimulus class gives rise both to higher hits and to higher false alarms (e.g., the pseudoword effect). On the basis of the dual-process account proposed by Joordens and Hockley (2000), we predict that mirror patterns occur when one stimulus class is more familiar and less distinctive than another, whereas concordant patterns occur when one stimulus class is more familiar than another. We tested these assumptions within a video game paradigm using novel stimuli that allow manipulations in terms of distinctiveness and familiarity (via similarity). When more distinctive, less familiar items are contrasted with less distinctive, more familiar items, a mirror pattern is observed. Systematically enhancing the familiarity of stimuli transforms the mirror pattern to a concordant pattern as predicted. Although our stimuli differ considerably from those used in examinations of the frequency-based mirror effect and the pseudoword effect, the implications of our findings with respect to those phenomena are also discussed.

Distinct zooplankton regime shift patterns across ecoregions of the U.S. Northeast continental shelf Large Marine Ecosystem

NASA Astrophysics Data System (ADS)

Morse, R. E.; Friedland, K. D.; Tommasi, D.; Stock, C.; Nye, J.

2017-01-01

We investigated regime shifts in seasonal zooplankton communities of the Northeast continental shelf Large Marine Ecosystem (NES) and its subcomponent ecoregions over a multi-decadal period (1977-2013). Our cross ecoregion analysis shows that regime shifts in different ecoregions often exhibited very distinct characteristics, emphasizing more granular fluctuations in NES plankton communities relative to previous work. Shifts early in the time series generally reflected an increase in abundance levels. The response of zooplankton abundance within fall communities was more similar among ecoregions than for spring communities. The Gulf of Maine exhibited highly distinct patterns from other ecoregions, with regime shifts identified in the early 1980s, early 2000s, and mid-2000s for spring communities. Regime shifts were identified in the early to mid-1990s for the NES, Georges Bank, and the Mid-Atlantic Bight ecoregions, while the fall communities experienced shifts in the early 1990s and late 1980s for the NES and Georges Bank, but in the late 1990s in the Mid-Atlantic Bight. A constrained correspondence analysis of zooplankton community against local and basin-scale climatological indices suggests that water temperature, stratification, and the Atlantic multidecadal oscillation (AMO) were the predominant factors in driving the zooplankton community composition.

The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Drosophila Airways

PubMed Central

Matsuda, Ryo; Hosono, Chie; Saigo, Kaoru; Samakovlis, Christos

2015-01-01

The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions. These local variations are crucial for organ function and organismal fitness. Organotypic patterns and tube geometries in branched networks are typically controlled by variations of extrinsic signaling but the impact of intrinsic factors on branch patterns and shapes is not well explored. Here, we show that the intersection of extrinsic hedgehog(hh) and WNT/wingless (wg) signaling with the tube-intrinsic Hox code of distinct segments specifies the tube pattern and shape of the Drosophila airways. In the cephalic part of the airways, hh signaling induces expression of the transcription factor (TF) knirps (kni) in the anterior dorsal trunk (DTa1). kni represses the expression of another TF spalt major (salm), making DTa1 a narrow and long tube. In DTa branches of more posterior metameres, Bithorax Complex (BX-C) Hox genes autonomously divert hh signaling from inducing kni, thereby allowing DTa branches to develop as salm-dependent thick and short tubes. Moreover, the differential expression of BX-C genes is partly responsible for the anterior-to-posterior gradual increase of the DT tube diameter through regulating the expression level of Salm, a transcriptional target of WNT/wg signaling. Thus, our results highlight how tube intrinsic differential competence can diversify tube morphology without changing availabilities of extrinsic factors. PMID:25615601

Brain-based decoding of mentally imagined film clips and sounds reveals experience-based information patterns in film professionals.

PubMed

de Borst, Aline W; Valente, Giancarlo; Jääskeläinen, Iiro P; Tikka, Pia

2016-04-01

In the perceptual domain, it has been shown that the human brain is strongly shaped through experience, leading to expertise in highly-skilled professionals. What has remained unclear is whether specialization also shapes brain networks underlying mental imagery. In our fMRI study, we aimed to uncover modality-specific mental imagery specialization of film experts. Using multi-voxel pattern analysis we decoded from brain activity of professional cinematographers and sound designers whether they were imagining sounds or images of particular film clips. In each expert group distinct multi-voxel patterns, specific for the modality of their expertise, were found during classification of imagery modality. These patterns were mainly localized in the occipito-temporal and parietal cortex for cinematographers and in the auditory cortex for sound designers. We also found generalized patterns across perception and imagery that were distinct for the two expert groups: they involved frontal cortex for the cinematographers and temporal cortex for the sound designers. Notably, the mental representations of film clips and sounds of cinematographers contained information that went beyond modality-specificity. We were able to successfully decode the implicit presence of film genre from brain activity during mental imagery in cinematographers. The results extend existing neuroimaging literature on expertise into the domain of mental imagery and show that experience in visual versus auditory imagery can alter the representation of information in modality-specific association cortices. Copyright © 2016 Elsevier Inc. All rights reserved.

Short-Term EEG Spectral Pattern as a Single Event in EEG Phenomenology

PubMed Central

Fingelkurts, Al. A; Fingelkurts, An. A

2010-01-01

Spectral decomposition, to this day, still remains the main analytical paradigm for the analysis of EEG oscillations. However, conventional spectral analysis assesses the mean characteristics of the EEG power spectra averaged out over extended periods of time and/or broad frequency bands, thus resulting in a “static” picture which cannot reflect adequately the underlying neurodynamic. A relatively new promising area in the study of EEG is based on reducing the signal to elementary short-term spectra of various types in accordance with the number of types of EEG stationary segments instead of using averaged power spectrum for the whole EEG. It is suggested that the various perceptual and cognitive operations associated with a mental or behavioural condition constitute a single distinguishable neurophysiological state with a distinct and reliable spectral pattern. In this case, one type of short-term spectral pattern may be considered as a single event in EEG phenomenology. To support this assumption the following issues are considered in detail: (a) the relations between local EEG short-term spectral pattern of particular type and the actual state of the neurons in underlying network and a volume conduction; (b) relationship between morphology of EEG short-term spectral pattern and the state of the underlying neurodynamical system i.e. neuronal assembly; (c) relation of different spectral pattern components to a distinct physiological mechanism; (d) relation of different spectral pattern components to different functional significance; (e) developmental changes of spectral pattern components; (f) heredity of the variance in the individual spectral pattern and its components; (g) intra-individual stability of the sets of EEG short-term spectral patterns and their percent ratio; (h) discrete dynamics of EEG short-term spectral patterns. Functional relevance (consistency) of EEG short-term spectral patterns in accordance with the changes of brain functional state, cognitive task and with different neuropsychopathologies is demonstrated. PMID:21379390

Distinct neural patterns enable grasp types decoding in monkey dorsal premotor cortex

NASA Astrophysics Data System (ADS)

Hao, Yaoyao; Zhang, Qiaosheng; Controzzi, Marco; Cipriani, Christian; Li, Yue; Li, Juncheng; Zhang, Shaomin; Wang, Yiwen; Chen, Weidong; Chiara Carrozza, Maria; Zheng, Xiaoxiang

2014-12-01

Objective. Recent studies have shown that dorsal premotor cortex (PMd), a cortical area in the dorsomedial grasp pathway, is involved in grasp movements. However, the neural ensemble firing property of PMd during grasp movements and the extent to which it can be used for grasp decoding are still unclear. Approach. To address these issues, we used multielectrode arrays to record both spike and local field potential (LFP) signals in PMd in macaque monkeys performing reaching and grasping of one of four differently shaped objects. Main results. Single and population neuronal activity showed distinct patterns during execution of different grip types. Cluster analysis of neural ensemble signals indicated that the grasp related patterns emerged soon (200-300 ms) after the go cue signal, and faded away during the hold period. The timing and duration of the patterns varied depending on the behaviors of individual monkey. Application of support vector machine model to stable activity patterns revealed classification accuracies of 94% and 89% for each of the two monkeys, indicating a robust, decodable grasp pattern encoded in the PMd. Grasp decoding using LFPs, especially the high-frequency bands, also produced high decoding accuracies. Significance. This study is the first to specify the neuronal population encoding of grasp during the time course of grasp. We demonstrate high grasp decoding performance in PMd. These findings, combined with previous evidence for reach related modulation studies, suggest that PMd may play an important role in generation and maintenance of grasp action and may be a suitable locus for brain-machine interface applications.

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.

PubMed

Hellweger, Ferdi L; van Sebille, Erik; Fredrick, Neil D

2014-09-12

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.

Strong inter-population cooperation leads to partner intermixing in microbial communities

DOE PAGES

Momeni, Babak; Brileya, Kristen A.; Fields, Matthew W.; ...

2013-01-22

Patterns of spatial positioning of individuals within microbial communities are often critical to community function. However, understanding patterning in natural communities is hampered by the multitude of cell–cell and cell–environment interactions as well as environmental variability. Here, through simulations and experiments on communities in defined environments, we examined how ecological interactions between two distinct partners impacted community patterning. We found that in strong cooperation with spatially localized large fitness benefits to both partners, a unique pattern is generated: partners spatially intermixed by appearing successively on top of each other, insensitive to initial conditions and interaction dynamics. Intermixing was experimentally observedmore » in two obligatory cooperative systems: an engineered yeast community cooperating through metabolite-exchanges and a methane-producing community cooperating through redox-coupling. Even in simulated communities consisting of several species, most of the strongly-cooperating pairs appeared intermixed. Thus, when ecological interactions are the major patterning force, strong cooperation leads to partner intermixing.« less

Spontaneous formation of spiral-like patterns with distinct periodic physical properties by confined electrodeposition of Co-In disks

NASA Astrophysics Data System (ADS)

Golvano-Escobal, Irati; Gonzalez-Rosillo, Juan Carlos; Domingo, Neus; Illa, Xavi; López-Barberá, José Francisco; Fornell, Jordina; Solsona, Pau; Aballe, Lucia; Foerster, Michael; Suriñach, Santiago; Baró, Maria Dolors; Puig, Teresa; Pané, Salvador; Nogués, Josep; Pellicer, Eva; Sort, Jordi

2016-07-01

Spatio-temporal patterns are ubiquitous in different areas of materials science and biological systems. However, typically the motifs in these types of systems present a random distribution with many possible different structures. Herein, we demonstrate that controlled spatio-temporal patterns, with reproducible spiral-like shapes, can be obtained by electrodeposition of Co-In alloys inside a confined circular geometry (i.e., in disks that are commensurate with the typical size of the spatio-temporal features). These patterns are mainly of compositional nature, i.e., with virtually no topographic features. Interestingly, the local changes in composition lead to a periodic modulation of the physical (electric, magnetic and mechanical) properties. Namely, the Co-rich areas show higher saturation magnetization and electrical conductivity and are mechanically harder than the In-rich ones. Thus, this work reveals that confined electrodeposition of this binary system constitutes an effective procedure to attain template-free magnetic, electric and mechanical surface patterning with specific and reproducible shapes.

Recurrent Activation of Neural Circuits during Attention to Global and Local Visual Information.

PubMed

Iglesias-Fuster, Jorge; Piña-Novo, Daniela; Ontivero-Ortega, Marlis; Lage-Castellanos, Agustín; Valdés-Sosa, Mitchell

2018-05-28

The attentional selection of different hierarchical level within compound (Navon) figures has been studied with event related potentials (ERPs), by controlling the ERPs obtained during attention to the global or the local echelon. These studies, using the canonical Navon figures, have produced contradictory results, with doubts regarding the scalp distribution of the effects. Moreover, the evidence about the temporal evolution of the processing of these two levels is not clear. Here, we unveiled global and local letters at distinct times, which enabled separation of their ERP responses. We combine this approach with the temporal generalization methodology, a novel multivariate technique which facilitates exploring the temporal structure of these ERPs. Opposite lateralization patterns were obtained for the selection negativities generated when attending global and local distracters (D statistics, p < .005), with maxima in right and left occipito-temporal scalp regions, respectively (η2 = .111, p < .01; η2 = .042, p < .04). However, both discrimination negativities elicited when comparing targets and distractors at the global or the local level were lateralized to the left hemisphere (η2 = .25, p < .03 and η2 = .142, p < .05 respectively). Recurrent activation patterns were found for both global and local stimuli, with scalp topographies corresponding to early preparatory stages reemerging during the attentional selection process, thus indicating recursive attentional activation. This implies that selective attention to global and local hierarchical levels recycles similar neural correlates at different time points. These neural correlates appear to be mediated by visual extra-striate areas.

Excellent Local Control Rates and Distinctive Patterns of Failure in Myxoid Liposarcoma Treated With Conservation Surgery and Radiotherapy

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

Guadagnolo, B. Ashleigh; Zagars, Gunar K.; Ballo, Matthew T.

2008-03-01

Purpose: To evaluate the local control rates and patterns of metastatic relapse in patients with localized myxoid liposarcoma treated with conservation surgery and radiotherapy (RT). Patients and Methods: Between 1960 and 2003, 127 patients with non-metastatic myxoid liposarcoma were treated with conservation surgery and RT at our institution. The median patient age was 39 years (range, 14-79 years). Of the 127 patients, 46% underwent preoperative RT (median dose, 50 Gy) and 54% underwent postoperative RT (median dose, 60 Gy). Also, 28% received doxorubicin-based chemotherapy as a part of their treatment. Results: The median follow-up was 9.1 years. The overall survivalmore » rate at 5 and 10 years was 87% and 79%, respectively. The corresponding disease-free survival rates were 81% and 73%. The local control rate at {>=}5 years was 97%. The actuarial rate of distant metastases at 5 and 10 years was 15% and 24%, respectively. Of the 27 patients who developed distant metastases, 48% did so in the retroperitoneum, 22% in other extrapulmonary soft tissues, 22% in the lung, 15% in bone, and 4% in the liver. Conclusion: The results of our study have shown that RT and conservation surgery for localized myxoid liposarcoma provide excellent local control. Distant metastatic relapse tended to occur in the retroperitoneum and other nonpulmonary soft tissues. Therefore, staging and surveillance imaging should include the abdomen and pelvis, as well as the thorax, for patients with localized myxoid liposarcoma.« less

Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei.

PubMed

Bass, Hank W; Hoffman, Gregg G; Lee, Tae-Jin; Wear, Emily E; Joseph, Stacey R; Allen, George C; Hanley-Bowdoin, Linda; Thompson, William F

2015-11-01

Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.

Membrane localization of insulin receptor substrate-2 (IRS-2) is associated with decreased overall survival in breast cancer

PubMed Central

Clark, Jennifer L.; Dresser, Karen; Hsieh, Chung-Cheng; Sabel, Michael; Kleer, Celina G.; Khan, Ashraf

2011-01-01

Recent studies have identified a role for insulin receptor substrate-2 (IRS-2) in promoting motility and metastasis in breast cancer. However, no published studies to date have examined IRS-2 expression in human breast tumors. We examined IRS-2 expression by immunohistochemistry (IHC) in normal breast tissue, benign breast lesions, and malignant breast tumors from the institutional pathology archives and a tumor microarray from a separate institution. Three distinct IRS-2 staining patterns were noted: diffusely cytoplasmic, punctate cytoplasmic, and localized to the cell membrane. The individual and pooled datasets were analyzed for associations of IRS-2 staining pattern with core clinical parameters and clinical outcomes. Univariate analysis revealed a trend toward decreased overall survival (OS) with IRS-2 membrane staining, and this association became significant upon multivariate analysis (P = 0.01). In progesterone receptor negative (PR−) tumors, in particular, IRS-2 staining at the membrane correlated with significantly worse OS than other IRS-2 staining patterns (P < 0.001). When PR status and IRS-2 staining pattern were evaluated in combination, PR− tumors with IRS-2 at the membrane were associated with a significantly decreased OS when compared with all other combinations (P = 0.002). Evaluation of IRS-2 staining patterns could potentially be used to identify patients with PR− tumors who would most benefit from aggressive treatment. PMID:21258861

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

DOE PAGES

Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

2015-09-04

Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing ofmore » ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha –1 yr –1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. As a result, given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.« less

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

USGS Publications Warehouse

Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

2015-01-01

Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha−1 yr−1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

Mathematical modeling and experimental validation of the spatial distribution of boron in the root of Arabidopsis thaliana identify high boron accumulation in the tip and predict a distinct root tip uptake function.

PubMed

Shimotohno, Akie; Sotta, Naoyuki; Sato, Takafumi; De Ruvo, Micol; Marée, Athanasius F M; Grieneisen, Verônica A; Fujiwara, Toru

2015-04-01

Boron, an essential micronutrient, is transported in roots of Arabidopsis thaliana mainly by two different types of transporters, BORs and NIPs (nodulin26-like intrinsic proteins). Both are plasma membrane localized, but have distinct transport properties and patterns of cell type-specific accumulation with different polar localizations, which are likely to affect boron distribution. Here, we used mathematical modeling and an experimental determination to address boron distributions in the root. A computational model of the root is created at the cellular level, describing the boron transporters as observed experimentally. Boron is allowed to diffuse into roots, in cells and cell walls, and to be transported over plasma membranes, reflecting the properties of the different transporters. The model predicts that a region around the quiescent center has a higher concentration of soluble boron than other portions. To evaluate this prediction experimentally, we determined the boron distribution in roots using laser ablation-inductivity coupled plasma-mass spectrometry. The analysis indicated that the boron concentration is highest near the tip and is lower in the more proximal region of the meristem zone, similar to the pattern of soluble boron distribution predicted by the model. Our model also predicts that upward boron flux does not continuously increase from the root tip toward the mature region, indicating that boron taken up in the root tip is not efficiently transported to shoots. This suggests that root tip-absorbed boron is probably used for local root growth, and that instead it is the more mature root regions which have a greater role in transporting boron toward the shoots. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Mathematical Modeling and Experimental Validation of the Spatial Distribution of Boron in the Root of Arabidopsis thaliana Identify High Boron Accumulation in the Tip and Predict a Distinct Root Tip Uptake Function

PubMed Central

Shimotohno, Akie; Sotta, Naoyuki; Sato, Takafumi; De Ruvo, Micol; Marée, Athanasius F.M.; Grieneisen, Verônica A.; Fujiwara, Toru

2015-01-01

Boron, an essential micronutrient, is transported in roots of Arabidopsis thaliana mainly by two different types of transporters, BORs and NIPs (nodulin26-like intrinsic proteins). Both are plasma membrane localized, but have distinct transport properties and patterns of cell type-specific accumulation with different polar localizations, which are likely to affect boron distribution. Here, we used mathematical modeling and an experimental determination to address boron distributions in the root. A computational model of the root is created at the cellular level, describing the boron transporters as observed experimentally. Boron is allowed to diffuse into roots, in cells and cell walls, and to be transported over plasma membranes, reflecting the properties of the different transporters. The model predicts that a region around the quiescent center has a higher concentration of soluble boron than other portions. To evaluate this prediction experimentally, we determined the boron distribution in roots using laser ablation-inductivity coupled plasma-mass spectrometry. The analysis indicated that the boron concentration is highest near the tip and is lower in the more proximal region of the meristem zone, similar to the pattern of soluble boron distribution predicted by the model. Our model also predicts that upward boron flux does not continuously increase from the root tip toward the mature region, indicating that boron taken up in the root tip is not efficiently transported to shoots. This suggests that root tip-absorbed boron is probably used for local root growth, and that instead it is the more mature root regions which have a greater role in transporting boron toward the shoots. PMID:25670713

An imidazole functionalized pentameric thiophene displays different staining patterns in normal and malignant cells

NASA Astrophysics Data System (ADS)

Nilsson, Peter; Magnusson, Karin; Appelqvist, Hanna; Cieslar-Pobuda, Artur; Bäck, Marcus; Kågedal, Bertil; Jonasson, Jon; Los, Marek

2015-10-01

Molecular tools for fluorescent imaging of cells and their components are vital for understanding the function and activity of cells. Here, we report an imidazole functionalized pentameric oligothiophene, p-HTIm, that can be utilized for fluorescent imaging of cells. p-HTIm fluorescence in normal cells appeared in a peripheral punctate pattern partially co-localized with lysosomes, whereas a one-sided perinuclear Golgi associated localization of the dye was observed in malignant cells. The uptake of p-HTIm was temperature dependent and the intracellular target was reached within 1 h after staining. The ability of p-HTIm to stain cells was reduced when the imidazole side chain was chemically altered, verifying that specific imidazole side-chain functionalities are necessary for achieving the observed cellular staining. Our findings confirm that properly functionalized oligothiophenes can be utilized as fluorescent tools for vital staining of cells and that the selectivity towards distinct intracellular targets are highly dependent on the side-chain functionalities along the conjugated thiophene backbone.

Silent Sentence Completion Shows Superiority Localizing Wernicke's Area and Activation Patterns of Distinct Language Paradigms Correlate with Genomics: Prospective Study.

PubMed

Salek, Kamel El; Hassan, Islam S; Kotrotsou, Aikaterini; Abrol, Srishti; Faro, Scott H; Mohamed, Feroze B; Zinn, Pascal O; Wei, Wei; Li, Nan; Kumar, Ashok J; Weinberg, Jeffrey S; Wefel, Jeffrey S; Kesler, Shelli R; Liu, Ho-Ling Anthony; Hou, Ping; Stafford, R Jason; Prabhu, Sujit; Sawaya, Raymond; Colen, Rivka R

2017-09-21

Preoperative mapping of language areas using fMRI greatly depends on the paradigms used, as different tasks harness distinct capabilities to activate speech processing areas. In this study, we compared the ability of 3 covert speech paradigms: Silent Sentence Completion (SSC), category naming (CAT) and verbal fluency (FAS), in localizing the Wernicke's area and studied the association between genomic markers and functional activation. Fifteen right-handed healthy volunteers and 35 mixed-handed patients were included. We focused on the anatomical areas of posterosuperior, middle temporal and angular gyri corresponding to Wernicke's area. Activity was deemed significant in a region of interest if P < 0.05. Association between fMRI activation and genomic mutation status was obtained. Results demonstrated SSC's superiority at localizing Wernicke's area. SSC demonstrated functional activity in 100% of cancer patients and healthy volunteers; which was significantly higher than those for FAS and CAT. Patients with 1p/19q non-co-deleted had higher extent of activation on SSC (P < 0.02). Those with IDH-1 wild-type were more likely to show no activity on CAT (P < 0.05). SSC is a robust paradigm for localizing Wernicke's area, making it an important clinical tool for function-preserving surgeries. We also found a correlation between tumor genomics and functional activation, which deserves more comprehensive study.

Spatial patterning in PM2.5 constituents under an inversion-focused sampling design across an urban area of complex terrain

PubMed Central

Tunno, Brett J; Dalton, Rebecca; Michanowicz, Drew R; Shmool, Jessie L C; Kinnee, Ellen; Tripathy, Sheila; Cambal, Leah; Clougherty, Jane E

2016-01-01

Health effects of fine particulate matter (PM2.5) vary by chemical composition, and composition can help to identify key PM2.5 sources across urban areas. Further, this intra-urban spatial variation in concentrations and composition may vary with meteorological conditions (e.g., mixing height). Accordingly, we hypothesized that spatial sampling during atmospheric inversions would help to better identify localized source effects, and reveal more distinct spatial patterns in key constituents. We designed a 2-year monitoring campaign to capture fine-scale intra-urban variability in PM2.5 composition across Pittsburgh, PA, and compared both spatial patterns and source effects during “frequent inversion” hours vs 24-h weeklong averages. Using spatially distributed programmable monitors, and a geographic information systems (GIS)-based design, we collected PM2.5 samples across 37 sampling locations per year to capture variation in local pollution sources (e.g., proximity to industry, traffic density) and terrain (e.g., elevation). We used inductively coupled plasma mass spectrometry (ICP-MS) to determine elemental composition, and unconstrained factor analysis to identify source suites by sampling scheme and season. We examined spatial patterning in source factors using land use regression (LUR), wherein GIS-based source indicators served to corroborate factor interpretations. Under both summer sampling regimes, and for winter inversion-focused sampling, we identified six source factors, characterized by tracers associated with brake and tire wear, steel-making, soil and road dust, coal, diesel exhaust, and vehicular emissions. For winter 24-h samples, four factors suggested traffic/fuel oil, traffic emissions, coal/industry, and steel-making sources. In LURs, as hypothesized, GIS-based source terms better explained spatial variability in inversion-focused samples, including a greater contribution from roadway, steel, and coal-related sources. Factor analysis produced source-related constituent suites under both sampling designs, though factors were more distinct under inversion-focused sampling. PMID:26507005

Functioning of Fluorescent Proteins in Aggregates in Anthozoa Species and in Recombinant Artificial Models

PubMed Central

Povarova, Natalia V.; Petri, Natalia D.; Blokhina, Anna E.; Bogdanov, Alexey M.; Lukyanov, Konstantin A.

2017-01-01

Despite great advances in practical applications of fluorescent proteins (FPs), their natural function is poorly understood. FPs display complex spatio-temporal expression patterns in living Anthozoa coral polyps. Here we applied confocal microscopy, specifically, the fluorescence recovery after photobleaching (FRAP) technique to analyze intracellular localization and mobility of endogenous FPs in live tissues. We observed three distinct types of protein distributions in living tissues. One type of distribution, characteristic for Anemonia, Discosoma and Zoanthus, is free, highly mobile cytoplasmic localization. Another pattern is seen in FPs localized to numerous intracellular vesicles, observed in Clavularia. The third most intriguing type of intracellular localization is with respect to the spindle-shaped aggregates and lozenge crystals several micrometers in size observed in Zoanthus samples. No protein mobility within those structures was detected by FRAP. This finding encouraged us to develop artificial aggregating FPs. We constructed “trio-FPs” consisting of three tandem copies of tetrameric FPs and demonstrated that they form multiple bright foci upon expression in mammalian cells. High brightness of the aggregates is advantageous for early detection of weak promoter activities. Simultaneously, larger aggregates can induce significant cytostatic and cytotoxic effects and thus such tags are not suitable for long-term and high-level expression. PMID:28704934

Ultastructural analysis on acetylcholinesterase localization in the cerebellar cortex of teleosts.

PubMed

Contestabile, A; Villani, L; Ciani, F

1977-12-28

The histochemical localization of acetylcholinesterase (AChE) was studied by electron microscopy in the cerebellar cortex of the goldfish and the catfish. The patterns of enzyme distribution show noticeable differences in the two teleost species at the level of the corresponding cerebellar structures. Among the most distinctive features is the prevailing intracellular localization of enzyme activity in the goldfish and the prevailing extracellular localization in the catfish in the molecular layer and, to a lesser extent, the granular layer. Only quantitative differences in the ability to synthesize AChE can be recorded among the different cerebellar neurons in the two species, since all these neurons exhibit different amounts of enzyme activity linked to their cytoplasmic structures. Comparing the results obtained with those of previous histochemical, experimental and developmental researches, the hypothesis seems well founded that the embryonic pool of cerebellar neurons is made up of AChE-synthesizing nruroblasts which, during development, loss or maintain to a different the mechanisms for AChE synthesis. In addition the light and electron microscope histochemistry reveals at different levels of resolution that the final pattern of AChE distribution in the cerebellar cortex is the sum of different degress of AChE synthesis by cerebellar neurons and different degrees of enzyme release in extracellular spaces.

A Role for Caenorhabditis elegans Importin IMA-2 in Germ Line and Embryonic Mitosis

PubMed Central

Geles, Kenneth G.; Johnson, Jeffrey J.; Jong, Sena; Adam, Stephen A.

2002-01-01

The importin α family of nuclear-cytoplasmic transport factors mediates the nuclear localization of proteins containing classical nuclear localization signals. Metazoan animals express multiple importin α proteins, suggesting their possible roles in cell differentiation and development. Adult Caenorhabditis elegans hermaphrodites express three importin α proteins, IMA-1, IMA-2, and IMA-3, each with a distinct expression and localization pattern. IMA-2 was expressed exclusively in germ line cells from the early embryonic through adult stages. The protein has a dynamic pattern of localization dependent on the stage of the cell cycle. In interphase germ cells and embryonic cells, IMA-2 is cytoplasmic and nuclear envelope associated, whereas in developing oocytes, the protein is cytoplasmic and intranuclear. During mitosis in germ line cells and embryos, IMA-2 surrounded the condensed chromosomes but was not directly associated with the mitotic spindle. The timing of IMA-2 nuclear localization suggested that the protein surrounded the chromosomes after fenestration of the nuclear envelope in prometaphase. Depletion of IMA-2 by RNA-mediated gene interference (RNAi) resulted in embryonic lethality and a terminal aneuploid phenotype. ima-2(RNAi) embryos have severe defects in nuclear envelope formation, accumulating nucleoporins and lamin in the cytoplasm. We conclude that IMA-2 is required for proper chromosome dynamics in germ line and early embryonic mitosis and is involved in nuclear envelope assembly at the conclusion of mitosis. PMID:12221121

Distribution of calmodulin in pea seedlings: immunocytochemical localization in plumules and root apices

NASA Technical Reports Server (NTRS)

Dauwalder, M.; Roux, S. J.; Hardison, L.

1986-01-01

Immunofluorescence techniques have been used to study the distribution of calmodulin in several tissues in young etiolated pea (Pisum sativum L.) seedlings. A fairly uniform staining was seen in the nucleoplasm and background cytoplasm of most cell types. Cell walls and nucleoli were not stained. In addition, patterned staining reactions were seen in many cells. In cells of the plumule, punctate staining of the cytoplasm was common, and in part this stain appeared to be associated with the plastids. A very distinctive staining of amyloplasts was seen in the columella of the root cap. Staining associated with cytoskeletal elements could be shown in division stages. By metaphase, staining of the spindle region was quite evident. In epidermal cells of the stem and along the underside of the leaf there was an intense staining of the vacuolar contents. Guard cells lacked this vacuolar stain. Vacuolar staining was sometimes seen in cells of the stele, but the most distinctive pattern in the stele was associated with young conducting cells of the xylem. These staining patterns are consistent with the idea that the interactions of plastids and the cytoskeletal may be one of the Ca(2+)-mediated steps in the response of plants to environmental stimuli. Nuclear functions may also be controlled, at least in part, by Ca2+.

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

PubMed

Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, Nallasivam; Mehra, Rohit; Kominsky, Hal D; Siddiqui, Javed; Yu, Jindan; Qin, Zhaohui S; Chinnaiyan, Arul M

2011-07-01

Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 × 10(-16)). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.

Targeted DNA Sequencing Reveals Patterns of Local Progression in the Pancreatic Remnant Following Resection of Intraductal Papillary Mucinous Neoplasm (IPMN) of the Pancreas

PubMed Central

Pea, Antonio; Yu, Jun; Rezaee, Neda; Luchini, Claudio; He, Jin; Molin, Marco Dal; Griffin, James F.; Fedor, Helen; Fesharakizadeh, Shahriar; Salvia, Roberto; Weiss, Matthew J.; Bassi, Claudio; Cameron, John L.; Zheng, Lei; Scarpa, Aldo; Hruban, Ralph H.; Lennon, Anne Marie; Goggins, Michael

2016-01-01

Objective The aim of this study was to characterize patterns of local progression following resection for pancreatic intraductal papillary mucinous neoplasms (IPMN) using targeted next-generation sequencing (NGS). Background Progression of neoplastic disease in the remnant pancreas following resection of IPMN may include development of a new IPMN or ductal adenocarcinoma (PDAC). However, it is not clear whether this progression represents recurrence of the same neoplasm or an independent second neoplasm. Methods Targeted-NGS on genes commonly mutated in IPMN and PDAC was performed on tumors from (1) 13 patients who developed disease progression in the remnant pancreas following resection of IPMN; and (2) 10 patients who underwent a resection for PDAC and had a concomitant IPMN. Mutations in the tumors were compared in order to determine the relationship between neoplasms. In parallel, clinical and pathological characteristics of 260 patients who underwent resection of noninvasive IPMN were reviewed to identify risk factors associated with local progression. Results We identified 3 mechanisms underlying local progression in the remnant pancreas: (1) residual microscopic disease at the resection margin, (2) intraparenchymal spread of neoplastic cells, leading to an anatomically separate but genetically related recurrence, and (3) multifocal disease with genetically distinct lesions. Analysis of the 260 patients with noninvasive IPMNs showed that family history of pancreatic cancer (P = 0.027) and high-grade dysplasia (HGD) (P = 0.003) were independent risk factors for the development of an IPMN with HGD or an invasive carcinoma in the remnant pancreas. Conclusions Using NGS, we identify distinct mechanisms for development of metachronous or synchronous neoplasms in patients with IPMN. Patients with a primary IPMN with HGD or with positive family history are at an increased risk to develop subsequent high-risk neoplasms in the remnant pancreas. PMID:27433916

Identification and characterization of novel NuMA isoforms

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

Wu, Jin, E-mail: petersdu2112@hotmail.com; Xu, Zhe; Core Laboratory for Clinical Medical Research, Beijing Tiantan Hospital, Capital Medical University, Beijing

2014-11-21

Highlights: • Seven NuMA isoforms generated by alternative splicing were categorized into 3 groups: long, middle and short. • Both exons 15 and 16 in long NuMA were “hotspot” for alternative splicing. • Lower expression of short NuMA was observed in cancer cells compared with nonneoplastic controls. • Distinct localization pattern of short isoforms indicated different function from that of long and middle NuMA. - Abstract: The large nuclear mitotic apparatus (NuMA) has been investigated for over 30 years with functions related to the formation and maintenance of mitotic spindle poles during mitosis. However, the existence and functions of NuMAmore » isoforms generated by alternative splicing remains unclear. In the present work, we show that at least seven NuMA isoforms (categorized into long, middle and short groups) generated by alternative splicing from a common NuMA mRNA precursor were discovered in HeLa cells and these isoforms differ mainly at the carboxyl terminus and the coiled-coil domains. Two “hotspot” exons with molecular mass of 3366-nt and 42-nt tend to be spliced during alternative splicing in long and middle groups. Furthermore, full-length coding sequences of long and middle NuMA obtained by using fusion PCR were constructed into GFP-tagged vector to illustrate their cellular localization. Long NuMA mainly localized in the nucleus with absence from nucleoli during interphase and translocated to the spindle poles in mitosis. Middle NuMA displayed the similar cell cycle-dependent distribution pattern as long NuMA. However, expression of NuMA short isoforms revealed a distinct subcellular localization. Short NuMA were present in the cytosol during the whole cycle, without colocalization with mitotic apparatus. These results have allowed us tentatively to explore a new research direction for NuMA’s various functions.« less

Self-Induced Switchings between Multiple Space-Time Patterns on Complex Networks of Excitable Units

NASA Astrophysics Data System (ADS)

Ansmann, Gerrit; Lehnertz, Klaus; Feudel, Ulrike

2016-01-01

We report on self-induced switchings between multiple distinct space-time patterns in the dynamics of a spatially extended excitable system. These switchings between low-amplitude oscillations, nonlinear waves, and extreme events strongly resemble a random process, although the system is deterministic. We show that a chaotic saddle—which contains all the patterns as well as channel-like structures that mediate the transitions between them—is the backbone of such a pattern-switching dynamics. Our analyses indicate that essential ingredients for the observed phenomena are that the system behaves like an inhomogeneous oscillatory medium that is capable of self-generating spatially localized excitations and that is dominated by short-range connections but also features long-range connections. With our findings, we present an alternative to the well-known ways to obtain self-induced pattern switching, namely, noise-induced attractor hopping, heteroclinic orbits, and adaptation to an external signal. This alternative way can be expected to improve our understanding of pattern switchings in spatially extended natural dynamical systems like the brain and the heart.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

PubMed Central

Scheikl, Daniela; Tellier, Aurélien

2017-01-01

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved. PMID:28133579

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations.

PubMed

Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

2017-01-01

Wild tomatoes are a valuable source of disease resistance germplasm for tomato ( Solanum lycopersicum ) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense , both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense . We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens ( Alternaria solani , Phytophthora infestans and a Fusarium sp .) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense , resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

Granger Causality Relationships between Local Field Potentials in an Animal Model of Temporal Lobe Epilepsy

PubMed Central

Cadotte, Alex J.; DeMarse, Thomas B.; Mareci, Thomas H.; Parekh, Mansi; Talathi, Sachin S.; Hwang, Dong-Uk; Ditto, William L.; Ding, Mingzhou; Carney, Paul R.

2010-01-01

An understanding of the in vivo spatial emergence of abnormal brain activity during spontaneous seizure onset is critical to future early seizure detection and closed-loop seizure prevention therapies. In this study, we use Granger causality (GC) to determine the strength and direction of relationships between local field potentials (LFPs) recorded from bilateral microelectrode arrays in an intermittent spontaneous seizure model of chronic temporal lobe epilepsy before, during, and after Racine grade partial onset generalized seizures. Our results indicate distinct patterns of directional GC relationships within the hippocampus, specifically from the CA1 subfield to the dentate gryus, prior to and during seizure onset. Our results suggest sequential and hierarchical temporal relationships between the CA1 and dentate gyrus within and across hippocampal hemispheres during seizure. Additionally, our analysis suggests a reversal in the direction of GC relationships during seizure, from an abnormal pattern to more anatomically expected pattern. This reversal correlates well with the observed behavioral transition from tonic to clonic seizure in time-locked video. These findings highlight the utility of GC to reveal dynamic directional temporal relationships between multichannel LFP recordings from multiple brain regions during unprovoked spontaneous seizures. PMID:20304005

Granger causality relationships between local field potentials in an animal model of temporal lobe epilepsy.

PubMed

Cadotte, Alex J; DeMarse, Thomas B; Mareci, Thomas H; Parekh, Mansi B; Talathi, Sachin S; Hwang, Dong-Uk; Ditto, William L; Ding, Mingzhou; Carney, Paul R

2010-05-30

An understanding of the in vivo spatial emergence of abnormal brain activity during spontaneous seizure onset is critical to future early seizure detection and closed-loop seizure prevention therapies. In this study, we use Granger causality (GC) to determine the strength and direction of relationships between local field potentials (LFPs) recorded from bilateral microelectrode arrays in an intermittent spontaneous seizure model of chronic temporal lobe epilepsy before, during, and after Racine grade partial onset generalized seizures. Our results indicate distinct patterns of directional GC relationships within the hippocampus, specifically from the CA1 subfield to the dentate gyrus, prior to and during seizure onset. Our results suggest sequential and hierarchical temporal relationships between the CA1 and dentate gyrus within and across hippocampal hemispheres during seizure. Additionally, our analysis suggests a reversal in the direction of GC relationships during seizure, from an abnormal pattern to more anatomically expected pattern. This reversal correlates well with the observed behavioral transition from tonic to clonic seizure in time-locked video. These findings highlight the utility of GC to reveal dynamic directional temporal relationships between multichannel LFP recordings from multiple brain regions during unprovoked spontaneous seizures. (c) 2010 Elsevier B.V. All rights reserved.

Morphometry, Microstructure, and Wear Pattern of Neornithischian Dinosaur Teeth From the Upper Cretaceous Iharkút Locality (Hungary).

PubMed

Virág, Attila; Ősi, Attila

2017-08-01

Teeth of iguanodontian ornithopods and ceratopsians could be remarkably similar, thus the referral of isolated dental material to particular neornithischian clades can be highly problematic. These groups are represented by the rhabdodontid Mochlodon vorosi and the basal coronosaurian Ajkaceratops kozmai in the Upper Cretaceous Csehbánya Formation at Iharkút (western Hungary). Whereas teeth of Mochlodon are common elements at the locality, no dental material belonging to Ajkaceratops was identified until now. Here we used mathematical statistical approaches, as well as tooth wear and dental microstructure analysis in order to decide whether the teeth previously referred to Mochlodon can be treated as a homogenous sample, or some remains belong rather to Ajkaceratops. According to our results, there was a striking morphological and structural convergence between the teeth of both taxa. However, the wear study revealed the existence of two different patterns within the sample. One is characterized by straight and parallel microstriations that suggest orthal movements during the jaw closure. This pattern was associated with Mochlodon. The other pattern appeared only on a few teeth, and it can be differentiated by its distinctive curved microstriations that indicate circumpalinal chewing. Because curved striations have never been described in ornithopods, but are found in several neoceratopsians, this pattern was associated here with Ajkaceratops. Here we present the first teeth that can provisionally be referred to the latter genus. We believe that the methodology discussed in this article will facilitate distinguishing ceratopsian and ornithopod teeth in other localities as well. Anat Rec, 300:1439-1463, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Area-selective atomic layer deposition of Ru on electron-beam-written Pt(C) patterns versus SiO2 substratum

NASA Astrophysics Data System (ADS)

Junige, Marcel; Löffler, Markus; Geidel, Marion; Albert, Matthias; Bartha, Johann W.; Zschech, Ehrenfried; Rellinghaus, Bernd; van Dorp, Willem F.

2017-09-01

Area selectivity is an emerging sub-topic in the field of atomic layer deposition (ALD), which employs opposite nucleation phenomena to distinct heterogeneous starting materials on a surface. In this paper, we intend to grow Ru exclusively on locally pre-defined Pt patterns, while keeping a SiO2 substratum free from any deposition. In a first step, we study in detail the Ru ALD nucleation on SiO2 and clarify the impact of the set-point temperature. An initial incubation period with actually no growth was revealed before a formation of minor, isolated RuO x islands; clearly no continuous Ru layer formed on SiO2. A lower temperature was beneficial in facilitating a longer incubation and consequently a wider window for (inherent) selectivity. In a second step, we write C-rich Pt micro-patterns on SiO2 by focused electron-beam-induced deposition (FEBID), varying the number of FEBID scans at two electron beam acceleration voltages. Subsequently, the localized Pt(C) deposits are pre-cleaned in O2 and overgrown by Ru ALD. Already sub-nanometer-thin Pt(C) patterns, which were supposedly purified into some form of Pt(O x ), acted as very effective activation for the locally restricted, thus area-selective ALD growth of a pure, continuous Ru covering, whereas the SiO2 substratum sufficiently inhibited towards no growth. FEBID at lower electron energy reduced unwanted stray deposition and achieved well-resolved pattern features. We access the nucleation phenomena by utilizing a hybrid metrology approach, which uniquely combines in-situ real-time spectroscopic ellipsometry, in-vacuo x-ray photoelectron spectroscopy, ex-situ high-resolution scanning electron microscopy, and mapping energy-dispersive x-ray spectroscopy.

Local Material as a Character of Contemporary Interior Design in Indonesia

NASA Astrophysics Data System (ADS)

Susanto, Dalhar; Puti Angelia, Dini; Ningsih, Tria Amalia

2017-12-01

Excellent design needs to fulfill universal requirements (utility, aesthetic, ergonomic, durability, and safe). Besides of all the requirements, an excellent design has to be shown its distinctiveness, uniqueness, and identity. To create an excellent design, we can use one of locality approach, it means local material utilization. From time to time, the material is linking each other in unity with environment context, human, knowledge, culture, social, economy, user needs and material availability. The aspects are the important part to get the reflective identity and local values in architecture and interior design work in Indonesia. It can be proofed by some of the architecture and interior work precedent, like traditional or vernacular in Nusantara or contemporary interior design work from Indonesian designer who has recognized to promote the locality value. However interior design works in Indonesia cannot be shown the characteristic of Indonesia identity and locality currently, it is different than another country work, like Japan, Italy, or Scandinavia. Interior design work from these countries can be easily known with accentuating of characteristic their places, such as material, color, detail, or geometry pattern in the product that has been produced. Meanwhile, some of the region in Indonesia are tropical climate and brought about much of local material and it has potential to make a unique work which has the local identity. This paper will discuss the result of a searching potential of local material usefulness as interior design identity in Indonesia. This research is done by typology method, which means discover the presence of some of the architecture elements appears to be related material. The elements are the pattern, color, craftsmanship, building element, object, and type of material in some of the contemporary interior design work in Indonesia were considered superior and capable of lifting elements recognized locality.

Capturing the Two Dimensions of Residential Segregation at the Neighborhood Level for Health Research

PubMed Central

Oka, Masayoshi; Wong, David W. S.

2014-01-01

Two conceptual and methodological foundations of segregation studies are that (i) segregation involves more than one group, and (ii) segregation measures need to quantify how different population groups are distributed across space. Therefore, percentage of population belonging to a group is not an appropriate measure of segregation because it does not describe how populations are spread across different areal units or neighborhoods. In principle, evenness and isolation are the two distinct dimensions of segregation that capture the spatial patterns of population groups. To portray people’s daily environment more accurately, segregation measures need to account for the spatial relationships between areal units and to reflect the situations at the neighborhood scale. For these reasons, the use of local spatial entropy-based diversity index (SHi) and local spatial isolation index (Si) to capture the evenness and isolation dimensions of segregation, respectively, are preferable. However, these two local spatial segregation indexes have rarely been incorporated into health research. Rather ineffective and insufficient segregation measures have been used in previous studies. Hence, this paper empirically demonstrates how the two measures can reflect the two distinct dimensions of segregation at the neighborhood level, and argues conceptually and set the stage for their future use to effectively and meaningfully examine the relationships between residential segregation and health. PMID:25202687

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

DOE PAGES

Cui, Yi; Hu, Dehong; Markillie, Lye Meng; ...

2017-10-04

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

Sfr13, a member of a large family of asymmetrically localized Sfi1-repeat proteins, is important for basal body separation and stability in Tetrahymena thermophila

PubMed Central

Stemm-Wolf, Alexander J.; Meehl, Janet B.; Winey, Mark

2013-01-01

Summary Directed fluid flow, which is achieved by the coordinated beating of motile cilia, is required for processes as diverse as cellular swimming, developmental patterning and mucus clearance. Cilia are nucleated, anchored and aligned at the plasma membrane by basal bodies, which are cylindrical microtubule-based structures with ninefold radial symmetry. In the unicellular ciliate Tetrahymena thermophila, two centrin family members associated with the basal body are important for both basal body organization and stabilization. We have identified a family of 13 proteins in Tetrahymena that contain centrin-binding repeats related to those identified in the Saccharomyces cerevisiae Sfi1 protein. We have named these proteins Sfr1–Sfr13 (for Sfi1-repeat). Nine of the Sfr proteins localize in unique polarized patterns surrounding the basal body, suggesting non-identical roles in basal body organization and association with basal body accessory structures. Furthermore, the Sfr proteins are found in distinct basal body populations in Tetrahymena cells, indicating that they are responsive to particular developmental programs. A complete genetic deletion of one of the family members, Sfr13, causes unstable basal bodies and defects in daughter basal body separation from the mother, phenotypes also observed with centrin disruption. It is likely that the other Sfr family members are involved in distinct centrin functions, providing specificity to the tasks that centrins perform at basal bodies. PMID:23426847

Identification and Transcript Analysis of the TCP Transcription Factors in the Diploid Woodland Strawberry Fragaria vesca

PubMed Central

Wei, Wei; Hu, Yang; Cui, Meng-Yuan; Han, Yong-Tao; Gao, Kuan; Feng, Jia-Yue

2016-01-01

Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors play versatile functions in multiple processes of plant growth and development. However, no systematic study has been performed in strawberry. In this study, 19 FvTCP genes were identified in the diploid woodland strawberry (Fragaria vesca) accession Heilongjiang-3. Phylogenetic analysis suggested that the FvTCP genes were classified into two main classes, with the second class further divided into two subclasses, which was supported by the exon-intron organizations and the conserved motif structures. Promoter analysis revealed various cis-acting elements related to growth and development, hormone and/or stress responses. We analyzed FvTCP gene transcript accumulation patterns in different tissues and fruit developmental stages. Among them, 12 FvTCP genes exhibited distinct tissue-specific transcript accumulation patterns. Eleven FvTCP genes were down-regulated in different fruit developmental stages, while five FvTCP genes were up-regulated. Transcripts of FvTCP genes also varied with different subcultural propagation periods and were induced by hormone treatments and biotic and abiotic stresses. Subcellular localization analysis showed that six FvTCP-GFP fusion proteins showed distinct localizations in Arabidopsis mesophyll protoplasts. Notably, transient over-expression of FvTCP9 in strawberry fruits dramatically affected the expression of a series of genes implicated in fruit development and ripening. Taken together, the present study may provide the basis for functional studies to reveal the role of this gene family in strawberry growth and development. PMID:28066489

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

Local adaptation and oceanographic connectivity patterns explain genetic differentiation of a marine diatom across the North Sea–Baltic Sea salinity gradient

PubMed Central

Sjöqvist, C; Godhe, A; Jonsson, P R; Sundqvist, L; Kremp, A

2015-01-01

Drivers of population genetic structure are still poorly understood in marine micro-organisms. We exploited the North Sea–Baltic Sea transition for investigating the seascape genetics of a marine diatom, Skeletonema marinoi. Eight polymorphic microsatellite loci were analysed in 354 individuals from ten locations to analyse population structure of the species along a 1500-km-long salinity gradient ranging from 3 to 30 psu. To test for salinity adaptation, salinity reaction norms were determined for sets of strains originating from three different salinity regimes of the gradient. Modelled oceanographic connectivity was compared to directional relative migration by correlation analyses to examine oceanographic drivers. Population genetic analyses showed distinct genetic divergence of a low-salinity Baltic Sea population and a high-salinity North Sea population, coinciding with the most evident physical dispersal barrier in the area, the Danish Straits. Baltic Sea populations displayed reduced genetic diversity compared to North Sea populations. Growth optima of low salinity isolates were significantly lower than those of strains from higher native salinities, indicating local salinity adaptation. Although the North Sea–Baltic Sea transition was identified as a barrier to gene flow, migration between Baltic Sea and North Sea populations occurred. However, the presence of differentiated neutral markers on each side of the transition zone suggests that migrants are maladapted. It is concluded that local salinity adaptation, supported by oceanographic connectivity patterns creating an asymmetric migration pattern between the Baltic Sea and the North Sea, determines genetic differentiation patterns in the transition zone. PMID:25892181

Distinct Subglacial Drainage Patterns Revealed in High-Resolution Mapping of Basal Radar Reflectivity across Greenland

NASA Astrophysics Data System (ADS)

Chu, W.; Schroeder, D. M.; Seroussi, H. L.; Creyts, T. T.; Palmer, S. J.; Bell, R. E.

2016-12-01

Subglacial water beneath the Greenland Ice Sheet is linked to changes in sliding rate in both theoretical and field-based studies. These can lead to massive, widespread speed-ups or, conversely, very little response from the ice sheet. While distinct modes of subglacial drainage have been proposed to cause these different responses, the absence of Greenland-wide hydrological observations makes it difficult to examine how shifts in drainage occur and what controls them. By combining NASA IceBridge radar-sounding and ice-sheet modeling, we identified distinct subglacial drainage patterns across Greenland. Specifically, we examine Russell Glacier as a southern Greenland example and the Petermann-Humboldt glacier system as a northern example. In southern Greenland at Russell Glacier, the distribution of subglacial water varies seasonally depending on the surface melt supply and is strongly controlled by bed topography and properties. In the winter, water is stored on bedrock ridges but is absent in deep sediment-filled troughs. In the summer, water drains to the deep troughs that focus this water, flooding the bed to intensify sliding. Conversely, the subglacial drainage systems in northern Greenland are distinctly different. Beneath Petermann and Humboldt, subglacial water is present throughout the year and primarily fed by basal melt in the upstream reaches. In Petermann, this basal water is focused by the deep topography along the main ice trunk. These drainage networks are continuous up to 180 km from the glacier terminus, and likely facilitate the onset of fast flow. In contrast, in Humboldt the flat topography and the lack of water focusing produce more broadly distributed networks rather than locally focused systems. In Humboldt, onset of fast flow develops much closer to the ice edge where surface meltwater may contribute to the subglacial water budget. Our results provide insights into the relationship between surface melt, basal topography and properties over a wide range of controlling parameters. Local conditions often determine the degree to which subglacial systems focus and play an important role in determining individual catchment responses to surface melt.

Emergent pattern formation in an interstitial biofilm

NASA Astrophysics Data System (ADS)

Zachreson, Cameron; Wolff, Christian; Whitchurch, Cynthia B.; Toth, Milos

2017-01-01

Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the assumptions that rod-shaped bacteria furrow through a viscous environment and excrete extracellular polymeric substances which bias their rate of motion. Because the bacteria furrow through their environment, the substratum stiffness is a key control parameter behind the formation of distinct morphological patterns. By systematically varying this property (which we quantify with a stiffness coefficient γ ), we show that subtle changes in the substratum stiffness can give rise to a stable state characterized by a high degree of local order and long-range pattern formation. The ordered state exhibits characteristics typically associated with bacterial fitness advantages, even though it is induced by changes in environmental conditions rather than changes in biological parameters. Our findings are applicable to a broad range of biofilms and provide insights into the relationship between bacterial movement and their environment, and basic mechanisms behind self-organization of biophysical systems.

Distinct Mechanisms for Synchronization and Temporal Patterning of Odor-Encoding Neural Assemblies

NASA Astrophysics Data System (ADS)

MacLeod, Katrina; Laurent, Gilles

1996-11-01

Stimulus-evoked oscillatory synchronization of neural assemblies and temporal patterns of neuronal activity have been observed in many sensory systems, such as the visual and auditory cortices of mammals or the olfactory system of insects. In the locust olfactory system, single odor puffs cause the immediate formation of odor-specific neural assemblies, defined both by their transient synchronized firing and their progressive transformation over the course of a response. The application of an antagonist of ionotropic γ-aminobutyric acid (GABA) receptors to the first olfactory relay neuropil selectively blocked the fast inhibitory synapse between local and projection neurons. This manipulation abolished the synchronization of the odor-coding neural ensembles but did not affect each neuron's temporal response patterns to odors, even when these patterns contained periods of inhibition. Fast GABA-mediated inhibition, therefore, appears to underlie neuronal synchronization but not response tuning in this olfactory system. The selective desynchronization of stimulus-evoked oscillating neural assemblies in vivo is now possible, enabling direct functional tests of their significance for sensation and perception.

Identifying typical patterns of vulnerability: A 5-step approach based on cluster analysis

NASA Astrophysics Data System (ADS)

Sietz, Diana; Lüdeke, Matthias; Kok, Marcel; Lucas, Paul; Carsten, Walther; Janssen, Peter

2013-04-01

Specific processes that shape the vulnerability of socio-ecological systems to climate, market and other stresses derive from diverse background conditions. Within the multitude of vulnerability-creating mechanisms, distinct processes recur in various regions inspiring research on typical patterns of vulnerability. The vulnerability patterns display typical combinations of the natural and socio-economic properties that shape a systems' vulnerability to particular stresses. Based on the identification of a limited number of vulnerability patterns, pattern analysis provides an efficient approach to improving our understanding of vulnerability and decision-making for vulnerability reduction. However, current pattern analyses often miss explicit descriptions of their methods and pay insufficient attention to the validity of their groupings. Therefore, the question arises as to how do we identify typical vulnerability patterns in order to enhance our understanding of a systems' vulnerability to stresses? A cluster-based pattern recognition applied at global and local levels is scrutinised with a focus on an applicable methodology and practicable insights. Taking the example of drylands, this presentation demonstrates the conditions necessary to identify typical vulnerability patterns. They are summarised in five methodological steps comprising the elicitation of relevant cause-effect hypotheses and the quantitative indication of mechanisms as well as an evaluation of robustness, a validation and a ranking of the identified patterns. Reflecting scale-dependent opportunities, a global study is able to support decision-making with insights into the up-scaling of interventions when available funds are limited. In contrast, local investigations encourage an outcome-based validation. This constitutes a crucial step in establishing the credibility of the patterns and hence their suitability for informing extension services and individual decisions. In this respect, working at the local level provides a clear advantage since, to a large extent, limitations in globally available observational data constrain such a validation on the global scale. Overall, the five steps are outlined in detail in order to facilitate and motivate the application of pattern recognition in other research studies concerned with vulnerability analysis, including future applications to different vulnerability frameworks. Such applications could promote the refinement of mechanisms in specific contexts and advance methodological adjustments. This would further increase the value of identifying typical patterns in the properties of socio-ecological systems for an improved understanding and management of the relation between these systems and particular stresses.

Understanding women's experiences of distress during pregnancy in Dar es Salaam, Tanzania.

PubMed

Kaaya, S F; Mbwambo, J K; Fawzi, M C Smith; Van Den Borne, H; Schaalma, H; Leshabari, M T

2010-01-01

Several studies show depression is common during pregnancy. However, there is limited information in Tanzania on the magnitude of perceived distress during pregnancy and meanings ascribed to such distress. A descriptive survey collected data using unstructured interviews from 12 traditional practitioners and 10 peri-urban women with previous pregnancy related mental health concerns identified using a depression vignette. The objectives were to describe the sources and characteristics of distress during pregnancy, and idioms of distress that could inform cultural adaptation of depression screening tools. Narrative analysis showed an emergent category of "problematic pregnancies" framed women's recollections of prolonged periods of sadness. This experience was qualified using various idioms of distress that were differentially emphasized depending on informant's perceived causes of health concern. The idiom kusononeka was consistently used to describe extreme sadness across causal categories and clustered with at least two typical features of major depression. This suggested existence of a construct with similarities to biomedical criteria for depression. "Thinking too much" emerged as a distinctive expression associated with prolonged sadness. Distinctive expressions of social functioning impairments were identified that can inform depression severity assessments. In conclusion, contextual inquiry into experiences of psychological distress showed distinct local idioms that clustered in patterns similar to symptoms of biomedical depressive episodes. Further studies to assess the utility of local idioms of distress and distress related functional impairment in depression assessment tools are warranted.

Using Airborne Radar Stratigraphy to Model Surface Accumulation Anomaly and Basal Control over Deformed Basal Ice in Greenland

NASA Astrophysics Data System (ADS)

Das, I.; Bell, R. E.; Creyts, T. T.; Wolovick, M.

2013-12-01

Large deformed ice structures have been imaged at the base of northern Greenland ice sheet by IceBridge airborne radar. Numerous deformed structures lie along the base of both Petermann Glacier and Northeast Ice stream catchments covering 10-13% of the catchment area. These structures may be combinations of basal freeze-on and folded ice that overturns and inverts stratigraphy. In the interior, where the ice velocity is low, the radar imaged height of the deformed structures are frequently a significant fraction of the ice thickness. They are related to basal freeze on and stick-slip at the base of the ice sheet and may be triggered by subglacial water, sediments or local geological conditions. The larger ones (at times up to 700 m thick and 140 km long) perturb the ice stratigraphy and create prominent undulations on the ice surface and modify the local surface mass balance. Here, we investigate the relationship between the deformed structures and surface processes using shallow and deep ice radar stratigraphy. The surface undulations caused by the deformed structures modulate the pattern of local surface snow accumulation. Using normalized differences of several near-surface stratigraphic layers, we have calculated the accumulation anomaly over these deformed structures. The accumulation anomalies can be as high as 20% of the local surface accumulation over some of the larger surface depressions caused by these deformed structures. We observe distinct differences in the phases of the near-surface internal layers on the Petermann and Northeast catchments. These differences indicate that the deformed bodies over Petermann are controlled by conditions at the bed different from the Northeast Ice stream. The distinctly different near-surface stratigraphy over the deformed structures in the Petermann and Northeast catchments have opened up a number of questions including their formation and how they influence the ice dynamics, ice stratigraphy and surface mass balance. In this study we will model the different physical conditions at the bed and ice rheology from their distinct signatures in the near-surface strata. The results will identify the distinct mechanisms that form these bodies and their control over the surface morphology and snow accumulation.

Magnetic polarity stratigraphy of Inchasi: a Pliocene mammal-bearing locality from the Bolivian Andes deposited just before the Great American Interchange

NASA Astrophysics Data System (ADS)

MacFadden, Bruce J.; Anaya, Federico; Argollo, Jaime

1993-01-01

The newly discovered section at Inchasi, located about 50 km southeast of Potosi, Bolivia, in the eastern Cordillera, consists of about 120 m of undeformed terrestrial sediments containing fossil mammals. Paleomagnetic analysis of 54 sites indicates a polarity pattern with an estimated duration of about 0.64 Ma. The rich Inchasi local fauna indicates a Montehermosan and/or Chapadmalalan land mammal age (Pliocene). Given these constraints, Inchasi correlates from the interval between the late Gilbert (within the Cochiti subchron) to the early Gauss (within the Mammoth subchron) chrons; that is, between about 4.0 and 3.3 Ma. The distinct lack of North American mammals in the Inchasi local fauna provides some of the first well-calibrated evidence that the Great American Interchange occurred after about 3.0 Ma, as has been previously stated based on other calibrations of the earliest immigrant (Uquian) faunas.

Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

PubMed Central

Staley, Christopher

2016-01-01

ABSTRACT Recent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P < 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P < 0.001), where freshwater sands had significantly higher abundances of taxa within the Actinobacteria, Betaproteobacteria, and Verrucomicrobia than marine environments. In contrast, marine sands harbored greater abundances of Gammaproteobacteria and Planctomycetes, and those from Florida had more Deltaproteobacteria and Firmicutes. Marine beaches had significantly different phylogenetic community structures (P ≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P < 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment. IMPORTANCE This study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives. PMID:26921429

Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

PubMed Central

Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

2015-01-01

Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

'Where' and 'what' in visual search.

PubMed

Atkinson, J; Braddick, O J

1989-01-01

A line segment target can be detected among distractors of a different orientation by a fast 'preattentive' process. One view is that this depends on detection of a 'feature gradient', which enables subjects to locate where the target is without necessarily identifying what it is. An alternative view is that a target can be identified as distinctive in a particular 'feature map' without subjects knowing where it is in that map. Experiments are reported in which briefly exposed arrays of line segments were followed by a pattern mask, and the threshold stimulus-mask interval determined for three tasks: 'what'--subjects reported whether the target was vertical or horizontal among oblique distractors; 'coarse where'--subjects reported whether the target was in the upper or lower half of the array; 'fine where'--subjects reported whether or not the target was in a set of four particular array positions. The threshold interval was significantly lower for the 'coarse where' than for the 'what' task, indicating that, even though localization in this task depends on the target's orientation difference, this localization is possible without absolute identification of target orientation. However, for the 'fine where' task, intervals as long as or longer than those for the 'what' task were required. It appears either that different localization processes work at different levels of resolution, or that a single localization process, independent of identification, can increase its resolution at the expense of processing speed. These possibilities are discussed in terms of distinct neural representations of the visual field and fixed or variable localization processes acting upon them.

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Climate Change and Conservation Planning in California: The San Francisco Bay Area Upland Habitat Goals Approach

NASA Astrophysics Data System (ADS)

Branciforte, R.; Weiss, S. B.; Schaefer, N.

2008-12-01

Climate change threatens California's vast and unique biodiversity. The Bay Area Upland Habitat Goals is a comprehensive regional biodiversity assessment of the 9 counties surrounding San Francisco Bay, and is designing conservation land networks that will serve to protect, manage, and restore that biodiversity. Conservation goals for vegetation, rare plants, mammals, birds, fish, amphibians, reptiles, and invertebrates are set, and those goals are met using the optimization algorithm MARXAN. Climate change issues are being considered in the assessment and network design in several ways. The high spatial variability at mesoclimatic and topoclimatic scales in California creates high local biodiversity, and provides some degree of local resiliency to macroclimatic change. Mesoclimatic variability from 800 m scale PRISM climatic norms is used to assess "mesoclimate spaces" in distinct mountain ranges, so that high mesoclimatic variability, especially local extremes that likely support range limits of species and potential climatic refugia, can be captured in the network. Quantitative measures of network resiliency to climate change include the spatial range of key temperature and precipitation variables within planning units. Topoclimatic variability provides a finer-grained spatial patterning. Downscaling to the topoclimatic scale (10-50 m scale) includes modeling solar radiation across DEMs for predicting maximum temperature differentials, and topographic position indices for modeling minimum temperature differentials. PRISM data are also used to differentiate grasslands into distinct warm and cool types. The overall conservation strategy includes local and regional connectivity so that range shifts can be accommodated.

Spiral wave classification using normalized compression distance: Towards atrial tissue spatiotemporal electrophysiological behavior characterization.

PubMed

Alagoz, Celal; Guez, Allon; Cohen, Andrew; Bullinga, John R

2015-08-01

Analysis of electrical activation patterns such as re-entries during atrial fibrillation (Afib) is crucial in understanding arrhythmic mechanisms and assessment of diagnostic measures. Spiral waves are a phenomena that provide intuitive basis for re-entries occurring in cardiac tissue. Distinct spiral wave behaviors such as stable spiral waves, meandering spiral waves, and spiral wave break-up may have distinct electrogram manifestations on a mapping catheter. Hence, it is desirable to have an automated classification of spiral wave behavior based on catheter recordings for a qualitative characterization of spatiotemporal electrophysiological activity on atrial tissue. In this study, we propose a method for classification of spatiotemporal characteristics of simulated atrial activation patterns in terms of distinct spiral wave behaviors during Afib using two different techniques: normalized compressed distance (NCD) and normalized FFT (NFFTD). We use a phenomenological model for cardiac electrical propagation to produce various simulated spiral wave behaviors on a 2D grid and labeled them as stable, meandering, or breakup. By mimicking commonly used catheter types, a star shaped and a circular shaped both of which do the local readings from atrial wall, monopolar and bipolar intracardiac electrograms are simulated. Virtual catheters are positioned at different locations on the grid. The classification performance for different catheter locations, types and for monopolar or bipolar readings were also compared. We observed that the performance for each case differed slightly. However, we found that NCD performance is superior to NFFTD. Through the simulation study, we showed the theoretical validation of the proposed method. Our findings suggest that a qualitative wavefront activation pattern can be assessed during Afib without the need for highly invasive mapping techniques such as multisite simultaneous electrogram recordings.

Differential fMRI Activation Patterns to Noxious Heat and Tactile Stimuli in the Primate Spinal Cord

PubMed Central

Yang, Pai-Feng; Wang, Feng

2015-01-01

Mesoscale local functional organizations of the primate spinal cord are largely unknown. Using high-resolution fMRI at 9.4 T, we identified distinct interhorn and intersegment fMRI activation patterns to tactile versus nociceptive heat stimulation of digits in lightly anesthetized monkeys. Within a spinal segment, 8 Hz vibrotactile stimuli elicited predominantly fMRI activations in the middle part of ipsilateral dorsal horn (iDH), along with significantly weaker activations in ipsilateral (iVH) and contralateral (cVH) ventral horns. In contrast, nociceptive heat stimuli evoked widespread strong activations in the superficial part of iDH, as well as in iVH and contralateral dorsal (cDH) horns. As controls, only weak signal fluctuations were detected in the white matter. The iDH responded most strongly to both tactile and heat stimuli, whereas the cVH and cDH responded selectively to tactile versus nociceptive heat, respectively. Across spinal segments, iDH activations were detected in three consecutive segments in both tactile and heat conditions. Heat responses, however, were more extensive along the cord, with strong activations in iVH and cDH in two consecutive segments. Subsequent subunit B of cholera toxin tracer histology confirmed that the spinal segments showing fMRI activations indeed received afferent inputs from the stimulated digits. Comparisons of the fMRI signal time courses in early somatosensory area 3b and iDH revealed very similar hemodynamic stimulus–response functions. In summary, we identified with fMRI distinct segmental networks for the processing of tactile and nociceptive heat stimuli in the cervical spinal cord of nonhuman primates. SIGNIFICANCE STATEMENT This is the first fMRI demonstration of distinct intrasegmental and intersegmental nociceptive heat and touch processing circuits in the spinal cord of nonhuman primates. This study provides novel insights into the local functional organizations of the primate spinal cord for pain and touch, information that will be valuable for designing and optimizing therapeutic interventions for chronic pain management. PMID:26203144

Resist Globally, Infect Locally: A Transcontinental Test of Adaptation by Stickleback and Their Tapeworm Parasite.

PubMed

Weber, Jesse N; Kalbe, Martin; Shim, Kum Chuan; Erin, Noémie I; Steinel, Natalie C; Ma, Lei; Bolnick, Daniel I

2017-01-01

Parasite infections are a product of both ecological processes affecting host-parasite encounter rates and evolutionary dynamics affecting host susceptibility. However, few studies examine natural infection variation from both ecological and evolutionary perspectives. Here, we describe the ecological and evolutionary factors generating variation in infection rates by a tapeworm (Schistocephalus solidus) in a vertebrate host, the threespine stickleback (Gasterosteus aculeatus). To explore ecological aspects of infection, we measured tapeworm prevalence in Canadian stickleback inhabiting two distinct environments: marine and freshwater. Consistent with ecological control of infection, the tapeworm is very rare in marine environments, even though marine fish are highly susceptible. Conversely, commonly infected freshwater stickleback exhibit substantial resistance in controlled laboratory trials, suggesting that high exposure risk overwhelms their recently evolved resistance. We also tested for parasite adaptation to its host by performing transcontinental reciprocal infections, using stickleback and tapeworm populations from Europe and western Canada. More infections occurred in same-continent host-parasite combinations, indicating parasite "local" adaptation, at least on the scale of continents. However, the recently evolved immunity of freshwater hosts applies to both local and foreign parasites. The pattern of adaptation described here is not wholly compatible with either of the common models of host-parasite coevolution (i.e., matching infection or targeted recognition). Instead, we propose a hybrid, eco-evolutionary model to explain the remarkable pattern of global host resistance and local parasite infectivity.

Convergence and divergence across construction methods for human brain white matter networks: an assessment based on individual differences.

PubMed

Zhong, Suyu; He, Yong; Gong, Gaolang

2015-05-01

Using diffusion MRI, a number of studies have investigated the properties of whole-brain white matter (WM) networks with differing network construction methods (node/edge definition). However, how the construction methods affect individual differences of WM networks and, particularly, if distinct methods can provide convergent or divergent patterns of individual differences remain largely unknown. Here, we applied 10 frequently used methods to construct whole-brain WM networks in a healthy young adult population (57 subjects), which involves two node definitions (low-resolution and high-resolution) and five edge definitions (binary, FA weighted, fiber-density weighted, length-corrected fiber-density weighted, and connectivity-probability weighted). For these WM networks, individual differences were systematically analyzed in three network aspects: (1) a spatial pattern of WM connections, (2) a spatial pattern of nodal efficiency, and (3) network global and local efficiencies. Intriguingly, we found that some of the network construction methods converged in terms of individual difference patterns, but diverged with other methods. Furthermore, the convergence/divergence between methods differed among network properties that were adopted to assess individual differences. Particularly, high-resolution WM networks with differing edge definitions showed convergent individual differences in the spatial pattern of both WM connections and nodal efficiency. For the network global and local efficiencies, low-resolution and high-resolution WM networks for most edge definitions consistently exhibited a highly convergent pattern in individual differences. Finally, the test-retest analysis revealed a decent temporal reproducibility for the patterns of between-method convergence/divergence. Together, the results of the present study demonstrated a measure-dependent effect of network construction methods on the individual difference of WM network properties. © 2015 Wiley Periodicals, Inc.

Expression and regulation of Sef, a novel signaling inhibitor of receptor tyrosine kinases-mediated signaling in the nervous system.

PubMed

Grothe, Claudia; Claus, Peter; Haastert, Kirsten; Lutwak, Ela; Ron, Dina

2008-01-01

Fibroblast growth factors (FGFs) signal via four distinct high affinity cell surface tyrosine kinase receptors, termed FGFR1-FGFR4 (FGFR-FGF-receptor). Recently, a new modulator of the FGF signaling pathway, the transmembrane protein 'similar expression to FGF genes' (Sef), has been identified in zebrafish and subsequently in mammals. Sef from mouse and human inhibits FGF mitogenic activity. In the present study, we analyzed the expression of Sef in distinct rat brain areas, in the spinal cord and in peripheral nerves and spinal ganglia using semi-quantitative RT-PCR. Furthermore, we studied the cellular expression pattern of Sef in intact spinal ganglia and sciatic nerves and, in addition, after crush lesion, using in situ hybridization and immunohistochemistry. Sef transcripts were expressed in all brain areas evaluated and in the spinal cord. A neuronal expression was found in both intact and injured spinal ganglia. Intact sciatic nerves, however, showed little or no Sef expression. Seven days after injury, high Sef expression was concentrated to the crush site, and Schwann cells seemed to be the source of Sef. The labeling pattern of up-regulated Sef was complementary to the patterns of FGF-2 and FGFR1-3, which were localized proximal and distal to the crush site. These results suggest an involvement of Sef during the nerve regeneration process, possibly by fine-tuning the effects of FGF signaling.

Relationships between hippocampal sharp waves, ripples and fast gamma oscillation: influence of dentate and entorhinal cortical activity

PubMed Central

Sullivan, David; Csicsvari, Jozsef; Mizuseki, Kenji; Montgomery, Sean; Diba, Kamran; Buzsáki, György

2011-01-01

Summary Hippocampal sharp waves (SPW) and associated fast (‘ripple’) oscillations in the CA1 region are among the most synchronous physiological patterns in the mammalian brain. Using two-dimensional arrays of electrodes for recording local field potentials and unit discharges in freely moving rats, we studied the emergence of ripple oscillations (140–220 Hz) and compared their origin and cellular-synaptic mechanisms with fast gamma oscillations (90–140 Hz). We show that (a) hippocampal SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve the same networks and share similar mechanisms, (b) both the frequency and magnitude of fast oscillations is positively correlated with the magnitude of SPWs, (c) during both ripples and fast gamma oscillations the frequency of network oscillation is higher in CA1 than in CA3, (d) SPWs and associated firing of neurons are synchronous in the dorsal hippocampus and dorso-medial entorhinal cortex but ripples are confined to the CA1 pyramidal layer and its downstream targets and (e) the emergence of CA3 population bursts, a prerequisite for SPW-ripples, is biased by activity patterns in the dentate gyrus and entorhinal cortex, with highest probability of ripples associated with an ‘optimum’ level of dentate gamma power. We hypothesize that each hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude of the excitatory drive. PMID:21653864

A new methodological approach for worldwide beryllium-7 time series analysis

NASA Astrophysics Data System (ADS)

Bianchi, Stefano; Longo, Alessandro; Plastino, Wolfango

2018-07-01

Time series analyses of cosmogenic radionuclide 7Be and 22Na atmospheric activity concentrations and meteorological data observed at twenty-five International Monitoring System (IMS) stations of the Comprehensive Nuclear-Test-Ban Treaty Organisation (CTBTO) have shown great variability in terms of noise structures, harmonic content, cross-correlation patterns and local Hurst exponent behaviour. Noise content and its structure has been extracted and characterised for the two radionuclides time series. It has been found that the yearly component, which is present in most of the time series, is not stationary, but has a percentage weight that varies with time. Analysis of atmospheric activity concentrations of 7Be, measured at IMS stations, has shown them to be influenced by distinct meteorological patterns, mainly by atmospheric pressure and temperature.

Differential subcellular distribution of ion channels and the diversity of neuronal function.

PubMed

Nusser, Zoltan

2012-06-01

Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

Distinct winter patterns of tropical Pacific convection anomaly and the associated extratropical wave trains in the Northern Hemisphere

NASA Astrophysics Data System (ADS)

Ding, Shuoyi; Chen, Wen; Graf, Hans-F.; Guo, Yuanyuan; Nath, Debashis

2017-11-01

In this paper, distinct patterns of boreal winter convection anomalies over the tropical Pacific and associated wave trains in the extratropics are addressed. The first leading mode (EOF1) of convection anomalies as measured by outgoing longwave radiation demonstrates an east-west oscillation of deep convection with centers over the equatorial central Pacific (CP) and over the tropical western North Pacific and the Maritime Continent. The second leading mode (EOF2) is also a dipole pattern with opposite centers straddling 170°W, possibly modifying EOF1 to some extent. Combining the first two leading modes, five major categories of tropical convection anomalies can be identified for the period 1979/80-2012/13. The comparison between these five categories and the corresponding SST anomaly patterns indicates a nonlinear relationship between convection and SST. The combination of EOF1 and EOF2 with in-phase PCs exhibits an east-west dipole pattern with opposite signs over west of the dateline and the Maritime Continent. The negative phase of the two PCs, named La Niña pattern, induces a negative Pacific/North American—positive North Atlantic Oscillation teleconnection in the extratropics. Approximately opposite responses can be detected in its positive phase, named CP El Niño pattern. The negative PC2 superposing positive PC1, named EP El Niño pattern, shows the strongest convection anomalies with enhanced (depressed) convection over the eastern (western) Pacific and leads to a Tropical/Northern Hemisphere-like teleconnection pattern and an anomalous anticyclone extending from the North Pacific to the North Atlantic. The positive PC2 with neutral PC1, named western CP pattern, shows weakly enhanced convection to the west of the dateline as a response to local SST warming around the dateline. This convection anomaly pattern, although weak, is important and excites a northeastward wave train from the tropics to Greenland, resulting in surface air temperature cooling covering the northeastern North America and warmer and wetter conditions over Western Europe.

AIDS communications through social networks: catalyst for behaviour changes in Uganda.

PubMed

Low-Beer, Daniel; Stoneburner, Rand L

2004-05-01

To investigate distinctive communications through social networks which may be associated with population behaviour changes and HIV prevalence declines in Uganda compared to other countries. We undertook a comparative analysis of demographic and HIV behavioural data collected in Demographic and Health Surveys (DHS III) in Uganda, Kenya, Tanzania, Malawi, Zambia and Zimbabwe as well as Knowledge, Attitudes and Behaviours (KABP) surveys in Uganda in 1989 and 1995. AIDS behaviours, social communications and channels for communication about AIDS and people with AIDS were analysed by age, sex and country. Modelling was developed to investigate at what stage of the epidemic a majority of people will know someone with AIDS, given differing communication patterns through social networks. Finally AIDS reporting and Voluntary Counselling and Testing (VCT) trends were analysed to assess if the impact of social communications worked through clinical services and interventions or more directly at the population level in community contexts. Uganda showed unique patterns of communications through social networks including a shift from mass and institutional to personal channels for communicating about AIDS, 1989-1995. This was associated with higher levels of knowing someone with AIDS through social networks and, in turn, positive risk ratios for behaviour change including reducing casual sex and condom use. Youth had distinctively high levels of knowing someone with AIDS in Uganda, suggesting widespread community communication across age groups. Patterns of disclosure, AIDS diagnosis and reporting were influential on social communications about AIDS. Over 90%, 45% or under 20% of people know someone with AIDS at peak HIV incidence and high AIDS mortality, depending on whether communications through social networks are extensive or restricted. There are distinctive patterns for communicating through social networks about AIDS and people with AIDS in Uganda. They appear to work directly at population level rather than in response to clinical interventions and testing and may be important in the uptake of the latter services. This communication response provides an important basis for HIV prevention if it is to be scaled to the population level. Vertical prevention (and even treatment) interventions need to engage more closely with local, horizontal communication and behavioural responses to AIDS. Communication programmes have to take root at the level of social networks working though local networks of meetings, chiefs, churches and health personnel as well as the media. Mobilising basic social communications may be a necessary resource (as much as services and finance) to scale HIV prevention and treatment to the population level.

Long-lived force patterns and deformation waves at repulsive epithelial boundaries

NASA Astrophysics Data System (ADS)

Rodríguez-Franco, Pilar; Brugués, Agustí; Marín-Llauradó, Ariadna; Conte, Vito; Solanas, Guiomar; Batlle, Eduard; Fredberg, Jeffrey J.; Roca-Cusachs, Pere; Sunyer, Raimon; Trepat, Xavier

2017-10-01

For an organism to develop and maintain homeostasis, cell types with distinct functions must often be separated by physical boundaries. The formation and maintenance of such boundaries are commonly attributed to mechanisms restricted to the cells lining the boundary. Here we show that, besides these local subcellular mechanisms, the formation and maintenance of tissue boundaries involves long-lived, long-ranged mechanical events. Following contact between two epithelial monolayers expressing, respectively, EphB2 and its ligand ephrinB1, both monolayers exhibit oscillatory patterns of traction forces and intercellular stresses that tend to pull cell-matrix adhesions away from the boundary. With time, monolayers jam, accompanied by the emergence of deformation waves that propagate away from the boundary. This phenomenon is not specific to EphB2/ephrinB1 repulsion but is also present during the formation of boundaries with an inert interface and during fusion of homotypic epithelial layers. Our findings thus unveil a global physical mechanism that sustains tissue separation independently of the biochemical and mechanical features of the local tissue boundary.

Influence of White and Gray Matter Connections on Endogenous Human Cortical Oscillations

PubMed Central

Hawasli, Ammar H.; Kim, DoHyun; Ledbetter, Noah M.; Dahiya, Sonika; Barbour, Dennis L.; Leuthardt, Eric C.

2016-01-01

Brain oscillations reflect changes in electrical potentials summated across neuronal populations. Low- and high-frequency rhythms have different modulation patterns. Slower rhythms are spatially broad, while faster rhythms are more local. From this observation, we hypothesized that low- and high-frequency oscillations reflect white- and gray-matter communications, respectively, and synchronization between low-frequency phase with high-frequency amplitude represents a mechanism enabling distributed brain-networks to coordinate local processing. Testing this common understanding, we selectively disrupted white or gray matter connections to human cortex while recording surface field potentials. Counter to our original hypotheses, we found that cortex consists of independent oscillatory-units (IOUs) that maintain their own complex endogenous rhythm structure. IOUs are differentially modulated by white and gray matter connections. White-matter connections maintain topographical anatomic heterogeneity (i.e., separable processing in cortical space) and gray-matter connections segregate cortical synchronization patterns (i.e., separable temporal processing through phase-power coupling). Modulation of distinct oscillatory modules enables the functional diversity necessary for complex processing in the human brain. PMID:27445767

The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches.

PubMed

Carvalho, Margarida Lima; Costa Silva, Guilherme José da; Melo, Silvana; Ashikaga, Fernando Yuldi; Shimabukuro-Dias, Cristiane Kioko; Scacchetti, Priscilla Cardim; Devidé, Renato; Foresti, Fausto; Oliveira, Claudio

2018-01-31

The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus Hemiodontichthys Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River. Hemiodontichthys samples from the two localities in Purus River were also karyotyped in order to address the degree of chromosomal variation between populations. Through GMYC analysis of the COI tree, the patterns of genetic variation among local populations revealed to be higher than the ones found among distinct species from other genera of the subfamily Loricariinae, suggesting the existence of probable four cryptic species in this genus. The possible existence of a species complex in the genus is corroborated by the different cytogenetic patterns between Hemiodontichthys sp. 1 and sp. 2, revealing the necessity of a deep taxonomic review of the group.

Bipartite electronic superstructures in the vortex core of Bi2Sr2CaCu2O8+δ

PubMed Central

Machida, T.; Kohsaka, Y.; Matsuoka, K.; Iwaya, K.; Hanaguri, T.; Tamegai, T.

2016-01-01

The central issue in the physics of cuprate superconductivity is the mutual relationship among superconductivity, pseudogap and broken-spatial-symmetry states. A magnetic field B suppresses superconductivity, providing an opportunity to investigate the competition among these states. Although various B-induced electronic superstructures have been reported, their energy, spatial and momentum-space structures are unclear. Here, we show using spectroscopic-imaging scanning tunnelling microscopy on Bi2Sr2CaCu2O8+δ that there are two distinct B-induced electronic superstructures, both being localized in the vortex core but appearing at different energies. In the low-energy range where the nodal Bogoliubov quasiparticles are well-defined, we observe the so-called vortex checkerboard that we identify as the B-enhanced quasiparticle interference pattern. By contrast, in the high-energy region where the pseudogap develops, the broken-spatial-symmetry patterns that pre-exist at B=0 T is locally enhanced in the vortex core. This evidences the competition between superconductivity and the broken-spatial-symmetry state that is associated with the pseudogap. PMID:27230420

An Investigation of Topography Modulated Low Level Moisture Convergence Patterns in the Southern Appalachians Using WRF

NASA Astrophysics Data System (ADS)

Wilson, A. M.; Duan, Y.; Barros, A.

2015-12-01

The Southern Appalachian Mountains (SAM) region is a biodiversity hot-spot that is vulnerable to land use/land cover changes due to its proximity to the rapidly growing population in the Southeast U.S. Persistent near surface moisture and associated microclimates observed in this region have been documented since the colonization of the area. The landform in this area, in particular in the inner mountain region, is highly complex with nested valleys and ridges. The geometry of the terrain causes distinct diurnal and seasonal local flow patterns that result in highly complex interactions of this low level moisture with meso- and synoptic-scale cyclones passing through the region. The Weather Research and Forecasting model (WRF) was used to conduct high resolution simulations of several case studies of warm season precipitation in the SAM with different synoptic-scale conditions to investigate this interaction between local and larger-scale flow patterns. The aim is to elucidate the microphysical interactions among these shallow orographic clouds and preexisting precipitating cloud systems and identify uncertainties in the model microphysics using in situ measurements. Findings show that ridge-valley precipitation gradients, in particular the "reverse" to the classical orographic effect observed in inner mountain valleys, is linked to horizontal heterogeneity in the vertical structure of low level cloud and precipitation promoted through landform controls on local flow. Moisture convergence patterns follow the peaks and valleys as represented by WRF terrain, and the topography effectively controls their timing and spatial structure. The simulations support the hypothesis that ridge-valley precipitation gradients, and in particular the reverse orographic enhancement effect in inner mountain valleys, is linked to horizontal heterogeneity in the vertical structure of low level clouds and precipitation promoted through landform controls on moisture convergence.

Patterns of relapse in primary central nervous system lymphoma: inferences regarding the role of the neuro-vascular unit and monoclonal antibodies in treating occult CNS disease.

PubMed

Ambady, Prakash; Fu, Rongwei; Netto, Joao Prola; Kersch, Cymon; Firkins, Jenny; Doolittle, Nancy D; Neuwelt, Edward A

2017-06-02

The radiologic features and patterns of primary central nervous system lymphoma (PCNSL) at initial presentation are well described. High response rates can be achieved with first-line high-dose methotrexate (HD-MTX) based regimens, yet many relapse within 2 years of diagnosis. We describe the pattern of relapse and review the potential mechanisms involved in relapse. We identified 78 consecutive patients who attained complete radiographic response (CR) during or after first-line treatment for newly diagnosed PCNSL (CD20+, diffuse large B cell type). Patients were treated with HD-MTX based regimen in conjunction with blood-brain barrier disruption (HD-MTX/BBBD); 44 subsequently relapsed. Images and medical records of these 44 consecutive patients were retrospectively reviewed. The anatomical location of enhancing lesions at initial diagnosis and at the time of relapse were identified and compared. 37/44 patients fulfilled inclusion criteria and had new measureable enhancing lesions at relapse; the pattern and location of relapse of these 37 patients were identified. At relapse, the new enhancement was at a spatially distinct site in 30 of 37 patients. Local relapse was found only in seven patients. Unlike gliomas, the majority of PCNSL had radiographic relapse at spatially distinct anatomical locations within the brain behind a previously intact neurovascular unit (NVU), and in few cases outside, the central nervous system (CNS). This may suggest either (1) reactivation of occult reservoirs behind an intact NVU in the CNS (or ocular) or (2) seeding from bone marrow or other extra CNS sites. Recognizing patterns of relapse is key for early detection and may provide insight into potential mechanisms of relapse as well as help develop strategies to extend duration of complete response.

A tale of two agnosias: distinctions between form and integrative agnosia.

PubMed

Riddoch, M Jane; Humphreys, Glyn W; Akhtar, Nabeela; Allen, Harriet; Bracewell, R Martyn; Schofield, Andrew J

2008-02-01

The performance of two patients with visual agnosia was compared across a number of tests examining visual processing. The patients were distinguished by having dorsal and medial ventral extrastriate lesions. While inanimate objects were disadvantaged for the patient with a dorsal extrastriate lesion, animate items are disadvantaged for the patient with the medial ventral extrastriate lesion. The patients also showed contrasting patterns of performance on the Navon Test: The patient with a dorsal extrastriate lesion demonstrated a local bias while the patient with a medial ventral extrastriate lesion had a global bias. We propose that the dorsal and medial ventral visual pathways may be characterized at an extrastriate level by differences in local relative to more global visual processing and that this can link to visually based category-specific deficits in processing.

3D Mechanical Models of Crustal Deformation and the Effect of Erosion on the Strain Pattern in SE Alaska

NASA Astrophysics Data System (ADS)

Barker, A. D.; Koons, P. O.; Upton, P.; Hallet, B.

2008-12-01

Employing 3D mechanical modeling to investigate the susceptibility of strain patterns to distinct erosion conditions we have identified a strong connection between surface erosion and strain localization and vertical motion of crustal material. The specific model geometry and boundary conditions are relevant to the dynamic St. Elias orogen of SE Alaska, but the general results and interpretations are universal. To illustrate the effect of erosion we compare results to a reference model without imposed erosion. We consider the crustal response to boundary conditions representing erosion scenarios: 1) regional erosion (~1 mm a-1 over a region ~600 km on a side) and 2) focused incision (~6 mm a-1 in valleys ~10 km wide and 50-100 km long). Whereas regional erosion mimics broader scale mass wasting and periglacial weathering, focused incision represents efficient erosion confined to valley systems similar to the massive Bering, Malaspina and Bagley glaciers of the St. Elias range. Using these boundary conditions we demonstrate significant localization of strain and crustal uplift beneath the sites of erosion. We also show the strain localization pattern adjusts to spatial shifts in erosion arising from substantial (order of 100km) glacial advance or retreat. The magnitude of the strain is higher in each erosion model compared to the reference model. The difference of the strain magnitude between erosion models and reference model depends on the location of the imposed erosion: crustal strain localize most when the forethrust daylights in the zone being eroded. Sustained focused erosion decreases the overall crustal strength beneath the site of erosion due to thinning of the strong brittle crust. Strain naturally concentrates within the weakened zone. Upward advection of warm crust causes further weakening and thereby leads to a tectonic aneurysm.

Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts

PubMed Central

2014-01-01

Background Polycomb group proteins form multicomponent complexes that are important for establishing lineage-specific patterns of gene expression. Mammalian cells encode multiple permutations of the prototypic Polycomb repressive complex 1 (PRC1) with little evidence for functional specialization. An aim of this study is to determine whether the multiple orthologs that are co-expressed in human fibroblasts act on different target genes and whether their genomic location changes during cellular senescence. Results Deep sequencing of chromatin immunoprecipitated with antibodies against CBX6, CBX7, CBX8, RING1 and RING2 reveals that the orthologs co-localize at multiple sites. PCR-based validation at representative loci suggests that a further six PRC1 proteins have similar binding patterns. Importantly, sequential chromatin immunoprecipitation with antibodies against different orthologs implies that multiple variants of PRC1 associate with the same DNA. At many loci, the binding profiles have a distinctive architecture that is preserved in two different types of fibroblast. Conversely, there are several hundred loci at which PRC1 binding is cell type-specific and, contrary to expectations, the presence of PRC1 does not necessarily equate with transcriptional silencing. Interestingly, the PRC1 binding profiles are preserved in senescent cells despite changes in gene expression. Conclusions The multiple permutations of PRC1 in human fibroblasts congregate at common rather than specific sites in the genome and with overlapping but distinctive binding profiles in different fibroblasts. The data imply that the effects of PRC1 complexes on gene expression are more subtle than simply repressing the loci at which they bind. PMID:24485159

Graph theory network function in Parkinson's disease assessed with electroencephalography.

PubMed

Utianski, Rene L; Caviness, John N; van Straaten, Elisabeth C W; Beach, Thomas G; Dugger, Brittany N; Shill, Holly A; Driver-Dunckley, Erika D; Sabbagh, Marwan N; Mehta, Shyamal; Adler, Charles H; Hentz, Joseph G

2016-05-01

To determine what differences exist in graph theory network measures derived from electroencephalography (EEG), between Parkinson's disease (PD) patients who are cognitively normal (PD-CN) and matched healthy controls; and between PD-CN and PD dementia (PD-D). EEG recordings were analyzed via graph theory network analysis to quantify changes in global efficiency and local integration. This included minimal spanning tree analysis. T-tests and correlations were used to assess differences between groups and assess the relationship with cognitive performance. Network measures showed increased local integration across all frequency bands between control and PD-CN; in contrast, decreased local integration occurred in PD-D when compared to PD-CN in the alpha1 frequency band. Differences found in PD-MCI mirrored PD-D. Correlations were found between network measures and assessments of global cognitive performance in PD. Our results reveal distinct patterns of band and network measure type alteration and breakdown for PD, as well as with cognitive decline in PD. These patterns suggest specific ways that interaction between cortical areas becomes abnormal and contributes to PD symptoms at various stages. Graph theory analysis by EEG suggests that network alteration and breakdown are robust attributes of PD cortical dysfunction pathophysiology. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Transmissible cancer in Tasmanian devils: localized lineage replacement and host population response

PubMed Central

Hamede, Rodrigo K.; Pearse, Anne-Maree; Swift, Kate; Barmuta, Leon A.; Murchison, Elizabeth P.; Jones, Menna E.

2015-01-01

Tasmanian devil facial tumour disease (DFTD) is a clonally transmissible cancer threatening the Tasmanian devil (Sarcophilus harrisii) with extinction. Live cancer cells are the infectious agent, transmitted to new hosts when individuals bite each other. Over the 18 years since DFTD was first observed, distinct genetic and karyotypic sublineages have evolved. In this longitudinal study, we investigate the associations between tumour karyotype, epidemic patterns and host demographic response to the disease. Reduced host population effects and low DFTD infection rates were associated with high prevalence of tetraploid tumours. Subsequent replacement by a diploid variant of DFTD coincided with a rapid increase in disease prevalence, population decline and reduced mean age of the population. Our results suggest a role for tumour genetics in DFTD transmission dynamics and epidemic outcome. Future research, for this and other highly pathogenic emerging infectious diseases, should focus on understanding the evolution of host and pathogen genotypes, their effects on susceptibility and tolerance to infection, and their implications for designing novel genetic management strategies. This study provides evidence for a rapid localized lineage replacement occurring within a transmissible cancer epidemic and highlights the possibility that distinct DFTD genetic lineages may harbour traits that influence pathogen fitness. PMID:26336167

Radiotelemetric analysis of the effects of prevailing wind direction on Mormon cricket migratory band movement.

PubMed

Sword, G A; Lorch, P D; Gwynne, D T

2008-08-01

During outbreaks, flightless Mormon crickets [Anabrus simplex Haldeman (Orthoptera: Tettigoniidae)] form large mobile groups known as migratory bands. These bands can contain millions of individuals that march en masse across the landscape. The role of environmental cues in influencing the movement direction of migratory bands is poorly understood and has been the subject of little empirical study. We examined the effect of wind direction on Mormon cricket migratory band movement direction by monitoring the local weather conditions and daily movement patterns of individual insects traveling in bands over the same time course at three close, but spatially distinct sites. Although weather conditions were relatively homogeneous across sites, wind directions tended to be more variable across sites during the morning hours, the period during which directional movement begins. Migratory bands at different sites traveled in distinctly different directions. However, we failed to find any evidence to suggest that the observed variation in migratory band movement direction was correlated with local wind direction at any time during the day. These results support the notion that the cues mediating migratory band directionality are likely to be group specific and that a role for landscape-scale environmental cues such as wind direction is unlikely.

Comparison of Grammar in Neurodevelopmental Disorders: The Case of Binding in Williams Syndrome and Autism with and without Language Impairment

ERIC Educational Resources Information Center

Perovic, Alexandra; Modyanova, Nadya; Wexler, Ken

2013-01-01

This study investigates whether distinct neurodevelopmental disorders show distinct patterns of impairments in particular grammatical abilities and the relation of those grammatical patterns to general language delays and intellectual disabilities. We studied two disorders (autism and Williams syndrome [WS]) and two distinct properties (Principle…

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

PubMed Central

Nandi, Tannistha; Holden, Matthew T.G.; Didelot, Xavier; Mehershahi, Kurosh; Boddey, Justin A.; Beacham, Ifor; Peak, Ian; Harting, John; Baybayan, Primo; Guo, Yan; Wang, Susana; How, Lee Chee; Sim, Bernice; Essex-Lopresti, Angela; Sarkar-Tyson, Mitali; Nelson, Michelle; Smither, Sophie; Ong, Catherine; Aw, Lay Tin; Hoon, Chua Hui; Michell, Stephen; Studholme, David J.; Titball, Richard; Chen, Swaine L.; Parkhill, Julian

2015-01-01

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity. PMID:25236617

Spatial patterns in gravel habitats and communities in the central and eastern English Channel

NASA Astrophysics Data System (ADS)

Coggan, Roger; Barrio Froján, Christopher R. S.; Diesing, Markus; Aldridge, John

2012-10-01

The distribution of sediment type and benthic communities in the central and eastern English Channel is shown to be polarised around a distinctive local hydrodynamic feature. The seabed in the region includes an extensive area of gravel substrate which is both an important habitat for benthic marine fauna and a valuable source of material for the marine aggregate industry. Effective management of the area is predicated on an understanding of whether it represents a single homogeneous unit, or several different units that may need to be managed in different ways. The aim of this study was to provide information that would inform such management decisions. Spatial patterns in gravel habitats and communities were studied by investigating the physical environment through modelled and empirical data, and the distribution of infauna and epifauna along an east-west trending transect. A common spatial pattern was observed in both physical and biological parameters, but rather than indicating a simple longitudinal gradient, there was a distinct polarisation around a central feature, a bedload parting (BLP) zone situated between the Isle of Wight and Cotentin peninsula. Sediments and communities at the eastern and western ends of the transect were more similar to each other than to those in the middle. The strong hydrodynamic regime in the BLP area controls sediment distribution, transporting finer material, mainly sand, away from the mid transect area. The pattern in sand content of the substrate mirrors the magnitude of the potential bedload transport, which is complex in this region due to the interplay between the M2 and M4 tidal constituents and produced a series of erosional and depositional zones. The structure of benthic communities reflected the local substrate and hydrodynamic conditions, with sponges observed among the stable substrates and stronger currents that characterised the mid transect area, while infauna became more diverse towards the ends of the transect where substrates were more mobile. We conclude that the area should not be considered as a homogeneous unit for management purposes, despite its apparent uniformity on contemporary seabed sediment maps.

Spatio-temporal characteristics of the diurnal precipitation cycle over Sweden and the linkage to large-scale circulation

NASA Astrophysics Data System (ADS)

Walther, A.; Jeong, J.-H.; Chen, D.

2009-04-01

Rainfall events exhibit diurnal cycle in both frequency and amount, of which phase and amplitude show substantial geographic and seasonal variation. Although the diurnal cycle of precipitation is one of the fundamental characteristics to determine local weather and climate, most of sophisticated climate models still have great deficiencies in reproducing it. Thus more exact understanding of the diurnal precipitation cycle and its mechanisms is thought to be very important to improve climate models and their prediction results. In this work we investigate the diurnal cycle of precipitation in Sweden using ground based hourly observations for 1996-2008. For the precipitation amount and frequency, mean diurnal cycles are computed, and the peak timing and amplitude of the diurnal and semi-diurnal cycle of precipitation are estimated by the harmonic analysis method. Clear mean diurnal precipitation cycles as well as distinct spatial patterns for all seasons are derived. In summer, showing the most distinct pattern, the majority of the stations show a clear rainfall maximum in the afternoon (12-18 LST) except for the coastal part of Central Sweden where we see an early-morning peak (00-06 LST) and the east coast of southern Sweden where we find a morning peak (06-12 LST). The clear afternoon peak may be due to high insolation accumulated during the day time in summer leading to a local convection activity later on that day. These coastal bands mostly consist of the stations closest to the Baltic Sea. Meso-scale convection connected to temperature differences between sea and land combined with a favorable wind pattern seems to play a role here. In the transition seasons, spring and autumn, the amplitude is weaker and the spatial pattern of peak timing is less distinct than in summer. In spring the westcoast stations have a morning peak and stations in southeastern Sweden show an afternoon peak. In autumn we see a zonal division with a clear afternoon peak in southern Sweden. This might be due to a steeply decreasing energy input from the solar insolation in the northern parts causing less convection activity but still enough insolation to cause an afternoon peak in southern Sweden. In both seasons, spring and autumn, north of 60 degrees the pattern is mixed showing early-morning, morning and afternoon peaks. The winter pattern is characterized by afternoon peaks along the eastcoast and central South Sweden and morning peaks over the most of the other parts of the country. However, the amplitude of the diurnal cycle is much weaker compared to that in summer or autumn. In order to examine the large scale circulation which might modulate the diurnal cycle, the Lamb weather types are computed based on sea level pressure fields from the NCEP/NCAR reanalysis 2 dataset with daily and 6-hourly resolution, respectively. The Lamb types based on 6-hourly SLP underline the high temporal variability of atmospheric conditions over the research area. Throughout all seasons, on about 45% of the days two or more circulation classes are different. In 6.3% (JJA) to 8.4% (DJF) of the days can observe 4 different Lamb classes. Using Lamb types with 6-hourly resolution leads to a somewhat finer classification. On average, for about one third of the days with precipitation the daily Lamb type and the appropriate 6-hourly one are different. The most frequent large-scale circulation classes coupled to precipitation events are of cyclonic or directional type. The atmospheric circulation patterns do not follow a diurnal cycle, whereas the local observed precipitation does. Knowledge about the timing of the rainfall is important in order to assign the right underlying circulation patterns to precipitation events.

The G protein-coupled estrogen receptor (GPER) is expressed in two different subcellular localizations reflecting distinct tumor properties in breast cancer.

PubMed

Samartzis, Eleftherios P; Noske, Aurelia; Meisel, Alexander; Varga, Zsuzsanna; Fink, Daniel; Imesch, Patrick

2014-01-01

The G protein-coupled estrogen receptor (GPER) is a novel estrogen receptor that mediates proliferative effects induced by estrogen but also by tamoxifen. The aim of our study was to analyze the frequency of GPER in a large collective of primary invasive breast carcinomas, with special emphasis on the subcellular expression and to evaluate the association with clinicopathological parameters and patient overall survival. The tissue microarrays from formalin-fixed, paraffin embedded samples of primary invasive breast carcinomas (n = 981) were analyzed for GPER expression using immunohistochemistry. Expression data were compared to the clinicopathological parameters and overall survival. GPER localization was also analyzed in two immortalized breast cancer cell lines T47D and MCF7 by confocal immunofluorescence microscopy. A predominantly cytoplasmic GPER expression was found in 189 carcinomas (19.3%), whereas a predominantly nuclear expression was observed in 529 cases (53.9%). A simultaneous comparable positive expression of both patterns was found in 32 of 981 cases (3.2%), and negative staining was detected in 295 cases (30%). Confocal microscopy confirmed the occurrence of cytoplasmic and nuclear GPER expression in T47D and MCF7. Cytoplasmic GPER expression was significantly associated with non-ductal histologic subtypes, low tumor stage, better histologic differentiation, as well as Luminal A and B subtypes. In contrast, nuclear GPER expression was significantly associated with poorly differentiated carcinomas and the triple-negative subtype. In univariate analysis, cytoplasmic GPER expression was associated with better overall survival (p = 0.012). Our data suggest that predominantly cytoplasmic and/or nuclear GPER expression are two distinct immunohistochemical patterns in breast carcinomas and may reflect different biological features, reason why these patterns should be clearly distinguished in histological evaluations. Prospective studies will be needed to assess whether the expression status of GPER in breast carcinomas should be routinely observed by clinicians, for instance, before implementing endocrine breast cancer treatment.

The G Protein-Coupled Estrogen Receptor (GPER) Is Expressed in Two Different Subcellular Localizations Reflecting Distinct Tumor Properties in Breast Cancer

PubMed Central

Samartzis, Eleftherios P.; Noske, Aurelia; Meisel, Alexander; Varga, Zsuzsanna; Fink, Daniel; Imesch, Patrick

2014-01-01

Introduction The G protein-coupled estrogen receptor (GPER) is a novel estrogen receptor that mediates proliferative effects induced by estrogen but also by tamoxifen. The aim of our study was to analyze the frequency of GPER in a large collective of primary invasive breast carcinomas, with special emphasis on the subcellular expression and to evaluate the association with clinicopathological parameters and patient overall survival. Methods The tissue microarrays from formalin-fixed, paraffin embedded samples of primary invasive breast carcinomas (n = 981) were analyzed for GPER expression using immunohistochemistry. Expression data were compared to the clinicopathological parameters and overall survival. GPER localization was also analyzed in two immortalized breast cancer cell lines T47D and MCF7 by confocal immunofluorescence microscopy. Results A predominantly cytoplasmic GPER expression was found in 189 carcinomas (19.3%), whereas a predominantly nuclear expression was observed in 529 cases (53.9%). A simultaneous comparable positive expression of both patterns was found in 32 of 981 cases (3.2%), and negative staining was detected in 295 cases (30%). Confocal microscopy confirmed the occurrence of cytoplasmic and nuclear GPER expression in T47D and MCF7. Cytoplasmic GPER expression was significantly associated with non-ductal histologic subtypes, low tumor stage, better histologic differentiation, as well as Luminal A and B subtypes. In contrast, nuclear GPER expression was significantly associated with poorly differentiated carcinomas and the triple-negative subtype. In univariate analysis, cytoplasmic GPER expression was associated with better overall survival (p = 0.012). Conclusion Our data suggest that predominantly cytoplasmic and/or nuclear GPER expression are two distinct immunohistochemical patterns in breast carcinomas and may reflect different biological features, reason why these patterns should be clearly distinguished in histological evaluations. Prospective studies will be needed to assess whether the expression status of GPER in breast carcinomas should be routinely observed by clinicians, for instance, before implementing endocrine breast cancer treatment. PMID:24421881

Constraining the physical properties of compositionally distinctive surfaces on Mars from overlapping THEMIS observations

NASA Astrophysics Data System (ADS)

Ahern, A.; Rogers, D.

2017-12-01

Better constraints on the physical properties (e.g. grain size, rock abundance, cohesion, porosity and amount of induration) of Martian surface materials can lead to greater understanding of outcrop origin (e.g. via sedimentary, effusive volcanic, pyroclastic processes). Many outcrop surfaces on Mars likely contain near-surface (<3 cm) vertical heterogeneity in physical properties due to thin sediment cover, induration, and physical weathering, that can obscure measurement of the bulk thermal conductivity of the outcrop materials just below. Fortunately, vertical heterogeneity within near-surface materials can result in unique, and possibly predictable, diurnal and seasonal temperature patterns. The KRC thermal model has been utilized in a number of previous studies to predict thermal inertia of surface materials on Mars. Here we use KRC to model surface temperatures from overlapping Mars Odyssey THEMIS surface temperature observations that span multiple seasons and local times, in order to constrain both the nature of vertical heterogeneity and the underlying outcrop thermal inertia for various spectrally distinctive outcrops on Mars. We utilize spectral observations from TES and CRISM to constrain the particle size of the uppermost surface. For this presentation, we will focus specifically on chloride-bearing units in Terra Sirenum and Meridiani Planum, as well as mafic and feldspathic bedrock locations with distinct spectral properties, yet uncertain origins, in Noachis Terra and Nili Fossae. We find that many of these surfaces exhibit variations in apparent thermal inertia with season and local time that are consistent with low thermal inertia materials overlying higher thermal inertia substrates. Work is ongoing to compare surface temperature measurements with modeled two-layer scenarios in order to constrain the top layer thickness and bottom layer thermal inertia. The information will be used to better interpret the origins of these distinctive outcrops.

Measures for brain connectivity analysis: nodes centrality and their invariant patterns

NASA Astrophysics Data System (ADS)

da Silva, Laysa Mayra Uchôa; Baltazar, Carlos Arruda; Silva, Camila Aquemi; Ribeiro, Mauricio Watanabe; de Aratanha, Maria Adelia Albano; Deolindo, Camila Sardeto; Rodrigues, Abner Cardoso; Machado, Birajara Soares

2017-07-01

The high dynamical complexity of the brain is related to its small-world topology, which enable both segregated and integrated information processing capabilities. Several measures of connectivity estimation have already been employed to characterize functional brain networks from multivariate electrophysiological data. However, understanding the properties of each measure that lead to a better description of the real topology and capture the complex phenomena present in the brain remains challenging. In this work we compared four nonlinear connectivity measures and show that each method characterizes distinct features of brain interactions. The results suggest an invariance of global network parameters from different behavioral states and that more complete description may be reached considering local features, independently of the connectivity measure employed. Our findings also point to future perspectives in connectivity studies that combine distinct and complementary dependence measures in assembling higher dimensions manifolds.

Category representations in the brain are both discretely localized and widely distributed.

PubMed

Shehzad, Zarrar; McCarthy, Gregory

2018-06-01

Whether category information is discretely localized or represented widely in the brain remains a contentious issue. Initial functional MRI studies supported the localizationist perspective that category information is represented in discrete brain regions. More recent fMRI studies using machine learning pattern classification techniques provide evidence for widespread distributed representations. However, these latter studies have not typically accounted for shared information. Here, we find strong support for distributed representations when brain regions are considered separately. However, localized representations are revealed by using analytical methods that separate unique from shared information among brain regions. The distributed nature of shared information and the localized nature of unique information suggest that brain connectivity may encourage spreading of information but category-specific computations are carried out in distinct domain-specific regions. NEW & NOTEWORTHY Whether visual category information is localized in unique domain-specific brain regions or distributed in many domain-general brain regions is hotly contested. We resolve this debate by using multivariate analyses to parse functional MRI signals from different brain regions into unique and shared variance. Our findings support elements of both models and show information is initially localized and then shared among other regions leading to distributed representations being observed.

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.

Spin-dependent electron scattering at graphene edges on Ni(111).

PubMed

Garcia-Lekue, A; Balashov, T; Olle, M; Ceballos, G; Arnau, A; Gambardella, P; Sanchez-Portal, D; Mugarza, A

2014-02-14

We investigate the scattering of surface electrons by the edges of graphene islands grown on Ni(111). By combining local tunneling spectroscopy and ab initio electronic structure calculations we find that the hybridization between graphene and Ni states results in strongly reflecting graphene edges. Quantum interference patterns formed around the islands reveal a spin-dependent scattering of the Shockley bands of Ni, which we attribute to their distinct coupling to bulk states. Moreover, we find a strong dependence of the scattering amplitude on the atomic structure of the edges, depending on the orbital character and energy of the surface states.

Inverse halftoning via robust nonlinear filtering

NASA Astrophysics Data System (ADS)

Shen, Mei-Yin; Kuo, C.-C. Jay

1999-10-01

A new blind inverse halftoning algorithm based on a nonlinear filtering technique of low computational complexity and low memory requirement is proposed in this research. It is called blind since we do not require the knowledge of the halftone kernel. The proposed scheme performs nonlinear filtering in conjunction with edge enhancement to improve the quality of an inverse halftoned image. Distinct features of the proposed approach include: efficiently smoothing halftone patterns in large homogeneous areas, additional edge enhancement capability to recover the edge quality and an excellent PSNR performance with only local integer operations and a small memory buffer.

Spatially restricted electrical activation of retinal ganglion cells in the rabbit retina by hexapolar electrode return configuration

NASA Astrophysics Data System (ADS)

Habib, Amgad G.; Cameron, Morven A.; Suaning, Gregg J.; Lovell, Nigel H.; Morley, John W.

2013-06-01

Objective. Visual prostheses currently in development aim to restore some form of vision to patients suffering from diseases such as age-related macular degeneration and retinitis pigmentosa. Most rely on electrically stimulating inner retinal cells via electrodes implanted on or near the retina, resulting in percepts of light termed ‘phosphenes’. Activation of spatially distinct populations of cells in the retina is key for pattern vision to be produced. To achieve this, the electrical stimulation must be localized, activating cells only in the direct vicinity of the stimulating electrode(s). With this goal in mind, a hexagonal return (hexapolar) configuration has been proposed as an alternative to the traditional monopolar or bipolar return configurations for electrically stimulating the retina. This study investigated the efficacy of the hexapolar configuration in localizing the activation of retinal ganglion cells (RGCs), compared to a monopolar configuration. Approach. Patch-clamp electrophysiology was used to measure the activation thresholds of RGCs in whole-mount rabbit retina to monopolar and hexapolar electrical stimulation, applied subretinally. Main results. Hexapolar activation thresholds for RGCs located outside the hex guard were found to be significantly (>2 fold) higher than those located inside the area of tissue bounded by the hex guard. The hexapolar configuration localized the activation of RGCs more effectively than its monopolar counterpart. Furthermore, no difference in hexapolar thresholds or localization was observed when using cathodic-first versus anodic-first stimulation. Significance. The hexapolar configuration may provide an improved method for electrically stimulating spatially distinct populations of cells in retinal tissue.

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird.

PubMed

Tigano, Anna; Shultz, Allison J; Edwards, Scott V; Robertson, Gregory J; Friesen, Vicki L

2017-04-01

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick-billed murre ( Uria lomvia ) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick-billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome-wide markers mapped to a newly assembled thick-billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non-breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

Average sedimentary rock rare Earth element patterns and crustal evolution: Some observations and implications from the 3800 Ma ISUA supracrustal belt, West Greenland

NASA Technical Reports Server (NTRS)

Dymek, R. F.; Boak, J. L.; Gromet, L. P.

1983-01-01

Rare earth element (REE) data is given on a set of clastic metasediments from the 3800 Ma Isua Supracrustal belt, West Greenland. Each of two units from the same sedimentary sequence has a distinctive REE pattern, but the average of these rocks bears a very strong resemblance to the REE pattern for the North American Shale Composite (NASC), and departs considerably from previous estimates of REE patterns in Archaean sediments. The possibility that the source area for the Isua sediments resembled that of the NASC is regarded as highly unlikely. However, REE patterns like that in the NASC may be produced by sedimentary recycling of material yielding patterns such as are found at Isua. The results lead to the following tentative conclusions: (1) The REE patterns for Isua Seq. B MBG indicate the existence of crustal materials with fractionated REE and negative Eu anomalies at 3800 Ma, (2) The average Seq. B REE pattern resembles that of the North American Shale Composite (NASC), (3) If the Seq. B average is truly representative of its crustal sources, then this early crust could have been extensively differentiated. In this regard, a proper understanding of the NASC pattern, and its relationship to post-Archaean crustal REE reservoirs, is essential, (4) The Isua results may represent a local effect.

Live cell imaging of phosphoinositide dynamics during Legionella infection.

PubMed

Weber, Stephen; Hilbi, Hubert

2014-01-01

The "accidental" pathogen Legionella pneumophila replicates intracellularly in a distinct compartment, the Legionella-containing vacuole (LCV). To form this specific pathogen vacuole, the bacteria translocate via the Icm/Dot type IV secretion system approximately 300 different effector proteins into the host cell. Several of these secreted effectors anchor to the cytoplasmic face of the LCV membrane by binding to phosphoinositide (PI) lipids. L. pneumophila thus largely controls the localization of secreted bacterial effectors and the recruitment of host factors to the LCV through the modulation of the vacuole membrane PI pattern. The LCV PI pattern and its dynamics can be studied in real-time using fluorescently labeled protein probes stably produced by the soil amoeba Dictyostelium discoideum. In this chapter, we describe a protocol to (1) construct and handle amoeba model systems as a tool for observing PIs in live cell imaging, (2) capture rapid changes in membrane PI patterning during uptake events, and (3) observe the dynamics of LCV PIs over the course of a Legionella infection.

Learning place cells, grid cells and invariances with excitatory and inhibitory plasticity

PubMed Central

2018-01-01

Neurons in the hippocampus and adjacent brain areas show a large diversity in their tuning to location and head direction, and the underlying circuit mechanisms are not yet resolved. In particular, it is unclear why certain cell types are selective to one spatial variable, but invariant to another. For example, place cells are typically invariant to head direction. We propose that all observed spatial tuning patterns – in both their selectivity and their invariance – arise from the same mechanism: Excitatory and inhibitory synaptic plasticity driven by the spatial tuning statistics of synaptic inputs. Using simulations and a mathematical analysis, we show that combined excitatory and inhibitory plasticity can lead to localized, grid-like or invariant activity. Combinations of different input statistics along different spatial dimensions reproduce all major spatial tuning patterns observed in rodents. Our proposed model is robust to changes in parameters, develops patterns on behavioral timescales and makes distinctive experimental predictions. PMID:29465399

Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.

PubMed

Kietrys, Anna M; Velema, Willem A; Kool, Eric T

2017-11-29

Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultradeep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.

Multi-approaches analysis reveals local adaptation in the emmer wheat (Triticum dicoccoides) at macro- but not micro-geographical scale.

PubMed

Volis, Sergei; Ormanbekova, Danara; Yermekbayev, Kanat; Song, Minshu; Shulgina, Irina

2015-01-01

Detecting local adaptation and its spatial scale is one of the most important questions of evolutionary biology. However, recognition of the effect of local selection can be challenging when there is considerable environmental variation across the distance at the whole species range. We analyzed patterns of local adaptation in emmer wheat, Triticum dicoccoides, at two spatial scales, small (inter-population distance less than one km) and large (inter-population distance more than 50 km) using several approaches. Plants originating from four distinct habitats at two geographic scales (cold edge, arid edge and two topographically dissimilar core locations) were reciprocally transplanted and their success over time was measured as 1) lifetime fitness in a year of planting, and 2) population growth four years after planting. In addition, we analyzed molecular (SSR) and quantitative trait variation and calculated the QST/FST ratio. No home advantage was detected at the small spatial scale. At the large spatial scale, home advantage was detected for the core population and the cold edge population in the year of introduction via measuring life-time plant performance. However, superior performance of the arid edge population in its own environment was evident only after several generations via measuring experimental population growth rate through genotyping with SSRs allowing counting the number of plants and seeds per introduced genotype per site. These results highlight the importance of multi-generation surveys of population growth rate in local adaptation testing. Despite predominant self-fertilization of T. dicoccoides and the associated high degree of structuring of genetic variation, the results of the QST - FST comparison were in general agreement with the pattern of local adaptation at the two spatial scales detected by reciprocal transplanting.

Rainfall-triggered shallow landslides at catchment scale: Threshold mechanics-based modeling for abruptness and localization

NASA Astrophysics Data System (ADS)

von Ruette, J.; Lehmann, P.; Or, D.

2013-10-01

Rainfall-induced shallow landslides may occur abruptly without distinct precursors and could span a wide range of soil mass released during a triggering event. We present a rainfall-induced landslide-triggering model for steep catchments with surfaces represented as an assembly of hydrologically and mechanically interconnected soil columns. The abruptness of failure was captured by defining local strength thresholds for mechanical bonds linking soil and bedrock and adjacent columns, whereby a failure of a single bond may initiate a chain reaction of subsequent failures, culminating in local mass release (a landslide). The catchment-scale hydromechanical landslide-triggering model (CHLT) was applied to results from two event-based landslide inventories triggered by two rainfall events in 2002 and 2005 in two nearby catchments located in the Prealps in Switzerland. Rainfall radar data, surface elevation and vegetation maps, and a soil production model for soil depth distribution were used for hydromechanical modeling of failure patterns for the two rainfall events at spatial and temporal resolutions of 2.5 m and 0.02 h, respectively. The CHLT model enabled systematic evaluation of the effects of soil type, mechanical reinforcement (soil cohesion and lateral root strength), and initial soil water content on landslide characteristics. We compared various landslide metrics and spatial distribution of simulated landslides in subcatchments with observed inventory data. Model parameters were optimized for the short but intense rainfall event in 2002, and the calibrated model was then applied for the 2005 rainfall, yielding reasonable predictions of landslide events and volumes and statistically reproducing localized landslide patterns similar to inventory data. The model provides a means for identifying local hot spots and offers insights into the dynamics of locally resolved landslide hazards in mountainous regions.

Influence of hydrologic processes on reproduction of the introduced bivalve Potamocorbula amurensis in northern San Francisco Bay, California

USGS Publications Warehouse

Parchaso, F.; Thompson, J.K.

2002-01-01

Monthly censusing of reproductive condition of the Asian clam Potamocorbula amurensis at four sites in northern San Francisco Bay over a 9-yr period revealed year-to-year differences in local reproductive activity that are associated with patterns of hydrologic variability. Between 1989 and 1992, Northern California experienced a drought, whereas the period between 1993 and 1998 was marked by a mix of wet and dry years. We took advantage of the extreme year-to-year differences to examine reproductive responses to river inflow patterns. Populations of P. amurensis at the upstream sites in Suisun Bay and Carquinez Strait were more reproductively active during wet years than dry years. Conversely, at the downstream site in San Pablo Bay, the population was more reproductively active during dry years than wet years. We suggest that the different reproductive patterns observed reflect the clam's response to different sources of food. During wet years, organic matter from the rivers augments food supplies in Suisun Bay. During dry years, when inflow into the San Francisco Bay Estuary from the rivers is reduced, water transported from the adjacent ocean into the estuary as far as San Pablo Bay provides a supplemental food supply for the local production. The populations take advantage of these spatially distinct food supplies by initiating and maintaining local reproductive activity. We conclude that the ability of P. amurensis to consume and use various types of food to regulate its reproductive activity is part of the reason for its success as an invasive species.

Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks

PubMed Central

Niño-García, Juan Pablo; Ruiz-González, Clara; del Giorgio, Paul A

2016-01-01

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum. PMID:26849312

Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks.

PubMed

Niño-García, Juan Pablo; Ruiz-González, Clara; Del Giorgio, Paul A

2016-07-01

Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

Ontogenetic anatomy of the distal vagina: relevance for local tumor spread and implications for cancer surgery.

PubMed

Höckel, Michael; Horn, Lars-Christian; Illig, Romana; Dornhöfer, Nadja; Fritsch, Helga

2011-08-01

We have suggested to base cancer surgery on ontogenetic anatomy and the compartment theory of tumor permeation in order to improve local tumor control and to lower treatment-related morbidity. Following the validation of this concept for the uterine cervix, proximal vagina and vulva, this study explores its applicability for the distal vagina. Serial transverse sections of female embryos and fetuses aged 8-17 weeks were assessed for the morphological changes in the region defined by the deep urogenital sinus-vaginal plate complex. Histopathological pattern analysis of local tumor spread was performed with carcinomas of the lower genital tract involving the distal vagina to test the compartment theory. Ontogenetically, the female urethra, urethrovaginal septum, distal vagina and rectovaginal septum represent a morphogenetic unit derived from the deep urogenital sinus-vaginal plate complex. Herein, the posterior urethra, the urethrovaginal septum and the distal vagina form a distinct subcompartment differentiated from the dorsal wall of the urogenital sinus. From 150 consecutive patients with distal vaginectomy as part of their surgical treatment 26 carcinomas of the lower genital tract had infiltrated the distal vagina. All 22 tumors involving the ventral wall invaded the urethra/periurethral tissue. Of the five carcinomas involving the dorsal wall none invaded the rectum/mesorectum. The pattern of local tumor permeation of lower genital tract cancer in the distal vagina can be consistently explained with ontogenetic anatomy and the compartment theory. Copyright © 2011 Elsevier Inc. All rights reserved.

Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells.

PubMed

Briggs, Erica M; Ha, Susan; Mita, Paolo; Brittingham, Gregory; Sciamanna, Ilaria; Spadafora, Corrado; Logan, Susan K

2018-01-01

Long Interspersed Nuclear Element-1 (LINE-1) is an autonomous retrotransposon that generates new genomic insertions through the retrotransposition of a RNA intermediate. Expression of LINE-1 is tightly repressed in most somatic tissues to prevent DNA damage and ensure genomic integrity. However, the reactivation of LINE-1 has been documented in cancer and the role of LINE-1 protein expression and retrotransposition has become of interest in the development, progression, and adaptation of many epithelial neoplasms, including prostate cancer. Here, we examined endogenous LINE-1 protein expression and localization in a panel of prostate cancer cells and observed a diverse range of LINE-1 expression patterns between cell lines. Subcellular localization of LINE-1 proteins, ORF1p and ORF2p, revealed distinct expression patterns. ORF1p, a nucleic acid chaperone that binds LINE-1 mRNA, was predominantly expressed in the cytoplasm, with minor localization in the nucleus. ORF2p, containing endonuclease and reverse transcriptase domains, exhibited punctate foci in the nucleus and also displayed co-localization with PCNA and γH2AX. Using a retrotransposition reporter assay, we found variations in LINE-1 retrotransposition between cell lines. Overall, our findings reveal new insight into the expression and retrotransposition of LINE-1 in prostate cancer. The prostate cancer cells we investigated provide a unique model for investigating endogenous LINE-1 activity and provide a functional model for studying LINE-1 mechanisms in prostate cancer.

Local Circuits of V1 Layer 4B Neurons Projecting to V2 Thick Stripes Define Distinct Cell Classes and Avoid Cytochrome Oxidase Blobs

PubMed Central

Yarch, Jeff; Federer, Frederick

2017-01-01

Decades of anatomical studies on the primate primary visual cortex (V1) have led to a detailed diagram of V1 intrinsic circuitry, but this diagram lacks information about the output targets of V1 cells. Understanding how V1 local processing relates to downstream processing requires identification of neuronal populations defined by their output targets. In primates, V1 layers (L)2/3 and 4B send segregated projections to distinct cytochrome oxidase (CO) stripes in area V2: neurons in CO blob columns project to thin stripes while neurons outside blob columns project to thick and pale stripes, suggesting functional specialization of V1-to-V2 CO streams. However, the conventional diagram of V1 shows all L4B neurons, regardless of their soma location in blob or interblob columns, as projecting selectively to CO blobs in L2/3, suggesting convergence of blob/interblob information in L2/3 blobs and, possibly, some V2 stripes. However, it is unclear whether all L4B projection neurons show similar local circuitries. Using viral-mediated circuit tracing, we have identified the local circuits of L4B neurons projecting to V2 thick stripes in macaque. Consistent with previous studies, we found the somata of this L4B subpopulation to reside predominantly outside blob columns; however, unlike previous descriptions of local L4B circuits, these cells consistently projected outside CO blob columns in all layers. Thus, the local circuits of these L4B output neurons, just like their extrinsic projections to V2, preserve CO streams. Moreover, the intra-V1 laminar patterns of axonal projections identify two distinct neuron classes within this L4B subpopulation, including a rare novel neuron type, suggestive of two functionally specialized output channels. SIGNIFICANCE STATEMENT Conventional diagrams of primate primary visual cortex (V1) depict neuronal connections within and between different V1 layers, but lack information about the cells' downstream targets. This information is critical to understanding how local processing in V1 relates to downstream processing. We have identified the local circuits of a population of cells in V1 layer (L)4B that project to area V2. These cells' local circuits differ from classical descriptions of L4B circuits in both the laminar and functional compartments targeted by their axons, and identify two neuron classes. Our results demonstrate that both local intra-V1 and extrinsic V1-to-V2 connections of L4B neurons preserve CO-stream segregation, suggesting that across-stream integration occurs downstream of V1, and that output targets dictate local V1 circuitry. PMID:28077720

Distinct localization of peripheral and central types of choline acetyltransferase in the rat cochlea.

PubMed

Kitanishi, Tsuyoshi; Aimi, Yoshinari; Kitano, Hiroya; Suzuki, Mikio; Kimura, Hiroshi; Saito, Atsushi; Shimizu, Takeshi; Tooyama, Ikuo

2013-10-30

We previously discovered a splice variant of choline acetyltransferase (ChAT) mRNA, and designated the variant protein pChAT because of its preferential expression in peripheral neuronal structures. In this study, we examined the immunohistochemical localization of pChAT in rat cochlea and compared the distribution pattern to those of common ChAT (cChAT) and acetylcholinesterase. Some neuronal cell bodies and fibers in the spiral ganglia showed immunoreactivity for pChAT, predominantly the small spiral ganglion cells, indicating outer hair cell type II neurons. In contrast, cChAT- and acetylcholinesterase-positive structures were localized to fibers and not apparent in ganglion cells. After ablation of the cochlear nuclei, many pChAT-positive cochlear nerve fibers became clearly visible, whereas fibers immunopositive for cChAT and acetylcholine esterase disappeared. These results suggested that pChAT and cChAT are localized in different systems of the rat cochlea; pChAT in the afferent and cChAT in the efferent structures.

Distinct Localization of Peripheral and Central Types of Choline Acetyltransferase in the Rat Cochlea

PubMed Central

Kitanishi, Tsuyoshi; Aimi, Yoshinari; Kitano, Hiroya; Suzuki, Mikio; Kimura, Hiroshi; Saito, Atsushi; Shimizu, Takeshi; Tooyama, Ikuo

2013-01-01

We previously discovered a splice variant of choline acetyltransferase (ChAT) mRNA, and designated the variant protein pChAT because of its preferential expression in peripheral neuronal structures. In this study, we examined the immunohistochemical localization of pChAT in rat cochlea and compared the distribution pattern to those of common ChAT (cChAT) and acetylcholinesterase. Some neuronal cell bodies and fibers in the spiral ganglia showed immunoreactivity for pChAT, predominantly the small spiral ganglion cells, indicating outer hair cell type II neurons. In contrast, cChAT- and acetylcholinesterase-positive structures were localized to fibers and not apparent in ganglion cells. After ablation of the cochlear nuclei, many pChAT-positive cochlear nerve fibers became clearly visible, whereas fibers immunopositive for cChAT and acetylcholine esterase disappeared. These results suggested that pChAT and cChAT are localized in different systems of the rat cochlea; pChAT in the afferent and cChAT in the efferent structures. PMID:24194628

Lung respiratory rhythm and pattern generation in the bullfrog: role of neurokinin-1 and mu-opioid receptors.

PubMed

Davies, B L; Brundage, C M; Harris, M B; Taylor, B E

2009-07-01

Location of the lung respiratory rhythm generator (RRG) in the bullfrog brainstem was investigated by examining neurokinin-1 and mu-opioid receptor (NK1R, muOR) colocalization by immunohistochemistry and characterizing the role of these receptors in lung rhythm and episodic pattern generation. NK1R and muOR occurred in brainstems from all developmental stages. In juvenile bullfrogs a distinct area of colocalization was coincident with high-intensity fluorescent labeling of muOR; high-intensity labeling of muOR was not distinctly and consistently localized in tadpole brainstems. NK1R labeling intensity did not change with development. Similarity in colocalization is consistent with similarity in responses to substance P (SP, NK1R agonist) and DAMGO (muOR agonist) when bath applied to bullfrog brainstems of different developmental stages. In early stage tadpoles and juvenile bullfrogs, SP increased and DAMGO decreased lung burst frequency. In juvenile bullfrogs, SP increased lung burst frequency, episode frequency, but decreased number of lung bursts per episode and lung burst duration. In contrast, DAMGO decreased lung burst frequency and burst cycle frequency, episode frequency, and number of lung bursts per episode but increased all other lung burst parameters. Based on these results, we hypothesize that NK1R and muOR colocalization together with a metamorphosis-related increase in muOR intensity marks the location of the lung RRG but not necessarily the lung episodic pattern generator.

Differential distribution of the sodium‐activated potassium channels slick and slack in mouse brain

PubMed Central

Knaus, Hans‐Günther; Schwarzer, Christoph

2015-01-01

ABSTRACT The sodium‐activated potassium channels Slick (Slo2.1, KCNT2) and Slack (Slo2.2, KCNT1) are high‐conductance potassium channels of the Slo family. In neurons, Slick and Slack channels are involved in the generation of slow afterhyperpolarization, in the regulation of firing patterns, and in setting and stabilizing the resting membrane potential. The distribution and subcellular localization of Slick and Slack channels in the mouse brain have not yet been established in detail. The present study addresses this issue through in situ hybridization and immunohistochemistry. Both channels were widely distributed and exhibited distinct distribution patterns. However, in some brain regions, their expression overlapped. Intense Slick channel immunoreactivity was observed in processes, varicosities, and neuronal cell bodies of the olfactory bulb, granular zones of cortical regions, hippocampus, amygdala, lateral septal nuclei, certain hypothalamic and midbrain nuclei, and several regions of the brainstem. The Slack channel showed primarily a diffuse immunostaining pattern, and labeling of cell somata and processes was observed only occasionally. The highest Slack channel expression was detected in the olfactory bulb, lateral septal nuclei, basal ganglia, and distinct areas of the midbrain, brainstem, and cerebellar cortex. In addition, comparing our data obtained from mouse brain with a previously published study on rat brain revealed some differences in the expression and distribution of Slick and Slack channels in these species. J. Comp. Neurol. 524:2093–2116, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:26587966

High-resolution isotopic evidence of specialised cattle herding in the European Neolithic

PubMed Central

Doppler, Thomas; Heyd, Volker; Knipper, Corina; Kuhn, Thomas; Lehmann, Moritz F.; Pike, Alistair W. G.; Schibler, Jörg

2017-01-01

Reconstructing stock herding strategies and land use is key to comprehending past human social organization and economy. We present laser-ablation strontium and carbon isotope data from 25 cattle (Bos taurus) to reconstruct mobility and infer herding management at the Swiss lakeside settlement of Arbon Bleiche 3, occupied for only 15 years (3384–3370 BC). Our results reveal three distinct isotopic patterns that likely reflect different herding strategies: 1) localized cattle herding, 2) seasonal movement, and 3) herding away from the site year-round. Different strategies of herding are not uniformly represented in various areas of the settlement, which indicates specialist modes of cattle management. The pressure on local fodder capacities and the need for alternative herding regimes must have involved diverse access to grazing resources. Consequently, the increasing importance of cattle in the local landscape was likely to have contributed to the progress of socio-economic differentiation in early agricultural societies in Europe. PMID:28746367

A cloning and expression analysis of pregnancy-associated glycoproteins expressed in trophoblasts of the white-tail deer placenta.

PubMed

Brandt, Gretchen A; Parks, Tina E; Killian, Gary; Ealy, Alan D; Green, Jonathan A

2007-11-01

The pregnancy-associated glycoproteins (PAGs) are placental proteins that have been cloned from swine, sheep, goats, and cattle, but never from animals within the Cervidae family. The goal of this work was to characterize PAGs in white-tailed deer. Placenta and uterine tissues were collected from pregnant does at days 85 and 90 of pregnancy. RNA from cotyledons was used to amplify deer PAGs by RT-PCR. Ten distinct cDNAs were cloned and sequenced. Some normally conserved amino acids comprising the catalytic site were found to be altered in deer PAGs 4, 5, and 8; another PAG, (PAG-9) was a splice variant that lacked exon 7. In each case, these mutations would likely preclude proteolytic activity for these proteins. A phylogenetic analysis revealed that most of the deer PAGs fell within the ancient PAG grouping. The remainder fell within the more modern (BNC-specific) PAG group. Western blotting was performed with anti-PAG antibodies and this analysis revealed that deer PAGs comprise a heterogeneous group based on different antigenicities and electrophoretic mobilities. Immunohistochemistry and in situ hybridization revealed some unique localization patterns of PAGs in the deer placentome compared to those in other ruminants. Most notably, deer PAGs 4 and 5, which according to the phylogeny, are "ancient PAGs," were expected to be present in all trophoblasts; instead, they were localized to the BNC. Although many of the PAGs identified here are very similar to those in Bovidae, some are clearly distinct in their expression pattern and probably possess functional roles unique to cervid reproduction. (c) 2007 Wiley-Liss, Inc.

Recanalization and flow regulate venous thrombus resolution and Matrix metalloproteinases expression in vivo

PubMed Central

Chabasse, Christine; Siefert, Suzanne A.; Chaudry, Mohammed; Hoofnagle, Mark H.; Lal, Brajesh K.; Sarkar, Rajabrata

2016-01-01

Objective We examined the role of thrombus recanalization and ongoing blood flow in the process of thrombus resolution by comparing two murine in vivo models of deep venous thrombosis. Design of study In CD1 mice, we performed surgical inferior vena cava (IVC) ligation (stasis thrombosis), stenosis (thrombosis with recanalization) or sham procedure. We analyzed thrombus weight over time as a measure of thrombus resolution, and quantified the mRNA and protein levels of Membrane-Type Matrix Metalloproteinases (MT-MMPs) as well as effectors of the plasmin complex at day 4, 8 and 12 post-surgery. Results Despite similar initial thrombus size, the presence of ongoing blood flow (stenosis model) was associated with a 45.91% subsequent improvement in thrombus resolution at day 8, and 12.57% at day 12, as compared with stasis thrombosis (ligation model). Immunoblot and real-time PCR demonstrated a difference in MMP-2 and MMP-9 activity at day 8 between the two models (P=.03 and P=.006 respectively), as well as a difference in MT2-MMP gene expression at day 8 (P=.044) and day 12 (P=0.03) and MT1-MMP protein expression at day 4 (P=.021). Histological analyses revealed distinct areas of recanalization in the thrombi of the stenosis model compared to the ligation model, as well as the recruitment of inflammatory cells, especially macrophages, and a focal pattern of localized expression of MT1-MMP and MT3-MMP proteins surrounding the areas of recanalization in the stenosis model. Conclusions Recanalization and ongoing blood flow accelerate deep venous thrombus resolution in vivo, and are associated with distinct patterns of MT1- and MT3-MMP expression and macrophages localization in areas of intra-thrombus recanalization. PMID:26993683

Recanalization and flow regulate venous thrombus resolution and matrix metalloproteinase expression in vivo.

PubMed

Chabasse, Christine; Siefert, Suzanne A; Chaudry, Mohammed; Hoofnagle, Mark H; Lal, Brajesh K; Sarkar, Rajabrata

2015-01-01

We examined the role of thrombus recanalization and ongoing blood flow in the process of thrombus resolution by comparing two murine in vivo models of deep venous thrombosis. In CD1 mice, we performed surgical inferior vena cava ligation (stasis thrombosis), stenosis (thrombosis with recanalization), or sham procedure. We analyzed thrombus weight over time as a measure of thrombus resolution and quantified the messenger RNA and protein levels of membrane-type matrix metalloproteinases (MT-MMPs) as well as effectors of the plasmin complex at days 4, 8, and 12 after surgery. Despite similar initial thrombus size, the presence of ongoing blood flow (stenosis model) was associated with a 45.91% subsequent improvement in thrombus resolution at day 8 and 12.57% at day 12 compared with stasis thrombosis (ligation model). Immunoblot and real-time polymerase chain reaction analysis demonstrated a difference in MMP-2 and MMP-9 activity at day 8 between the two models (P = .03 and P = .006, respectively) as well as a difference in MT2-MMP gene expression at day 8 (P = .044) and day 12 (P = .03) and MT1-MMP protein expression at day 4 (P = .021). Histologic analyses revealed distinct areas of recanalization in the thrombi of the stenosis model compared with the ligation model as well as the recruitment of inflammatory cells, especially macrophages, and a focal pattern of localized expression of MT1-MMP and MT3-MMP proteins surrounding the areas of recanalization in the stenosis model. Recanalization and ongoing blood flow accelerate deep venous thrombus resolution in vivo and are associated with distinct patterns of MT1-MMP and MT3-MMP expression and macrophage localization in areas of intrathrombus recanalization. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

DRINKING PATTERNS AND DSM-IV ALCOHOL USE DISORDERS’ CRITERIA IN ARGENTINEAN EMERGENCY DEPARTMENT PATIENTS

PubMed Central

Cremonte, Mariana; Cherpitel, Cheryl J.; Borges, Guilherme; Peltzer, Raquel I.; Santángelo, Pablo R.

2011-01-01

Background Previous studies have shown cultural variations in normative drinking and furthermore, in the quantity and frequency of drinking related to alcohol use disorders. Aim The main goal of this study is to characterize alcohol drinking patterns in Argentinean Emergency Department patients, and secondly, to explore the association between those drinking patterns and DSM-IV alcohol use disorders. Method Data were collected from a probability sample of patients admitted to the Emergency Department of a large public hospital in Mar del Plata, Argentina. Data analyzed here pertain to those who reported consuming at least one drink during the last twelve months (n=529). A factor analysis of multiple correspondences and a hierarchic classification were performed. For the factor analysis, usual quantity and frequency of drinking (for the last 12 months) were considered active variables; number of DSM-IV dependence criteria met, positive or negative diagnostic status for abuse, positive or negative diagnostic status for dependence (both for the last 12 months), and socio-demographic characteristics (age, gender and economic level) were considered illustrative variables. Results The first five factorial axes were retained, accounting for 88% of the total variance. Hierarchic classification resulted in six distinctive classes of drinking patterns. Two patterns were associated with a positive diagnosis of abuse and dependence, respectively. One, drinking between 4 and 6 drinks per occasion mostly on a weekly basis, was associated with a diagnosis of abuse; this pattern was also associated with meeting one or two dependence criteria (dependence orphans). The other, drinking 7 or more drinks per occasion, was associated with a diagnosis of dependence, and also with a diagnostic orphan condition. This class, composed primarily of males, was not characterized by any particular frequency of drinking. The other four drinking patterns were not associated with a positive diagnosis of an alcohol use disorder. Two of them were characterized by drinking low quantities with a low frequency (either monthly or yearly). Participants in both of these classes tended to be female. The other two patterns were characterized by drinking less than 3 drinks per occasion, either daily or weekly: the former associated with being older than 35 years, and the later with no distinctive socio-demographic characteristics. Conclusions Results demonstrated six distinct drinking patterns, two of them related to a positive diagnosis of an alcohol use disorder. Our findings support previous research indicating that dependence orphans share some characteristics with abuse and dependence cases. Given the lack of similar studies in the region, these findings, although descriptive, enrich the knowledge of alcohol use disorders in the regional context. Furthermore, they may contribute to the development of local drinking guidelines and prevention strategies. PMID:22984352

Local and global inhibition in bilingual word production: fMRI evidence from Chinese-English bilinguals

PubMed Central

Guo, Taomei; Liu, Hongyan; Misra, Maya; Kroll, Judith F.

2011-01-01

The current study examined the neural correlates associated with local and global inhibitory processes used by bilinguals to resolve interference between competing responses. Two groups of participants completed both blocked and mixed picture naming tasks while undergoing functional magnetic resonance imaging (fMRI). One group first named a set of pictures in L1, and then named the same pictures in L2. The other group first named pictures in L2, and then in L1. After the blocked naming tasks, both groups performed a mixed language naming task (i.e., naming pictures in either language according to a cue). The comparison between the blocked and mixed naming tasks, collapsed across groups, was defined as the local switching effect, while the comparison between blocked naming in each language was defined as the global switching effect. Distinct patterns of neural activation were found for local inhibition as compared to global inhibition in bilingual word production. Specifically, the results suggest that the dorsal anterior cingulate cortex (ACC) and the supplementary motor area (SMA) play important roles in local inhibition, while the dorsal left frontal gyrus and parietal cortex are important for global inhibition. PMID:21440072

Pneumothorax detection in chest radiographs using local and global texture signatures

NASA Astrophysics Data System (ADS)

Geva, Ofer; Zimmerman-Moreno, Gali; Lieberman, Sivan; Konen, Eli; Greenspan, Hayit

2015-03-01

A novel framework for automatic detection of pneumothorax abnormality in chest radiographs is presented. The suggested method is based on a texture analysis approach combined with supervised learning techniques. The proposed framework consists of two main steps: at first, a texture analysis process is performed for detection of local abnormalities. Labeled image patches are extracted in the texture analysis procedure following which local analysis values are incorporated into a novel global image representation. The global representation is used for training and detection of the abnormality at the image level. The presented global representation is designed based on the distinctive shape of the lung, taking into account the characteristics of typical pneumothorax abnormalities. A supervised learning process was performed on both the local and global data, leading to trained detection system. The system was tested on a dataset of 108 upright chest radiographs. Several state of the art texture feature sets were experimented with (Local Binary Patterns, Maximum Response filters). The optimal configuration yielded sensitivity of 81% with specificity of 87%. The results of the evaluation are promising, establishing the current framework as a basis for additional improvements and extensions.

Marine Ostracod Provinciality in the Late Ordovician of Palaeocontinental Laurentia and Its Environmental and Geographical Expression

PubMed Central

Mohibullah, Mohibullah; Williams, Mark; Vandenbroucke, Thijs R. A.; Sabbe, Koen; Zalasiewicz, Jan A.

2012-01-01

Background We examine the environmental, climatic and geographical controls on tropical ostracod distribution in the marine Ordovician of North America. Methodology/Principal Findings Analysis of the inter-regional distribution patterns of Ordovician Laurentian ostracods, focussing particularly on the diverse Late Ordovician Sandbian (ca 461 to 456 Ma) faunas, demonstrates strong endemicity at the species-level. Local endemism is very pronounced, ranging from 25% (e.g. Foxe basin) to 75% (e.g. Michigan basin) in each basin, a pattern that is also reflected in other benthic faunas such as brachiopods. Multivariate (ordination) analyses of the ostracod faunas allow demarcation of a Midcontinent Province and a southern Marginal Province in Laurentia. While these are most clearly differentiated at the stratigraphical level of the bicornis graptolite biozone, analyses of the entire dataset suggest that these provinces remain distinct throughout the Sandbian interval. Differences in species composition between the provinces appear to have been controlled by changes in physical parameters (e.g. temperature and salinity) related to water depth and latitude and a possible regional geographic barrier, and these differences persist into the Katian and possibly the Hirnantian. Local environmental parameters, perhaps operating at the microhabitat scale, may have been significant in driving local speciation events from ancestor species in each region. Conclusions/Significance Our work establishes a refined methodology for assessing marine benthic arthropod micro-benthos provinciality for the Early Palaeozoic. PMID:22900000

Wave Propagation and Localization via Quasi-Normal Modes and Transmission Eigenchannels

NASA Astrophysics Data System (ADS)

Wang, Jing; Shi, Zhou; Davy, Matthieu; Genack, Azriel Z.

2013-10-01

Field transmission coefficients for microwave radiation between arrays of points on the incident and output surfaces of random samples are analyzed to yield the underlying quasi-normal modes and transmission eigenchannels of each realization of the sample. The linewidths, central frequencies, and transmitted speckle patterns associated with each of the modes of the medium are found. Modal speckle patterns are found to be strongly correlated leading to destructive interference between modes. This explains distinctive features of transmission spectra and pulsed transmission. An alternate description of wave transport is obtained from the eigenchannels and eigenvalues of the transmission matrix. The maximum transmission eigenvalue, τ1 is near unity for diffusive waves even in turbid samples. For localized waves, τ1 is nearly equal to the dimensionless conductance, which is the sum of all transmission eigenvalues, g = Στn. The spacings between the ensemble averages of successive values of lnτn are constant and equal to the inverse of the bare conductance in accord with predictions by Dorokhov. The effective number of transmission eigenvalues Neff determines the contrast between the peak and background of radiation focused for maximum peak intensity. The connection between the mode and channel approaches is discussed.

Wave Propagation and Localization via Quasi-Normal Modes and Transmission Eigenchannels

NASA Astrophysics Data System (ADS)

Wang, Jing; Shi, Zhou; Davy, Matthieu; Genack, Azriel Z.

Field transmission coefficients for microwave radiation between arrays of points on the incident and output surfaces of random samples are analyzed to yield the underlying quasi-normal modes and transmission eigenchannels of each realization of the sample. The linewidths, central frequencies, and transmitted speckle patterns associated with each of the modes of the medium are found. Modal speckle patterns are found to be strongly correlated leading to destructive interference between modes. This explains distinctive features of transmission spectra and pulsed transmission. An alternate description of wave transport is obtained from the eigenchannels and eigenvalues of the transmission matrix. The maximum transmission eigenvalue, τ1 is near unity for diffusive waves even in turbid samples. For localized waves, τ1 is nearly equal to the dimensionless conductance, which is the sum of all transmission eigenvalues, g = Στn. The spacings between the ensemble averages of successive values of lnτn are constant and equal to the inverse of the bare conductance in accord with predictions by Dorokhov. The effective number of transmission eigenvalues Neff determines the contrast between the peak and background of radiation focused for maximum peak intensity. The connection between the mode and channel approaches is discussed.

Numerical Study of Winter Diurnal Convection Over the City of Krasnoyarsk: Effects of Non-freezing River, Undulating Fog and Steam Devils

NASA Astrophysics Data System (ADS)

Hrebtov, M.; Hanjalić, K.

2017-06-01

We performed a numerical simulation of penetrative convection of an inversion-topped weakly stratified atmospheric boundary layer over urban terrain with a strong localized source of heat and moisture. With some simplifications, the case mimics the real environment of the Krasnoyarsk region in Russia where the non-freezing river Yenisei acts as a thermal and humidity source during winter, generating an undulating fog pattern along the river accompanied with scattered `steam devils'. An idealized full diurnal cycle was simulated using an unsteady Reynolds-averaged Navier-Stokes (RANS) three-equation algebraic flux model and the novel buoyancy-accounting functions for treating the ground boundary conditions. The results show a significant effect of the river on the net temperature and moisture distribution. The localized heat and moisture source leads to strong horizontal convection and marked non-uniformity of humidity concentration in the air. An interplay of several distinct large-scale vortex systems leads to a wavy pattern of moisture plumes over the river. The simulations deal with rare natural phenomena and show the capability of the RANS turbulence closure to capture the main features of flow and scalar fields on an affordable, relatively coarse, computational grid.

Functional connectivity changes detected with magnetoencephalography after mild traumatic brain injury

PubMed Central

Dimitriadis, Stavros I.; Zouridakis, George; Rezaie, Roozbeh; Babajani-Feremi, Abbas; Papanicolaou, Andrew C.

2015-01-01

Mild traumatic brain injury (mTBI) may affect normal cognition and behavior by disrupting the functional connectivity networks that mediate efficient communication among brain regions. In this study, we analyzed brain connectivity profiles from resting state Magnetoencephalographic (MEG) recordings obtained from 31 mTBI patients and 55 normal controls. We used phase-locking value estimates to compute functional connectivity graphs to quantify frequency-specific couplings between sensors at various frequency bands. Overall, normal controls showed a dense network of strong local connections and a limited number of long-range connections that accounted for approximately 20% of all connections, whereas mTBI patients showed networks characterized by weak local connections and strong long-range connections that accounted for more than 60% of all connections. Comparison of the two distinct general patterns at different frequencies using a tensor representation for the connectivity graphs and tensor subspace analysis for optimal feature extraction showed that mTBI patients could be separated from normal controls with 100% classification accuracy in the alpha band. These encouraging findings support the hypothesis that MEG-based functional connectivity patterns may be used as biomarkers that can provide more accurate diagnoses, help guide treatment, and monitor effectiveness of intervention in mTBI. PMID:26640764

Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

PubMed Central

Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

1998-01-01

All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

Differential timing of granule cell production during cerebellum development underlies generation of the foliation pattern.

PubMed

Legué, Emilie; Gottshall, Jackie L; Jaumouillé, Edouard; Roselló-Díez, Alberto; Shi, Wei; Barraza, Luis Humberto; Washington, Senna; Grant, Rachel L; Joyner, Alexandra L

2016-09-08

The mouse cerebellum (Cb) has a remarkably complex foliated three-dimensional (3D) structure, but a stereotypical cytoarchitecture and local circuitry. Little is known of the cellular behaviors and genes that function during development to determine the foliation pattern. In the anteroposterior axis the mammalian cerebellum is divided by lobules with distinct sizes, and the foliation pattern differs along the mediolateral axis defining a medial vermis and two lateral hemispheres. In the vermis, lobules are further grouped into four anteroposterior zones (anterior, central, posterior and nodular zones) based on genetic criteria, and each has distinct lobules. Since each cerebellar afferent group projects to particular lobules and zones, it is critical to understand how the 3D structure of the Cb is acquired. During cerebellar development, the production of granule cells (gcs), the most numerous cell type in the brain, is required for foliation. We hypothesized that the timing of gc accumulation is different in the four vermal zones during development and contributes to the distinct lobule morphologies. In order to test this idea, we used genetic inducible fate mapping to quantify accumulation of gcs in each lobule during the first two postnatal weeks in mice. The timing of gc production was found to be particular to each lobule, and delayed in the central zone lobules relative to the other zones. Quantification of gc proliferation and differentiation at three time-points in lobules representing different zones, revealed the delay involves a later onset of maximum differentiation and prolonged proliferation of gc progenitors in the central zone. Similar experiments in Engrailed mutants (En1 (-/+) ;En2 (-/-) ), which have a smaller Cb and altered foliation pattern preferentially outside the central zone, showed that gc production, proliferation and differentiation are altered such that the differences between zones are attenuated compared to wild-type mice. Our results reveal that gc production is differentially regulated in each zone of the cerebellar vermis, and our mutant analysis indicates that the dynamics of gc production plays a role in determining the 3D structure of the Cb.

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change

USGS Publications Warehouse

Sork, Victoria L.; Davis, Frank W.; Westfall, Robert; Flint, Alan L.; Ikegami, Makihiko; Wang, Hongfang; Grivet, Delphine

2010-01-01

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata N??e, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions. ?? 2010 Blackwell Publishing Ltd.

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.

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change.

PubMed

Sork, Victoria L; Davis, Frank W; Westfall, Robert; Flint, Alan; Ikegami, Makihiko; Wang, Hongfang; Grivet, Delphine

2010-09-01

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions.

Distinct domains within the NITROGEN LIMITATION ADAPTATION protein mediate its subcellular localization and function in the nitrate-dependent phosphate homeostasis pathway

USDA-ARS?s Scientific Manuscript database

The NITROGEN LIMITATION ADAPTATION (NLA) protein is a RING-type E3 ubiquitin ligase that plays an essential role in the regulation of nitrogen and phosphate homeostasis. NLA is localized to two distinct subcellular sites, the plasma membrane and nucleus, and contains four distinct domains: i) a RING...

Recognition of distinctive patterns of gallium-67 distribution in sarcoidosis

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

Sulavik, S.B.; Spencer, R.P.; Weed, D.A.

1990-12-01

Assessment of gallium-67 ({sup 67}Ga) uptake in the salivary and lacrimal glands and intrathoracic lymph nodes was made in 605 consecutive patients including 65 with sarcoidosis. A distinctive intrathoracic lymph node {sup 67}Ga uptake pattern, resembling the Greek letter lambda, was observed only in sarcoidosis (72%). Symmetrical lacrimal gland and parotid gland {sup 67}Ga uptake (panda appearance) was noted in 79% of sarcoidosis patients. A simultaneous lambda and panda pattern (62%) or a panda appearance with radiographic bilateral, symmetrical, hilar lymphadenopathy (6%) was present only in sarcoidosis patients. The presence of either of these patterns was particularly prevalent in roentgenmore » Stages I (80%) or II (74%). We conclude that simultaneous (a) lambda and panda images, or (b) a panda image with bilateral symmetrical hilar lymphadenopathy on chest X-ray represent distinctive patterns which are highly specific for sarcoidosis, and may obviate the need for invasive diagnostic procedures.« less

Hydrochemical determination of source water contributions to Lake Lungo and Lake Ripasottile (central Italy)

USGS Publications Warehouse

Archer, Claire; Noble, Paula; Kreamer, David; Piscopo, Vincenzo; Petitta, Marco; Rosen, Michael R.; Poulson, Simon R.; Piovesan, Gianluca; Mensing, Scott

2017-01-01

Lake Lungo and Lake Ripasottile are two shallow (4-5 m) lakes located in the Rieti Basin, central Italy, that have been described previously as surface outcroppings of the groundwater table. In this work, the two lakes as well as springs and rivers that represent their potential source waters are characterized physio-chemically and isotopically, using a combination of environmental tracers. Temperature and pH were measured and water samples were analyzed for alkalinity, major ion concentration, and stable isotope (δ2H, δ18O, δ13C of dissolved inorganic carbon, and δ34S and δ18O of sulfate) composition. Chemical data were also investigated in terms of local meteorological data (air temperature, precipitation) to determine the sensitivity of lake parameters to changes in the surrounding environment. Groundwater represented by samples taken from Santa Susanna Spring was shown to be distinct with SO42- and Mg2+ content of 270 and 29 mg/L, respectively, and heavy sulfate isotopic composition(δ34S=15.2 ‰ and δ18O=10‰). Outflow from the Santa Susanna Spring enters Lake Ripasottile via a canal and both spring and lake water exhibits the same chemical distinctions and comparatively low seasonal variability. Major ion concentrations in Lake Lungo are similar to the Vicenna Riara Spring and are interpreted to represent the groundwater locally recharged within the plain. The δ13CDIC exhibit the same groupings as the other chemical parameters, providing supporting evidence of the source relationships. Lake Lungo exhibited exceptional ranges of δ13CDIC (±5 ‰) and δ2H, δ18O (±5 ‰ and ±7 ‰, respectively), attributed to sensitivity to seasonal changes. The hydrochemistry results, particularly major ion data, highlight how the two lakes, though geographically and morphologically similar, represent distinct hydrochemical facies. These data also show a different response in each lake to temperature and precipitation patterns in the basin that may be attributed to lake water retention time. The sensitivity of each lake to meteorological patterns can be used to understand the potential effects from long-term climate variability.

Development of coherent neuronal activity patterns in mammalian cortical networks: common principles and local hetereogeneity.

PubMed

Egorov, Alexei V; Draguhn, Andreas

2013-01-01

Many mammals are born in a very immature state and develop their rich repertoire of behavioral and cognitive functions postnatally. This development goes in parallel with changes in the anatomical and functional organization of cortical structures which are involved in most complex activities. The emerging spatiotemporal activity patterns in multi-neuronal cortical networks may indeed form a direct neuronal correlate of systemic functions like perception, sensorimotor integration, decision making or memory formation. During recent years, several studies--mostly in rodents--have shed light on the ontogenesis of such highly organized patterns of network activity. While each local network has its own peculiar properties, some general rules can be derived. We therefore review and compare data from the developing hippocampus, neocortex and--as an intermediate region--entorhinal cortex. All cortices seem to follow a characteristic sequence starting with uncorrelated activity in uncoupled single neurons where transient activity seems to have mostly trophic effects. In rodents, before and shortly after birth, cortical networks develop weakly coordinated multineuronal discharges which have been termed synchronous plateau assemblies (SPAs). While these patterns rely mostly on electrical coupling by gap junctions, the subsequent increase in number and maturation of chemical synapses leads to the generation of large-scale coherent discharges. These patterns have been termed giant depolarizing potentials (GDPs) for predominantly GABA-induced events or early network oscillations (ENOs) for mostly glutamatergic bursts, respectively. During the third to fourth postnatal week, cortical areas reach their final activity patterns with distinct network oscillations and highly specific neuronal discharge sequences which support adult behavior. While some of the mechanisms underlying maturation of network activity have been elucidated much work remains to be done in order to fully understand the rules governing transition from immature to mature patterns of network activity. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Spatiotemporal patterns of infant bronchiolitis in a Tennessee Medicaid population.

PubMed

Sloan, Chantel D; Gebretsadik, Tebeb; Wu, Pingsheng; Carroll, Kecia N; Mitchel, Edward F; Hartert, Tina V

2013-09-01

Respiratory syncytial virus (RSV) is a major cause of worldwide morbidity and mortality in infants, primarily through the induction of bronchiolitis. RSV epidemics are highly seasonal, occurring in the winter months in the northern hemisphere. Within the United States, RSV epidemic dynamics vary both spatially and temporally. This analysis employs a retrospective space–time scan statistic to locate spatiotemporal clustering of infant bronchiolitis in a very large Tennessee (TN) Medicaid cohort. We studied infants less than 6 months of age (N = 52,468 infants) who had an outpatient visit, emergency department visit, or hospitalization for bronchiolitis between 1995 and 2008. The scan statistic revealed distinctive and consistent patterns of deviation in epidemic timing. Eastern TN (Knoxville area) showed clustering in January and February, and Central TN (Nashville area) in November and December. This is likely due to local variation in geography-associated factors which should be taken into consideration in future modeling of RSV epidemics.

Geographic patterns of genetic variation and conservation consequences in three South American rodents.

PubMed

Miranda, Gustavo B; Andrades-Miranda, Jaqueline; Oliveira, Luiz F B; Langguth, Alfredo; Mattevi, Margarete S

2007-12-01

In this study, the geographic patterns of genetic variation of three rodent species belonging to the tribe Oryzomyini were investigated using the mitochondrial cytochrome b and nuclear IRBP genes in biomes that are undergoing degradation processes to a greater or lesser degree. The samples are from 25 collecting localities distributed throughout the Amazon, Cerrado, Atlantic Forest, and Pampa biomes. The results show that the three species have a population and geographic structure, besides being in demographic equilibrium. The phylogenetic analyses performed on Euryoryzomys russatus and Hylaeamys megacephalus showed these specimens grouped in three distinct clades forming geographic gradients (North-South direction in H. megacephalus). Intraspecific genetic divergence was higher in H. megacephalus (4.53%), followed by E. russatus (1.79%), and lowest in Sooretamys angouya (0.88%). The results obtained indicate that, necessarily, the management strategies to preserve genetic diversity should be different for each species, since each of them presented specific population parameters.

Topology of three-dimensional separated flows

NASA Technical Reports Server (NTRS)

Tobak, M.; Peake, D. J.

1981-01-01

Based on the hypothesis that patterns of skin-friction lines and external streamlines reflect the properties of continuous vector fields, topology rules define a small number of singular points (nodes, saddle points, and foci) that characterize the patterns on the surface and on particular projections of the flow (e.g., the crossflow plane). The restricted number of singular points and the rules that they obey are considered as an organizing principle whose finite number of elements can be combined in various ways to connect together the properties common to all steady three dimensional viscous flows. Introduction of a distinction between local and global properties of the flow resolves an ambiguity in the proper definition of a three dimensional separated flow. Adoption of the notions of topological structure, structural stability, and bifurcation provides a framework to describe how three dimensional separated flows originate and succeed each other as the relevant parameters of the problem are varied.

The Remote Sensing of Mineral Aerosols and their Impact on Phytoplankton Productivity

NASA Technical Reports Server (NTRS)

Tindale, Neil W.

1997-01-01

The overall objective of this experiment was to test the iron hypothesis does the addition of iron to nutrient rich surface waters enhance productivity? Our specific objectives in this experiment included sampling and studying the marine aerosol size and type (which are related to chemical reactivity) during the PlumEx cruise to determine the importance of local (Galapagos Islands) versus long-range sources of atmospheric material. Detailed results of single particle analysis of our samples are being prepared for publication in two papers. We collect aerosol samples and they have been analyzed for trace metals and other elements. We are mapped aerosol distribution and the desert source areas around the Arabian Sea region. We did record a clear relationship between the aerosol radiance and synoptic weather patterns with distinct signals over the ocean northwest and southwest of Australia. While the interpretation was limited an aerosol climatology pattern was presented.

Folkecology and commons management in the Maya Lowlands

PubMed Central

Atran, Scott; Medin, Douglas; Ross, Norbert; Lynch, Elizabeth; Coley, John; Ek’, Edilberto Ucan; Vapnarsky, Valentina

1999-01-01

Three groups living off the same rainforest habitat manifest strikingly distinct behaviors, cognitions, and social relationships relative to the forest. Only the area’s last native Maya reveal systematic awareness of ecological complexity involving animals, plants, and people and practices clearly favoring forest regeneration. Spanish-speaking immigrants prove closer to native Maya in thought, action, and social networking than do immigrant Maya. There is no overriding “local,” “Indian,” or “immigrant” relationship to the environment. Results indicate that exclusive concern with rational self-interest and institutional constraints do not sufficiently account for commons behavior and that cultural patterning of cognition and access to relevant information are significant predictors. Unlike traditional accounts of relations between culture, cognition, and behavior, the models offered are not synthetic interpretations of people’s thoughts and behaviors but are emergent cultural patterns derived statistically from measurements of individual cognitions and behaviors. PMID:10377461

Competition between relatives and the evolution of dispersal in a parasitoid wasp

PubMed Central

INNOCENT, T. M.; ABE, J.; WEST, S. A.; REECE, S. E.

2014-01-01

Evolutionary theory predicts that levels of dispersal vary in response to the extent of local competition for resources and the relatedness between potential competitors. Here, we test these predictions by making use of a female dispersal dimorphism in the parasitoid wasp Melittobia australica. We show that there are two distinct female morphs, which differ in morphology, pattern of egg production, and dispersal behaviour. As predicted by theory, we found that greater competition for resources resulted in increased production of dispersing females. In contrast, we did not find support for the prediction that high relatedness between competitors increases the production of dispersing females in Melittobia. Finally, we exploit the close links between the evolutionary processes leading to selection for dispersal and for biased sex ratios to examine whether the pattern of dispersal can help distinguish between competing hypotheses for the lack of sex ratio adjustment in Melittobia. PMID:20492084

The landscape ecology and microbiota of the human nose, mouth and throat

PubMed Central

Proctor, Diana M.; Relman, David A.

2017-01-01

Landscape ecology examines the relationships between the spatial arrangement of different landforms and the processes that give rise to spatial and temporal patterns in local community structure. These relationships that underlie the patterns of the microbial communities that inhabit the human body, and in particular, those of the nose, mouth and throat, deserve greater attention. Important questions include what defines the size of a population (i.e., ‘patch’) in a given body site; what defines the boundaries of distinct patches within a single body site, and where and over what spatial scales within a body site are gradients detected. This review looks at the landscape ecology in the upper respiratory tract and mouth, and seeks greater clarity about the physiological factors, whether immunological, chemical or physical, that govern microbial community composition and function, and the ecological traits that underlie health and disease. PMID:28407480

Substance P binding sites in the nucleus tractus solitarius of the cat

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

Maley, B.E.; Sasek, C.A.; Seybold, V.S.

1988-11-01

Substance P binding sites in the nucleus tractus solitarius were visualized with receptor autoradiography using Bolton-Hunter (/sup 125/I)substance P. Substance P binding sites were found to have distinct patterns within the cat nucleus tractus solitarius. The majority of substance P binding sites were present in the medial, intermediate and the peripheral rim of the parvocellular subdivisions. Lower amounts of substance P binding sites were present in the commissural, ventrolateral, interstitial and dorsolateral subdivisions. No substance P binding sites were present in the central region of the parvocellular subdivision or the solitary tract. The localization of substance P binding sites inmore » the nucleus tractus solitarius is very similar to the patterns of substance P immunoreactive fibers previously described for this region. Results of this study add further support for a functional role of substance P in synaptic circuits of the nucleus tractus solitarius.« less

Evidence for triple-junction rifting focussed on local magmatic centres along Parga Chasma, Venus

NASA Astrophysics Data System (ADS)

Graff, J. R.; Ernst, R. E.; Samson, C.

2018-05-01

Parga Chasma is a discontinuous rift system marking the southern boundary of the Beta-Atla-Themis (BAT) region on Venus. Along a 1500 km section of Parga Chasma, detailed mapping of Magellan Synthetic Aperture Radar images has revealed 5 coronae, 11 local rift zones distinct from a regional extension pattern, and 47 graben-fissure systems with radiating (28), linear (12) and circumferential (7) geometries. The magmatic centres of these graben-fissure systems typically coincide with coronae or large volcanoes, although a few lack any central magmatic or tectonic feature (i.e. are cryptic). Some of the magmatic centres are interpreted as the foci of triple-junction rifting that form the 11 local rift zones. Cross-cutting relationships between graben-fissure systems and local rift faults reveal synchronous formation, implying a genetic association. Additionally, cross-cutting relationships show that local rifting events postdate the regional extension along Parga Chasma, further indicating multiple stages of rifting. Evidence for multiple centres of younger magmatism and local rifting against a background of regional extension provides an explanation for the discontinuous morphology of Parga Chasma. Examination of the Atlantic Rift System (prior to ocean opening) on Earth provides an analogue to the rift morphologies observed on Venus.

Grid point extraction and coding for structured light system

NASA Astrophysics Data System (ADS)

Song, Zhan; Chung, Ronald

2011-09-01

A structured light system simplifies three-dimensional reconstruction by illuminating a specially designed pattern to the target object, thereby generating a distinct texture on it for imaging and further processing. Success of the system hinges upon what features are to be coded in the projected pattern, extracted in the captured image, and matched between the projector's display panel and the camera's image plane. The codes have to be such that they are largely preserved in the image data upon illumination from the projector, reflection from the target object, and projective distortion in the imaging process. The features also need to be reliably extracted in the image domain. In this article, a two-dimensional pseudorandom pattern consisting of rhombic color elements is proposed, and the grid points between the pattern elements are chosen as the feature points. We describe how a type classification of the grid points plus the pseudorandomness of the projected pattern can equip each grid point with a unique label that is preserved in the captured image. We also present a grid point detector that extracts the grid points without the need of segmenting the pattern elements, and that localizes the grid points in subpixel accuracy. Extensive experiments are presented to illustrate that, with the proposed pattern feature definition and feature detector, more features points in higher accuracy can be reconstructed in comparison with the existing pseudorandomly encoded structured light systems.

ADAM33 polymorphisms are associated with asthma and a distinctive palm dermatoglyphic pattern

PubMed Central

XUE, WEILIN; HAN, WEI; ZHOU, ZHAO-SHAN

2013-01-01

A close correlation between asthma and palm dermatoglyphic patterns has been observed in previous studies, but the underlying genetic mechanisms have not been investigated. A disintegrin and metalloprotein-33 (ADAM33) polymorphisms are important in the development of asthma and other atopic diseases. To investigate the underlying mechanisms of the association between asthma and distinctive palm dermatoglyphic patterns, thirteen ADAM33 single-nucleotide polymorphisms (SNPs) were analyzed for the association between asthma and palm dermatoglyphic patterns in a population of 400 asthmatic patients and 200 healthy controls. Based on the results, five SNPs, rs44707 (codominant model, P=0.031; log-additive model, P=0.0084), rs2787094 (overdominant model, P=0.049), rs678881 (codominant model, P=0.028; overdominant model, P=0.0083), rs677044 (codominant model, P=0.013; log-additive model, P=0.0033) and rs512625 (dominant model, P=0.033), were associated with asthma in this population. Two SNPs, rs44707 (dominant model, P=0.042) and rs2787094 (codominant model, P=0.014; recessive model, P=0.0038), were observed in the asthma patients with the distinctive palm pattern. As rs44707 and rs2787094 are associated with asthma and a distinctive palm pattern, the data suggest that ADAM33 polymorphisms are correlated with asthma and may be the underlying genetic basis of the association between asthma and palm dermatoglyphic patterns. PMID:24141861

The Emerging Pattern of Civil-Military Relations in Islamist States

DTIC Science & Technology

2013-03-01

Turkey, and Egypt , this thesis argues that a distinct pattern of civil-military relations is beginning to emerge in which Islamist governments rely on...important implications for how Islamist governments assert their authority over the military. 14. SUBJECT TERMS Iran, Turkey, Egypt , Civil...institutions. Drawing on the reform experiences in Iran, Turkey, and Egypt , this thesis argues that a distinct pattern of civil-military relations is

Horizontal and Vertical Cultural Differences in the Content of Advertising Appeals

PubMed Central

Shavitt, Sharon; Johnson, Timothy P.; Zhang, Jing

2014-01-01

The distinction between vertical (emphasizing hierarchy) and horizontal (valuing equality) cultures yields novel predictions regarding the prevalence of advertising appeals. A content analysis of 1211 magazine advertisements in five countries (Denmark, Korea, Poland, Russia, U.S.) revealed differences in ad content that underscore the value of this distinction. Patterns in the degree to which ads emphasized status benefits and uniqueness benefits corresponded to the countries' vertical/horizontal cultural classification. These and other patterns of ad benefits are analyzed and the predictions afforded by the vertical/horizontal distinction versus the broader individualism-collectivism distinction are compared and tested. PMID:25554720

Creating fair lineups for suspects with distinctive features.

PubMed

Zarkadi, Theodora; Wade, Kimberley A; Stewart, Neil

2009-12-01

In their descriptions, eyewitnesses often refer to a culprit's distinctive facial features. However, in a police lineup, selecting the only member with the described distinctive feature is unfair to the suspect and provides the police with little further information. For fair and informative lineups, the distinctive feature should be either replicated across foils or concealed on the target. In the present experiments, replication produced more correct identifications in target-present lineups--without increasing the incorrect identification of foils in target-absent lineups--than did concealment. This pattern, and only this pattern, is predicted by the hybrid-similarity model of recognition.

Horizontal and Vertical Cultural Differences in the Content of Advertising Appeals.

PubMed

Shavitt, Sharon; Johnson, Timothy P; Zhang, Jing

2011-05-01

The distinction between vertical (emphasizing hierarchy) and horizontal (valuing equality) cultures yields novel predictions regarding the prevalence of advertising appeals. A content analysis of 1211 magazine advertisements in five countries (Denmark, Korea, Poland, Russia, U.S.) revealed differences in ad content that underscore the value of this distinction. Patterns in the degree to which ads emphasized status benefits and uniqueness benefits corresponded to the countries' vertical/horizontal cultural classification. These and other patterns of ad benefits are analyzed and the predictions afforded by the vertical/horizontal distinction versus the broader individualism-collectivism distinction are compared and tested.

Spitzenkorper, exocyst, and polarisome components in Candida albicans hyphae show different patterns of localization and have distinct dynamic properties.

PubMed

Jones, Laura A; Sudbery, Peter E

2010-10-01

During the extreme polarized growth of fungal hyphae, secretory vesicles are thought to accumulate in a subapical region called the Spitzenkörper. The human fungal pathogen Candida albicans can grow in a budding yeast or hyphal form. When it grows as hyphae, Mlc1 accumulates in a subapical spot suggestive of a Spitzenkörper-like structure, while the polarisome components Spa2 and Bud6 localize to a surface crescent. Here we show that the vesicle-associated protein Sec4 also localizes to a spot, confirming that secretory vesicles accumulate in the putative C. albicans Spitzenkörper. In contrast, exocyst components localize to a surface crescent. Using a combination of fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) experiments and cytochalasin A to disrupt actin cables, we showed that Spitzenkörper-located proteins are highly dynamic. In contrast, exocyst and polarisome components are stably located at the cell surface. It is thought that in Saccharomyces cerevisiae exocyst components are transported to the cell surface on secretory vesicles along actin cables. If each vesicle carried its own complement of exocyst components, then it would be expected that exocyst components would be as dynamic as Sec4 and would have the same pattern of localization. This is not what we observe in C. albicans. We propose a model in which a stream of vesicles arrives at the tip and accumulates in the Spitzenkörper before onward delivery to the plasma membrane mediated by exocyst and polarisome components that are more stable residents of the cell surface.

Objective classification of atmospheric circulation over southern Scandinavia

NASA Astrophysics Data System (ADS)

Linderson, Maj-Lena

2001-02-01

A method for calculating circulation indices and weather types following the Lamb classification is applied to southern Scandinavia. The main objective is to test the ability of the method to describe the atmospheric circulation over the area, and to evaluate the extent to which the pressure patterns determine local precipitation and temperature in Scania, southernmost Sweden. The weather type classification method works well and produces distinct groups. However, the variability within the group is large with regard to the location of the low pressure centres, which may have implications for the precipitation over the area. The anticyclonic weather type dominates, together with the cyclonic and westerly types. This deviates partly from the general picture for Sweden and may be explained by the southerly location of the study area. The cyclonic type is most frequent in spring, although cloudiness and amount of rain are lowest during this season. This could be explained by the occurrence of weaker cyclones or low air humidity during this time of year. Local temperature and precipitation were modelled by stepwise regression for each season, designating weather types as independent variables. Only the winter season-modelled temperature and precipitation show a high and robust correspondence to the observed temperature and precipitation, even though <60% of the precipitation variance is explained. In the other seasons, the connection between atmospheric circulation and the local temperature and precipitation is low. Other meteorological parameters may need to be taken into account. The time and space resolution of the mean sea level pressure (MSLP) grid may affect the results, as many important features might not be covered by the classification. Local physiography may also influence the local climate in a way that cannot be described by the atmospheric circulation pattern alone, stressing the importance of using more than one observation series.

A new species of Aspidura Wagler, 1830 (Squamata: Colubridae: Natricinae) from Sri Pada sanctuary (Peak Wilderness), Sri Lanka.

PubMed

Wickramasinghe, L J Mendis; Vidanapathirana, Dulan Ranga; Kandambi, H K Dushantha; Pyron, R Alexander; Wickramasinghe, Nethu

2017-11-13

We describe a new species, Aspidura ravanai sp. nov., representing the eighth species of the genus known from Sri Lanka. The new species is readily distinguished from all other congeners by its colour pattern, scalation, and genetic distinctiveness. Our molecular results indicated that Aspidura began diversifying in the Miocene approximately 18 Ma, and A. ravanai sp. nov. diverged from its likely sister lineage A. trachyprocta at least 6.2 Ma. The species is currently known only from the type locality, on the western slopes of Sri Pada Peak in the central highlands of Sri Lanka.

Shaping climate change in the North Atlantic sector: The role of the atmospheric response to local SST changes vs. large-scale changes

NASA Astrophysics Data System (ADS)

Hand, Ralf; Keenlyside, Noel; Omrani, Nour-Eddine; Greatbatch, Richard; Bader, Jürgen

2017-04-01

Climate change simulations robustly show a warming hole in the sub-polar North Atlantic that results from slowing of the AMOC countering the global warming signal. Here we investigate how the distinct SST spatial structures, which include a sharpening of the Gulf Stream SST gradients, influence climate change in the NA sector in winter. For this we analyse the RCP8.5 scenario simulation of the MPI Earth System Model. Additional sensitivity experiments with the atmospheric model component, ECHAM5, are performed to deconstruct the effect of the local spatial structure of the SST change from those arising from large-scale warming of the ocean, remote SST pattern changes and changed radiative forcings. The MPI model simulation shows a signifcant decrease in precipitation to the south of the GS extension region in the future, despite a strong increase in underlying SST. While directly to the north there is a significant increase in precipitation. These distinct features in the precipitation response over the North Atlantic result from the local SST. Over the Gulf Stream, the differential structure of the precipitation changes reflects the changes of the local SST gradients there. Over the subpolar gyre the increase in precipitation is partly suppressed. In this region the Subpolar Gyre the weakened AMOC causes a SST warming, that is much weaker than the warming other regions of the ocean show at the same latitude. The large-scale response, which includes the overall increase in precipitation over the NA is due to the overall warming, remote SSTs and/or directly connected to the radiative forcing.

Amnesia, rehearsal, and temporal distinctiveness models of recall.

PubMed

Brown, Gordon D A; Della Sala, Sergio; Foster, Jonathan K; Vousden, Janet I

2007-04-01

Classical amnesia involves selective memory impairment for temporally distant items in free recall (impaired primacy) together with relative preservation of memory for recency items. This abnormal serial position curve is traditionally taken as evidence for a distinction between different memory processes, with amnesia being associated with selectively impaired long-term memory. However recent accounts of normal serial position curves have emphasized the importance of rehearsal processes in giving rise to primacy effects and have suggested that a single temporal distinctiveness mechanism can account for both primacy and recency effects when rehearsal is considered. Here we explore the pattern of strategic rehearsal in a patient with very severe amnesia. When the patient's rehearsal pattern is taken into account, a temporal distinctiveness model can account for the serial position curve in both amnesic and control free recall. The results are taken as consistent with temporal distinctiveness models of free recall, and they motivate an emphasis on rehearsal patterns in understanding amnesic deficits in free recall.

Comparison of isozyme patterns between Spirometra erinacei and Spirometra mansonoides by isoelectric focusing.

PubMed

Fukumoto, S; Tsuboi, T; Hirai, K; Phares, C K

1992-08-01

No differences were observed in the isozyme patterns of 4 enzymes examined between fresh samples stored at -80 C and samples stored at room temperature for 10 days after lyophilization, which supports the validity of comparing lyophilized samples to fresh frozen tissue. Mature proglottids as well as plerocercoids of Spirometra erinacei from Japan and Australia were indistinguishable by comparison of isozyme patterns after isoelectric focusing. The isozyme patterns of acid phosphatase, glucosephosphate isomerase (GPI), and mannosephosphate isomerase from plerocercoids of Spirometra mansonoides were distinctly different from those of plerocercoids of S. erinacei. The adenylate kinase isozyme patterns of the mature proglottids of S. mansonoides were also distinctly different from those of the mature proglottids and the plerocercoids of S. erinacei. The GPI isozyme pattern of the mature proglottids of S. mansonoides was also distinguishable from the GPI patterns of those of S. erinacei. These electrophoretic data suggest that the S. erinacei from Japan and Australia are closely related, if not identical, but that S. mansonoides is genetically distinct from S. erinacei.

Mercury in mosses Hylocomium splendens (Hedw.) B.S.G. and Pleurozium schreberi (Brid.) Mitt. from Poland and Alaska: Understanding the origin of pollution sources

USGS Publications Warehouse

Migaszewski, Z.M.; Galuszka, A.; Dole, ogonekgowska S.; Crock, J.G.; Lamothe, P.J.

2010-01-01

This report shows baseline concentrations of mercury in the moss species Hylocomium splendens and Pleurozium schreberi from the Kielce area and the remaining Holy Cross Mountains (HCM) region (south-central Poland), and Wrangell-Saint Elias National Park and Preserve (Alaska) and Denali National Park and Preserve (Alaska). Like mosses from many European countries, Polish mosses were distinctly elevated in Hg, bearing a signature of cross-border atmospheric transport combined with local point sources. In contrast, Alaskan mosses showed lower Hg levels, reflecting mostly the underlying geology. Compared to HCM, Alaskan and Kielce mosses exhibited more uneven spatial distribution patterns of Hg. This variation is linked to topography and location of local point sources (Kielce) and underlying geology (Alaska). Both H. splendens and P. schreberi showed similar bioaccumulative capabilities of Hg in all four study areas. ?? 2010 Elsevier Inc.

Toward a transnational history of the social sciences.

PubMed

Heilbron, Johan; Guilhot, Nicolas; Jeanpierre, Laurent

2008-01-01

Historical accounts of the social sciences have too often accepted local or national institutions as a self-evident framework of analysis, instead of considering them as being embedded in transnational relations of various kinds. Evolving patterns of transnational mobility and exchange cut through the neat distinction between the local, the national, and the inter-national, and thus represent an essential component in the dynamics of the social sciences, as well as a fruitful perspective for rethinking their historical development. In this programmatic outline, it is argued that a transnational history of the social sciences may be fruitfully understood on the basis of three general mechanisms, which have structured the transnational flows of people and ideas in decisive ways: (a) the functioning of international scholarly institutions, (b) the transnational mobility of scholars, and (c) the politics of trans-national exchange of nonacademic institutions. The article subsequently examines and illustrates each of these mechanisms.

MITOPRED: a web server for the prediction of mitochondrial proteins

PubMed Central

Guda, Chittibabu; Guda, Purnima; Fahy, Eoin; Subramaniam, Shankar

2004-01-01

MITOPRED web server enables prediction of nucleus-encoded mitochondrial proteins in all eukaryotic species. Predictions are made using a new algorithm based primarily on Pfam domain occurrence patterns in mitochondrial and non-mitochondrial locations. Pre-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. Automated updates are scheduled for the pre-calculated prediction database so as to provide access to the most current data. The server, its documentation and the data are available from http://mitopred.sdsc.edu. PMID:15215413

Chimera States in Continuous Media: Existence and Distinctness

NASA Astrophysics Data System (ADS)

Nicolaou, Zachary G.; Riecke, Hermann; Motter, Adilson E.

2017-12-01

The defining property of chimera states is the coexistence of coherent and incoherent domains in systems that are structurally and spatially homogeneous. The recent realization that such states might be common in oscillator networks raises the question of whether an analogous phenomenon can occur in continuous media. Here, we show that chimera states can exist in continuous systems even when the coupling is strictly local, as in many fluid and pattern forming media. Using the complex Ginzburg-Landau equation as a model system, we characterize chimera states consisting of a coherent domain of a frozen spiral structure and an incoherent domain of amplitude turbulence. We show that in this case, in contrast with discrete network systems, fluctuations in the local coupling field play a crucial role in limiting the coherent regions. We suggest these findings shed light on new possible forms of coexisting order and disorder in fluid systems.

Satellite animal tracking feasibility studies

NASA Technical Reports Server (NTRS)

Buechner, H. K.

1975-01-01

A study was initiated in Tsavo National Park to determine movements and home ranges of individual elephants and their relations to overall distribution patterns and environmental factors such as rainfall. Methods used were radio tracking and observations of visually identifiable individuals. Aerial counts provided data on overall distribution. Two bulls and two cows were radio-tagged in Tsavo West and two bulls and four cows in Tsavo East, providing home range and movement data. The movements of individuals were useful in interpreting relatively major shifts in elephant distribution. Results point to the following preliminary conclusions: (1) elephants in the Tsavo area undertook long distance movements in fairly direct response to localized rainfall; (2) a subdivision of the overall population into locally distinct units may exist during the dry season but did not occur after significant rainfall; and (3) food appears to be the primary factor governing movements and distribution of elephants in the area.

Origin of heterogeneous spiking patterns from continuously distributed ion channel densities: a computational study in spinal dorsal horn neurons.

PubMed

Balachandar, Arjun; Prescott, Steven A

2018-05-01

Distinct spiking patterns may arise from qualitative differences in ion channel expression (i.e. when different neurons express distinct ion channels) and/or when quantitative differences in expression levels qualitatively alter the spike generation process. We hypothesized that spiking patterns in neurons of the superficial dorsal horn (SDH) of spinal cord reflect both mechanisms. We reproduced SDH neuron spiking patterns by varying densities of K V 1- and A-type potassium conductances. Plotting the spiking patterns that emerge from different density combinations revealed spiking-pattern regions separated by boundaries (bifurcations). This map suggests that certain spiking pattern combinations occur when the distribution of potassium channel densities straddle boundaries, whereas other spiking patterns reflect distinct patterns of ion channel expression. The former mechanism may explain why certain spiking patterns co-occur in genetically identified neuron types. We also present algorithms to predict spiking pattern proportions from ion channel density distributions, and vice versa. Neurons are often classified by spiking pattern. Yet, some neurons exhibit distinct patterns under subtly different test conditions, which suggests that they operate near an abrupt transition, or bifurcation. A set of such neurons may exhibit heterogeneous spiking patterns not because of qualitative differences in which ion channels they express, but rather because quantitative differences in expression levels cause neurons to operate on opposite sides of a bifurcation. Neurons in the spinal dorsal horn, for example, respond to somatic current injection with patterns that include tonic, single, gap, delayed and reluctant spiking. It is unclear whether these patterns reflect five cell populations (defined by distinct ion channel expression patterns), heterogeneity within a single population, or some combination thereof. We reproduced all five spiking patterns in a computational model by varying the densities of a low-threshold (K V 1-type) potassium conductance and an inactivating (A-type) potassium conductance and found that single, gap, delayed and reluctant spiking arise when the joint probability distribution of those channel densities spans two intersecting bifurcations that divide the parameter space into quadrants, each associated with a different spiking pattern. Tonic spiking likely arises from a separate distribution of potassium channel densities. These results argue in favour of two cell populations, one characterized by tonic spiking and the other by heterogeneous spiking patterns. We present algorithms to predict spiking pattern proportions based on ion channel density distributions and, conversely, to estimate ion channel density distributions based on spiking pattern proportions. The implications for classifying cells based on spiking pattern are discussed. © 2018 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.

Estimating the effects of the transboundary transport and local emissions of atmospheric pollutants in South Korea during KORUS-AQ campaign

NASA Astrophysics Data System (ADS)

Lee, S.; Koo, J. H.; Hong, J.; Choi, M.; Kim, J.; Lim, H.; Holben, B. N.; Eck, T. F.; Ahn, J. Y.; Park, J.; Kim, S. K.

2017-12-01

The air quality of South Korea, located in the east of China, is affected by persistent westerlies, showing the relationship to the emission in upwind region. High aerosol concentration in South Korea is also attributed to local emissions. Particularly, the industrial complex and power plants are concentrated in the Chungcheongnam-do (CN), located by the southwest part of Seoul Metropolitan Area (SMA). In this study, we evaluate the contribution of both the transboundary transport of Chinese pollutants and local emissions in the CN to the air quality in South Korea during Korea-US Air Quality (KORUS-AQ) campaign, 1 May to 12 June in 2016. Based on the information of aerosol optical depth (AOD) obtained from ground-based Aerosol Robotic NETwork (AERONET) sunphotometer and surface in-situ Particulate Matter (PM) measurements at 19 stations, high and low aerosol pollution cases are classified first. Then, 2-day back-trajectories are calculated using National Ocean and Atmospheric Administration (NOAA) HYbrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model at each AERONET site to investigate whether transport pattern is different in accordance with the classified cases about aerosol amounts. As a result, we find the distinct pathway of air-mass transport from eastern China; When high AOD is observed at station located in the western coast of South Korea, air masses are directly transported from Shandong peninsular to the Korean peninsula. In contrast, air masses are mostly transported from northwestern or northern China during the period of low AOD conditions. When PM2.5 detected at SMA sites is greater than Korean government criteria (50 micrograms per cubic meter for 24-hour average PM2.5), SMA sites are mostly affected by air mass flows through the CN area. These results indicate that transport pattern can be different vertically and surface aerosol concentration has different transport pattern from the transport pattern related to the variation of total column aerosol.

Metagabbro associated with the shear zone on Prins Karls Forland (Svalbard, Arctic)

NASA Astrophysics Data System (ADS)

Maraszewska, Maria; Manecki, Maciej; Czerny, Jerzy; Schneider, David; Myhre, Per Inge; Faehnrich, Karol; Barnes, Christopher

2016-04-01

Prins Karls Forland (PKF) is a N-S elongated island situated west of Spitsbergen in the Svalbard archipelago, High Arctic. The northern part of the island is dominated by siliciclastic metasediments regionally metamorphosed to greenshist facies assemblages during one distinct stage of tectonism. Amphibolite facies garnet-mica schists, mica schists, quartzites and carbonate-silicate rocks exhibiting evidence of at least two distinct, strong deformation episodes (including mylonitization) locally outcrop on the east coast of PKF, termed the Pinkie Unit. A ~1 km wide shear zone containing ductile to brittle structures and distinct outcrops of greenstones (metagabbros and greenschists), associated with magnetite ore, separates these two contrasting tectonic units. Ten samples of greenstones were collected on the slopes of Lauratzonfjellet and Boureefjellet for petrologic and geochemical analyses. Despite intense localized shearing, the metagabbros are undeformed and preserve coarse crystalline, magmatic texture, which is locally poikilitic. The primary magmatic assemblage consists of brown hornblende, plagioclase, biotite and opaque minerals, with accessory apatite and titanite. No relicts of pyroxenes are preserved. Formation of secondary uralite, sericite and chlorite is observed. Metamorphic assemblage consists of actinolite pseudomorhs after hornblende, epidote, and second generation biotite. Blue amphibole is observed in one sample from Boureefjellet; greenschists from Boureefjellet also contain fibrous blue amphibole, as well as garnets, actinolite, epidote and biotite. Some rocks sampled on Boureefjellet are more strongly deformed and exhibit probably two stages of metamorphism: amphibolite facies metamorphism resulting in blue amphibole-garnet assemblage followed by greenschist facies metamorphism resulting in actinolite-epidote-biotite paragenesis. Parallel and overlapping patterns on chondrite-normalized REE diagrams and spider diagrams indicate that these metagabbros are comagmatic. Enrichment in incompatible lighter elements and position of projections on discrimination diagrams suggest ocean island basalt (OIB) character of primary magmas. The age of these rocks is unknown and is an objective of ongoing investigation. This work is partially funded by AGH research grant no 11.11.140.319.

Genomic organization of the human mi-er1 gene and characterization of alternatively spliced isoforms: regulated use of a facultative intron determines subcellular localization.

PubMed

Paterno, Gary D; Ding, Zhihu; Lew, Yuan-Y; Nash, Gord W; Mercer, F Corinne; Gillespie, Laura L

2002-07-24

mi-er1 (previously called er1) is a fibroblast growth factor-inducible early response gene activated during mesoderm induction in Xenopus embryos and encoding a nuclear protein that functions as a transcriptional activator. The human orthologue of mi-er1 was shown to be upregulated in breast carcinoma cell lines and breast tumours when compared to normal breast cells. In this report, we investigate the structure of the human mi-er1 (hmi-er1) gene and characterize the alternatively spliced transcripts and protein isoforms. hmi-er1 is a single copy gene located at 1p31.2 and spanning 63 kb. It contains 17 exons and includes one skipped exon, a facultative intron and three polyadenylation signals to produce 12 transcripts encoding six distinct proteins. hmi-er1 transcripts were expressed at very low levels in most human adult tissues and the mRNA isoform pattern varied with the tissue. The 12 transcripts encode proteins containing a common internal sequence with variable N- and C-termini. Three distinct N- and two distinct C-termini were identified, giving rise to six protein isoforms. The two C-termini differ significantly in size and sequence and arise from alternate use of a facultative intron to produce hMI-ER1alpha and hMI-ER1beta. In all tissues except testis, transcripts encoding the beta isoform were predominant. hMI-ER1alpha lacks the predicted nuclear localization signal and transfection assays revealed that, unlike hMI-ER1beta, it is not a nuclear protein, but remains in the cytoplasm. Our results demonstrate that alternate use of a facultative intron regulates the subcellular localization of hMI-ER1 proteins and this may have important implications for hMI-ER1 function.

A locally adaptive kernel regression method for facies delineation

NASA Astrophysics Data System (ADS)

Fernàndez-Garcia, D.; Barahona-Palomo, M.; Henri, C. V.; Sanchez-Vila, X.

2015-12-01

Facies delineation is defined as the separation of geological units with distinct intrinsic characteristics (grain size, hydraulic conductivity, mineralogical composition). A major challenge in this area stems from the fact that only a few scattered pieces of hydrogeological information are available to delineate geological facies. Several methods to delineate facies are available in the literature, ranging from those based only on existing hard data, to those including secondary data or external knowledge about sedimentological patterns. This paper describes a methodology to use kernel regression methods as an effective tool for facies delineation. The method uses both the spatial and the actual sampled values to produce, for each individual hard data point, a locally adaptive steering kernel function, self-adjusting the principal directions of the local anisotropic kernels to the direction of highest local spatial correlation. The method is shown to outperform the nearest neighbor classification method in a number of synthetic aquifers whenever the available number of hard data is small and randomly distributed in space. In the case of exhaustive sampling, the steering kernel regression method converges to the true solution. Simulations ran in a suite of synthetic examples are used to explore the selection of kernel parameters in typical field settings. It is shown that, in practice, a rule of thumb can be used to obtain suboptimal results. The performance of the method is demonstrated to significantly improve when external information regarding facies proportions is incorporated. Remarkably, the method allows for a reasonable reconstruction of the facies connectivity patterns, shown in terms of breakthrough curves performance.

How do local and remote processes affect the distribution of iron in the Atlantic Ocean?

NASA Astrophysics Data System (ADS)

Tagliabue, A.; Boyd, P.; Rijkenberg, M. J. A.; Williams, R. G.

2016-02-01

Iron (Fe) plays an important role in governing the magnitudes and patterns of primary productivity, nitrogen fixation and phytoplankton community composition across the Atlantic Ocean. Variations in the supply of Fe to surface waters across the mixed layer interface, over seasonal to annual to decadal scales, are underpinned by it's vertical profile. Traditionally, nutrient profiles are understood in terms of surface depletion and subsurface regeneration, but for Fe this is more complicated due to the role of scavenging and organic complexation by ligands, as well as subsurface sources. This means that the Fe profile may be controlled locally, by sinking, regeneration and scavenging or remotely, by the upstream conditions of subducted water masses. Subduction drives the transfer of Fe across the interface between winter mixed layer and the ocean interior, but has received little attention thus far. Via the subduction of watermasses with distinct biogeochemical signatures to low latitudes, remote processes can regulate the Atlantic Ocean Fe distribution at local scales. Specifically, the formation of mode waters with excess Fe binding ligands (positive L*) enable these waters to stabilise any Fe flux from regeneration that would otherwise be lost by scavenging. The pattern of mode water ventilation then highlights those regions of the ocean where local processes are able to influence the Fe profile. Local process that augment L*, such as the production of ligands during particle regeneration, can also interact with the larger scale ventilation signature but do not alter the main trends. By applying our framework to recent GEOTRACES datasets over the Atlantic Ocean we are able to highlight regions where the Fe profile is forced locally or remotely, thereby providing an important process-based constraint on the biogeochemical models we rely on for future projections. Furthermore, we are able to appraise how the varying influence of local and remote processes drives the degree of agreement in the vertical profiles of Fe and macronutrients, which then sets the degree of surface water Fe limitation.

Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean.

PubMed

Li, W K W

2002-09-12

Many issues in biological oceanography are regional or global in scope; however, there are not many data sets of extensive areal coverage for marine plankton. In microbial ecology, a fruitful approach to large-scale questions is comparative analysis wherein statistical data patterns are sought from different ecosystems, frequently assembled from unrelated studies. A more recent approach termed macroecology characterizes phenomena emerging from large numbers of biological units by emphasizing the shapes and boundaries of statistical distributions, because these reflect the constraints on variation. Here, I use a set of flow cytometric measurements to provide macroecological perspectives on North Atlantic phytoplankton communities. Distinct trends of abundance in picophytoplankton and both small and large nanophytoplankton underlaid two patterns. First, total abundance of the three groups was related to assemblage mean-cell size according to the 3/4 power law of allometric scaling in biology. Second, cytometric diversity (an ataxonomic measure of assemblage entropy) was maximal at intermediate levels of water column stratification. Here, intermediate disturbance shapes diversity through an equitable distribution of cells in size classes, from which arises a high overall biomass. By subsuming local fluctuations, macroecology reveals meaningful patterns of phytoplankton at large scales.

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

Ants regulate colony spatial organization using multiple chemical road-signs

PubMed Central

Heyman, Yael; Shental, Noam; Brandis, Alexander; Hefetz, Abraham; Feinerman, Ofer

2017-01-01

Communication provides the basis for social life. In ant colonies, the prevalence of local, often chemically mediated, interactions introduces strong links between communication networks and the spatial distribution of ants. It is, however, unknown how ants identify and maintain nest chambers with distinct functions. Here, we combine individual tracking, chemical analysis and machine learning to decipher the chemical signatures present on multiple nest surfaces. We present evidence for several distinct chemical ‘road-signs' that guide the ants' movements within the dark nest. These chemical signatures can be used to classify nest chambers with different functional roles. Using behavioural manipulations, we demonstrate that at least three of these chemical signatures are functionally meaningful and allow ants from different task groups to identify their specific nest destinations, thus facilitating colony coordination and stabilization. The use of multiple chemicals that assist spatiotemporal guidance, segregation and pattern formation is abundant in multi-cellular organisms. Here, we provide a rare example for the use of these principles in the ant colony. PMID:28569746

Designation of a neotype and redescription of Hesione reticulata von Marenzeller, 1879 from Japan (Annelida, Hesionidae).

PubMed

Jimi, Naoto; Salazar-Vallejo, Sergio I; Kajihara, Hiroshi

2017-01-01

The hesionid polychaete Hesione reticulata von Marenzeller, 1879 was described from Enoshima Island, Japan and has been recorded also from the Red Sea. Depending on researchers, it has been regarded as either a distinct species or synonymous with older established ones. The type specimen has been lost. In order to clarify its taxonomic status, Hesione reticulata is herein redescribed, illustrated, and a neotype is proposed based on recent material collected near the type locality. The diagnostic features include the presence of several dorsal, discontinuous longitudinal bands, interrupted by pale segmental spots; prostomium with tiny antennae; a tuberculated dorsal integument; acicular lobes double; and neurochaetal blades with guards approaching the distal tooth. The dorsal color pattern in life enables a clear distinction from similar species such as Hesione intertexta Grube, 1878 amongst others. Mitochondrial COI barcoding sequences are deposited in the DNA Data Bank of Japan. A key to Hesione species from Japan is also included.

Distinctive clinical and histological features of Waldenström's macroglobulinemia and splenic marginal zone lymphoma.

PubMed

Arcaini, Luca; Varettoni, Marzia; Boveri, Emanuela; Orlandi, Ester; Rattotti, Sara; Zibellini, Silvia; Merli, Michele; Lucioni, Marco; Rizzi, Silvia; Gotti, Manuel; Morello, Lucia; Pascutto, Cristiana; Paulli, Marco

2011-02-01

We studied 122 patients with Waldenström's macroglobulinemia (WM) and 98 with splenic marginal zone lymphoma (SMZL); 29 SMZL patients (30%) had a serum MC (IgM in 17 patients). SMZL differed from WM for female prevalence, abdominal and superficial adenopathy, spleen and liver involvement, positive HCV. The median MC level was 2.0 g/dL in WM and 0.95 g/dL in SMZL (P<.001). On BM histology, SMZL was characterized by sinusoidal infiltration (70% of cases) and by a more frequent nodular pattern (P<.01) while WM had a higher incidence of interstitial BM localization. After a median follow-up of 5.3 years, median OS was not reached for SMZL and was 12 years for WM (P=.23; 14 years for asymptomatic WM, 8 years for symptomatic WM). In conclusion, despite similar outcomes of these 2 entities, SMZL appears as a disease with distinct clinical features and BM histology and a peculiar association with HCV infection.

Hydrodynamic Equations for Flocking Models without Velocity Alignment

NASA Astrophysics Data System (ADS)

Peruani, Fernando

2017-10-01

The spontaneous emergence of collective motion patterns is usually associated with the presence of a velocity alignment mechanism that mediates the interactions among the moving individuals. Despite of this widespread view, it has been shown recently that several flocking behaviors can emerge in the absence of velocity alignment and as a result of short-range, position-based, attractive forces that act inside a vision cone. Here, we derive the corresponding hydrodynamic equations of a microscopic position-based flocking model, reviewing and extending previous reported results. In particular, we show that three distinct macroscopic collective behaviors can be observed: i) the coarsening of aggregates with no orientational order, ii) the emergence of static, elongated nematic bands, and iii) the formation of moving, locally polar structures, which we call worms. The derived hydrodynamic equations indicate that active particles interacting via position-based interactions belong to a distinct class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems.

Ants regulate colony spatial organization using multiple chemical road-signs.

PubMed

Heyman, Yael; Shental, Noam; Brandis, Alexander; Hefetz, Abraham; Feinerman, Ofer

2017-06-01

Communication provides the basis for social life. In ant colonies, the prevalence of local, often chemically mediated, interactions introduces strong links between communication networks and the spatial distribution of ants. It is, however, unknown how ants identify and maintain nest chambers with distinct functions. Here, we combine individual tracking, chemical analysis and machine learning to decipher the chemical signatures present on multiple nest surfaces. We present evidence for several distinct chemical 'road-signs' that guide the ants' movements within the dark nest. These chemical signatures can be used to classify nest chambers with different functional roles. Using behavioural manipulations, we demonstrate that at least three of these chemical signatures are functionally meaningful and allow ants from different task groups to identify their specific nest destinations, thus facilitating colony coordination and stabilization. The use of multiple chemicals that assist spatiotemporal guidance, segregation and pattern formation is abundant in multi-cellular organisms. Here, we provide a rare example for the use of these principles in the ant colony.

Biogenic silica from the BDP93 drill site and adjacent areas of the Selenga Delta, Lake Baikal, Siberia

USGS Publications Warehouse

Colman, Steven M.; Peck, John A.; Hatton, Josephine; Karabanov, Eugene B.; King, John W.

1999-01-01

Biogenic silica contents of sediments on the lower Selenga Delta and Buguldeika saddle in Lake Baikal show distinct fluctuations that reflect changes in diatom productivity, and ultimately, climate. The pattern of the upper 50 m of the section, dating from about 334 ka, is similar to that of the marine oxygen-isotope record, increasingly so as the younger sediments become progressively finer grained and less locally derived with time. The last two interglaciations are marked by biogenic silica abundances similar to those of the Holocene. The equivalent of marine oxygen-isotope stage 3 is distinctly intermediate in character between full glacial and full interglacial biogenic silica values. Following near-zero values during the last glacial maximum, biogenic silica began to increase at about 13 ka. The rise in biogenic silica to Holocene values was interrupted by an abrupt decrease during Younger Dryas time, about 11 to 10 14C ka.

Diversity in shortjaw cisco (Coregonus zenithicus) in North America

USGS Publications Warehouse

Todd, T.N.; Steinhilber, M.

2002-01-01

Shortjaw cisco (Coregonus zenithicus) exhibit morphological variability across their geographic range in North America and could comprise more than one distinct morph or taxon. To investigate this, principal components analysis was applied to a data set that consisted of four variables from nine localities. All data were obtained from digital images of the specimens and the excised first gill arch. Confidence ellipses (95%) about the means of bivariate distributions of the principal components revealed that some populations were distinct from the others, but a continuity of overlap clouded understanding of pattern among the variation. Most populations had more and longer gillrakers than shortjaw cisco from George Lake (Manitoba) and Basswood Lake (Ontario) that had fewer and shorter gillrakers. This analysis supports the existence of a short- and few-rakered morph and a long- and many-rakered morph. However, most populations of shortjaw cisco from the Great Lakes across Canada to the Arctic share a similar morphology and likely represent a single, widespread species.

Pattern of calbindin-D28k and calretinin immunoreactivity in the brain of Xenopus laevis during embryonic and larval development.

PubMed

Morona, Ruth; González, Agustín

2013-01-01

The present study represents a detailed spatiotemporal analysis of the localization of calbindin-D28k (CB) and calretinin (CR) immunoreactive structures in the brain of Xenopus laevis throughout development, conducted with the aim to correlate the onset of the immunoreactivity with the development of compartmentalization of distinct subdivisions recently identified in the brain of adult amphibians and primarily highlighted when analyzed within a segmental paradigm. CR and CB are expressed early in the brain and showed a progressively increasing expression throughout development, although transient expression in some neuronal subpopulations was also noted. Common and distinct characteristics in Xenopus, as compared with reported features during development in the brain of mammals, were observed. The development of specific regions in the forebrain such as the olfactory bulbs, the components of the basal ganglia and the amygdaloid complex, the alar and basal hypothalamic regions, and the distinct diencephalic neuromeres could be analyzed on the basis of the distinct expression of CB and CR in subregions. Similarly, the compartments of the mesencephalon and the main rhombencephalic regions, including the cerebellum, were differently highlighted by their specific content in CB and CR throughout development. Our results show the usefulness of the analysis of the distribution of these proteins as a tool in neuroanatomy to interpret developmental aspects of many brain regions. Copyright © 2012 Wiley Periodicals, Inc.

Structural or pigmentary? Origin of the distinctive white stripe on the blue wing of a Morpho butterfly.

PubMed

Yoshioka, Shinya; Kinoshita, Shuichi

2006-01-22

A few species of Morpho butterflies have a distinctive white stripe pattern on their structurally coloured blue wings. Since the colour pattern of a butterfly wing is formed as a mosaic of differently coloured scales, several questions naturally arise: are the microstructures the same between the blue and white scales? How is the distinctive whiteness produced, structurally or by means of pigmentation? To answer these questions, we have performed structural and optical investigations of the stripe pattern of a butterfly, Morpho cypris. It is found that besides the dorsal and ventral scale layers, the wing substrate also has the corresponding stripe pattern. Quantitative optical measurements and analysis using a simple model for the wing structure reveal the origin of the higher reflectance which makes the white stripe brighter.

Noradrenaline, oxymetazoline and phorbol myristate acetate induce distinct functional actions and phosphorylation patterns of α1A-adrenergic receptors.

PubMed

Alcántara-Hernández, Rocío; Hernández-Méndez, Aurelio; Romero-Ávila, M Teresa; Alfonzo-Méndez, Marco A; Pupo, André S; García-Sáinz, J Adolfo

2017-12-01

In LNCaP cells that stably express α 1A -adrenergic receptors, oxymetazoline increased intracellular calcium and receptor phosphorylation, however, this agonist was a weak partial agonist, as compared to noradrenaline, for calcium signaling. Interestingly, oxymetazoline-induced receptor internalization and desensitization displayed greater effects than those induced by noradrenaline. Phorbol myristate acetate induced modest receptor internalization and minimal desensitization. α 1A -Adrenergic receptor interaction with β-arrestins (colocalization/coimmunoprecipitation) was induced by noradrenaline and oxymetazoline and, to a lesser extent, by phorbol myristate acetate. Oxymetazoline was more potent and effective than noradrenaline in inducing ERK 1/2 phosphorylation. Mass spectrometric analysis of immunopurified α 1A -adrenergic receptors from cells treated with adrenergic agonists and the phorbol ester clearly showed that phosphorylated residues were present both at the third intracellular loop and at the carboxyl tail. Distinct phosphorylation patterns were observed under the different conditions. The phosphorylated residues were: a) Baseline and all treatments: T233; b) noradrenaline: S220, S227, S229, S246, S250, S389; c) oxymetazoline: S227, S246, S381, T384, S389; and d) phorbol myristate acetate: S246, S250, S258, S351, S352, S401, S402, S407, T411, S413, T451. Our novel data, describing the α 1A -AR phosphorylation sites, suggest that the observed different phosphorylation patterns may participate in defining adrenoceptor localization and action, under the different conditions examined. Copyright © 2017 Elsevier B.V. All rights reserved.

Site Formation Processes and Hunter-Gatherers Use of Space in a Tropical Environment: A Geo-Ethnoarchaeological Approach from South India

PubMed Central

Friesem, David E.; Lavi, Noa; Madella, Marco; Ajithprasad, P.; French, Charles

2016-01-01

Hunter-gatherer societies have distinct social perceptions and practices which are expressed in unique use of space and material deposition patterns. However, the identification of archaeological evidence associated with hunter-gatherer activity is often challenging, especially in tropical environments such as rainforests. We present an integrated study combining ethnoarchaeology and geoarchaeology in order to study archaeological site formation processes related to hunter-gatherers’ ways of living in tropical forests. Ethnographic data was collected from an habitation site of contemporary hunter-gatherers in the forests of South India, aimed at studying how everyday activities and way of living dictate patterns of material deposition. Ethnoarchaeological excavations of abandoned open-air sites and a rock-shelter of the same group located deep in the forests, involved field observations and sampling of sediments from the abandoned sites and the contemporary site. Laboratory analyses included geochemical analysis (i.e., FTIR, ICP-AES), phytolith concentration analysis and soil micromorphology. The results present a dynamic spatial deposition pattern of macroscopic, microscopic and chemical materials, which stem from the distinctive ways of living and use of space by hunter-gatherers. This study shows that post-depositional processes in tropical forests result in poor preservation of archaeological materials due to acidic conditions and intensive biological activity within the sediments. Yet, the multiple laboratory-based analyses were able to trace evidence for activity surfaces and their maintenance practices as well as localized concentrations of activity remains such as the use of plants, metals, hearths and construction materials. PMID:27783683

Spatial and Temporal Patterns of Biocide Action against Staphylococcus epidermidis Biofilms▿ ‡

PubMed Central

Davison, William M.; Pitts, Betsey; Stewart, Philip S.

2010-01-01

The dynamic antimicrobial action of chlorine, a quaternary ammonium compound, glutaraldehyde, and nisin within biofilm cell clusters of Staphylococcus epidermidis was investigated using time-lapse confocal scanning laser microscopy. The technique allowed for the simultaneous imaging of changes in biofilm structure and disruption of cellular membrane integrity through the loss of an unbound fluorophore loaded into bacterial cells prior to antimicrobial challenge. Each of the four antimicrobial agents produced distinct spatial and temporal patterns of fluorescence loss. The antimicrobial action of chlorine was localized around the periphery of biofilm cell clusters. Chlorine was the only antimicrobial agent that caused any biofilm removal. Treatment with the quaternary ammonium compound caused membrane permeabilization that started at the periphery of cell clusters, then migrated steadily inward. A secondary pattern superimposed on the penetration dynamic suggested a subpopulation of less-susceptible cells. These bacteria lost fluorescence much more slowly than the majority of the population. Nisin caused a rapid and uniform loss of green fluorescence from all parts of the biofilm without any removal of biofilm. Glutaraldehyde caused no biofilm removal and also no loss of membrane integrity. Measurements of biocide penetration and action time at the center of cell clusters yielded 46 min for 10 mg liter−1 chlorine, 21 min for 50 mg liter−1 chlorine, 25 min for the quaternary ammonium compound, and 4 min for nisin. These results underscore the distinction between biofilm removal and killing and reinforce the critical role of biocide reactivity in determining the rate of biofilm penetration. PMID:20457816

Evolution of bacterial-like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer.

PubMed

Uhrig, R Glen; Kerk, David; Moorhead, Greg B

2013-12-01

Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Dysfunction of members in either the protein kinase or phosphatase family can have wide-ranging deleterious effects in both metazoans and plants alike. Previously, three bacterial-like phosphoprotein phosphatase classes were uncovered in eukaryotes and named according to the bacterial sequences with which they have the greatest similarity: Shewanella-like (SLP), Rhizobiales-like (RLPH), and ApaH-like (ALPH) phosphatases. Utilizing the wealth of data resulting from recently sequenced complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum likelihood methods to elucidate the pattern of evolution of eukaryotic bacterial-like phosphoprotein phosphatase sequences, which are predominantly distributed in photosynthetic eukaryotes. We uncovered a pattern of ancestral mitochondrial (SLP and RLPH) or archaeal (ALPH) gene entry into eukaryotes, supplemented by possible instances of lateral gene transfer between bacteria and eukaryotes. In addition to the previously known green algal and plant SLP1 and SLP2 protein forms, a more ancestral third form (SLP3) was found in green algae. Data from in silico subcellular localization predictions revealed class-specific differences in plants likely to result in distinct functions, and for SLP sequences, distinctive and possibly functionally significant differences between plants and nonphotosynthetic eukaryotes. Conserved carboxyl-terminal sequence motifs with class-specific patterns of residue substitutions, most prominent in photosynthetic organisms, raise the possibility of complex interactions with regulatory proteins.

Differential distribution of the sodium-activated potassium channels slick and slack in mouse brain.

PubMed

Rizzi, Sandra; Knaus, Hans-Günther; Schwarzer, Christoph

2016-07-01

The sodium-activated potassium channels Slick (Slo2.1, KCNT2) and Slack (Slo2.2, KCNT1) are high-conductance potassium channels of the Slo family. In neurons, Slick and Slack channels are involved in the generation of slow afterhyperpolarization, in the regulation of firing patterns, and in setting and stabilizing the resting membrane potential. The distribution and subcellular localization of Slick and Slack channels in the mouse brain have not yet been established in detail. The present study addresses this issue through in situ hybridization and immunohistochemistry. Both channels were widely distributed and exhibited distinct distribution patterns. However, in some brain regions, their expression overlapped. Intense Slick channel immunoreactivity was observed in processes, varicosities, and neuronal cell bodies of the olfactory bulb, granular zones of cortical regions, hippocampus, amygdala, lateral septal nuclei, certain hypothalamic and midbrain nuclei, and several regions of the brainstem. The Slack channel showed primarily a diffuse immunostaining pattern, and labeling of cell somata and processes was observed only occasionally. The highest Slack channel expression was detected in the olfactory bulb, lateral septal nuclei, basal ganglia, and distinct areas of the midbrain, brainstem, and cerebellar cortex. In addition, comparing our data obtained from mouse brain with a previously published study on rat brain revealed some differences in the expression and distribution of Slick and Slack channels in these species. J. Comp. Neurol. 524:2093-2116, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats.

PubMed

Schuelke, Taruna; Pereira, Tiago José; Hardy, Sarah M; Bik, Holly M

2018-04-01

Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies. Here, we investigated patterns in marine nematode microbiomes, by characterizing host-associated microbial taxa in 281 worms isolated from a range of habitat types (deep-sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and Gulf of Mexico). Microbiome profiles were generated from single worms spanning 33 distinct morphological genera, using a two-gene metabarcoding approach to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1-V2 region of the 18S rRNA gene targeting microbial eukaryotes. Contrary to our expectations, nematode microbiome profiles demonstrated no distinct patterns either globally (across depths and ocean basins) or locally (within site); prokaryotic and eukaryotic microbial assemblages did not correlate with nematode feeding morphology, host phylogeny or morphological identity, ocean region or marine habitat type. However, fine-scale analysis of nematode microbiomes revealed a variety of novel ecological interactions, including putative parasites and symbionts, and potential associations with bacterial/archaeal taxa involved in nitrogen and methane cycling. Our results suggest that in marine habitats, free-living nematodes may utilize diverse and generalist foraging strategies that are not correlated with host genotype or feeding morphology. Furthermore, some abiotic factors such as geographic region and habitat type do not appear to play an obvious role in structuring host-microbe associations or feeding preferences. © 2018 John Wiley & Sons Ltd.

Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis.

PubMed

Lenz, Tobias L; Eizaguirre, Christophe; Rotter, Björn; Kalbe, Martin; Milinski, Manfred

2013-02-01

Understanding the extent of local adaptation in natural populations and the mechanisms that allow individuals to adapt to their native environment is a major avenue in molecular ecology research. Evidence for the frequent occurrence of diverging ecotypes in species that inhabit multiple ecological habitats is accumulating, but experimental approaches to understanding the biological pathways as well as the underlying genetic mechanisms are still rare. Parasites are invoked as one of the major selective forces driving evolution and are themselves dependent on the ecological conditions in a given habitat. Immunological adaptation to local parasite communities is therefore expected to be a key component of local adaptation in natural populations. Here, we use next-generation sequencing technology to compare the transcriptome-wide response of experimentally infected three-spined sticklebacks from a lake and a river population, which are known to evolve under selection by distinct parasite communities. By comparing overall gene expression levels as well as the activation of functional pathways in response to parasite exposure, we identified potential differences between the two stickleback populations at several levels. Our results suggest locally adapted patterns of gene regulation in response to parasite exposure, which may reflect different local optima in the trade-off between the benefits and the disadvantages of mounting an immune response because of quantitative differences of the local parasite communities. © 2012 Blackwell Publishing Ltd.

How to pattern a leaf.

PubMed

Bolduc, N; O'Connor, D; Moon, J; Lewis, M; Hake, S

2012-01-01

Leaf development presents a tremendous resource for tackling the question of patterning in biology. Leaves can be simple or highly dissected. They may have elaborated parts such as the tendrils of a pea leaf or the rolled blade of a carnivorous pitcher plant. Despite the variation in size, shape, and function, all leaves initiate in the same manner: from the flanks of a meristem. The maize leaf is useful for analysis of patterning due to the wealth of mutants and the distinct tissues along the proximal distal axis. The blade is distal, the sheath is proximal, and the ligule forms at the blade/sheath boundary. Establishment of this boundary involves the transcription factors LIGULELESS1 and LIGULELESS2 and the kinase LIGULELESS NARROW. The meristem-specific protein KNOTTED1 (KN1) binds and modulates the lg2 gene. Given the localization of KN1 at the proximal end of the leaf from the time of inception, we hypothesize that KN1 has a role in establishing the very proximal end of the leaf, whereas an auxin maximum guides the growing distal tip.

Early Mesozoic rift basin architecture and sediment routing system in the Moroccan High Atlas

NASA Astrophysics Data System (ADS)

Perez, N.; Teixell, A.; Gomez, D.

2016-12-01

Late Permian to Triassic extensional systems associated with Pangea breakup governed the structural framework and rift basin architecture that was inherited by Cenozoic High Atlas Mountains in Morocco. U-Pb detrital zircon geochronologic and mapping results from Permo-Triassic deposits now incorporated into the High Atlas Mountains provide new constraints on the geometry and interconnectivity among synextensional depocenters. U-Pb detrital zircon data provide provenance constraints of Permo-Triassic deposits, highlighting temporal changes in sediment sources and revealing the spatial pattern of sediment routing along the rift. We also characterize the U-Pb detrital zircon geochronologic signature of distinctive interfingering fluvial, tidal, and aeolian facies that are preferentially preserved near the controlling normal faults. These results highlight complex local sediment mixing patterns potentially linked to the interplay between fault motion, eustatic, and erosion/transport processes. We compare our U-Pb geochronologic results with existing studies of Gondwanan and Laurentian cratonic blocks to investigate continent scale sediment routing pathways, and with analogous early Mesozoic extensional systems situated in South America (Mitu basin, Peru) and North America (Newark Basin) to assess sediment mixing patterns in rift basins.

Multifaceted plasma membrane Ca(2+) pumps: From structure to intracellular Ca(2+) handling and cancer.

PubMed

Padányi, Rita; Pászty, Katalin; Hegedűs, Luca; Varga, Karolina; Papp, Béla; Penniston, John T; Enyedi, Ágnes

2016-06-01

Plasma membrane Ca(2+) ATPases (PMCAs) are intimately involved in the control of intracellular Ca(2+) concentration. They reduce Ca(2+) in the cytosol not only by direct ejection, but also by controlling the formation of inositol-1,4,5-trisphosphate and decreasing Ca(2+) release from the endoplasmic reticulum Ca(2+) pool. In mammals four genes (PMCA1-4) are expressed, and alternative RNA splicing generates more than twenty variants. The variants differ in their regulatory characteristics. They localize into highly specialized membrane compartments and respond to the incoming Ca(2+) with distinct temporal resolution. The expression pattern of variants depends on cell type; a change in this pattern can result in perturbed Ca(2+) homeostasis and thus altered cell function. Indeed, PMCAs undergo remarkable changes in their expression pattern during tumorigenesis that might significantly contribute to the unbalanced Ca(2+) homeostasis of cancer cells. This article is part of a Special Issue entitled: Calcium and Cell Fate. Guest Editors: Jacques Haiech, Claus Heizmann, Joachim Krebs, Thierry Capiod and Olivier Mignen. Copyright © 2015 Elsevier B.V. All rights reserved.

Distinct patterns of notochord mineralization in zebrafish coincide with the localization of Osteocalcin isoform 1 during early vertebral centra formation

PubMed Central

2012-01-01

Background In chondrichthyans, basal osteichthyans and tetrapods, vertebral bodies have cartilaginous anlagen that subsequently mineralize (chondrichthyans) or ossify (osteichthyans). Chondrocytes that form the vertebral centra derive from somites. In teleost fish, vertebral centrum formation starts in the absence of cartilage, through direct mineralization of the notochord sheath. In a second step, the notochord is surrounded by somite-derived intramembranous bone. In several small teleost species, including zebrafish (Danio rerio), even haemal and neural arches form directly as intramembranous bone and only modified caudalmost arches remain cartilaginous. This study compares initial patterns of mineralization in different regions of the vertebral column in zebrafish. We ask if the absence or presence of cartilaginous arches influences the pattern of notochord sheath mineralization. Results To reveal which cells are involved in mineralization of the notochord sheath we identify proliferating cells, we trace mineralization on the histological level and we analyze cell ultrastructure by TEM. Moreover, we localize proteins and genes that are typically expressed by skeletogenic cells such as Collagen type II, Alkaline phosphatase (ALP) and Osteocalcin (Oc). Mineralization of abdominal and caudal vertebrae starts with a complete ring within the notochord sheath and prior to the formation of the bony arches. In contrast, notochord mineralization of caudal fin centra starts with a broad ventral mineral deposition, associated with the bases of the modified cartilaginous arches. Similar, arch-related, patterns of mineralization occur in teleosts that maintain cartilaginous arches throughout the spine. Throughout the entire vertebral column, we were able to co-localize ALP-positive signal with chordacentrum mineralization sites, as well as Collagen II and Oc protein accumulation in the mineralizing notochord sheath. In the caudal fin region, ALP and Oc signals were clearly produced both by the notochord epithelium and cells outside the notochord, the cartilaginous arches. Based on immunostaining, real time PCR and oc2:gfp transgenic fish, we identify Oc in the mineralizing notochord sheath as osteocalcin isoform 1 (Oc1). Conclusions If notochord mineralization occurs prior to arch formation, mineralization of the notochord sheath is ring-shaped. If notochord mineralization occurs after cartilaginous arch formation, mineralization of the notochord sheath starts at the insertion point of the arches, with a basiventral origin. The presence of ALP and Oc1, not only in cells outside the notochord, but also in the notochord epithelium, suggests an active role of the notochord in the mineralization process. The same may apply to Col II-positive chondrocytes of the caudalmost haemal arches that show ALP activity and Oc1 accumulation, since these chondrocytes do not mineralize their own cartilage matrix. Even without cartilaginous preformed vertebral centra, the cartilaginous arches may have an inductive role in vertebral centrum formation, possibly contributing to the distinct mineralization patterns of zebrafish vertebral column and caudal fin vertebral fusion. PMID:23043290

Distinct patterns of notochord mineralization in zebrafish coincide with the localization of Osteocalcin isoform 1 during early vertebral centra formation.

PubMed

Bensimon-Brito, Anabela; Cardeira, João; Cancela, Maria Leonor; Huysseune, Ann; Witten, Paul Eckhard

2012-10-09

In chondrichthyans, basal osteichthyans and tetrapods, vertebral bodies have cartilaginous anlagen that subsequently mineralize (chondrichthyans) or ossify (osteichthyans). Chondrocytes that form the vertebral centra derive from somites. In teleost fish, vertebral centrum formation starts in the absence of cartilage, through direct mineralization of the notochord sheath. In a second step, the notochord is surrounded by somite-derived intramembranous bone. In several small teleost species, including zebrafish (Danio rerio), even haemal and neural arches form directly as intramembranous bone and only modified caudalmost arches remain cartilaginous. This study compares initial patterns of mineralization in different regions of the vertebral column in zebrafish. We ask if the absence or presence of cartilaginous arches influences the pattern of notochord sheath mineralization. To reveal which cells are involved in mineralization of the notochord sheath we identify proliferating cells, we trace mineralization on the histological level and we analyze cell ultrastructure by TEM. Moreover, we localize proteins and genes that are typically expressed by skeletogenic cells such as Collagen type II, Alkaline phosphatase (ALP) and Osteocalcin (Oc). Mineralization of abdominal and caudal vertebrae starts with a complete ring within the notochord sheath and prior to the formation of the bony arches. In contrast, notochord mineralization of caudal fin centra starts with a broad ventral mineral deposition, associated with the bases of the modified cartilaginous arches. Similar, arch-related, patterns of mineralization occur in teleosts that maintain cartilaginous arches throughout the spine.Throughout the entire vertebral column, we were able to co-localize ALP-positive signal with chordacentrum mineralization sites, as well as Collagen II and Oc protein accumulation in the mineralizing notochord sheath. In the caudal fin region, ALP and Oc signals were clearly produced both by the notochord epithelium and cells outside the notochord, the cartilaginous arches. Based on immunostaining, real time PCR and oc2:gfp transgenic fish, we identify Oc in the mineralizing notochord sheath as osteocalcin isoform 1 (Oc1). If notochord mineralization occurs prior to arch formation, mineralization of the notochord sheath is ring-shaped. If notochord mineralization occurs after cartilaginous arch formation, mineralization of the notochord sheath starts at the insertion point of the arches, with a basiventral origin. The presence of ALP and Oc1, not only in cells outside the notochord, but also in the notochord epithelium, suggests an active role of the notochord in the mineralization process. The same may apply to Col II-positive chondrocytes of the caudalmost haemal arches that show ALP activity and Oc1 accumulation, since these chondrocytes do not mineralize their own cartilage matrix. Even without cartilaginous preformed vertebral centra, the cartilaginous arches may have an inductive role in vertebral centrum formation, possibly contributing to the distinct mineralization patterns of zebrafish vertebral column and caudal fin vertebral fusion.

Finger Vein Recognition Based on Local Directional Code

PubMed Central

Meng, Xianjing; Yang, Gongping; Yin, Yilong; Xiao, Rongyang

2012-01-01

Finger vein patterns are considered as one of the most promising biometric authentication methods for its security and convenience. Most of the current available finger vein recognition methods utilize features from a segmented blood vessel network. As an improperly segmented network may degrade the recognition accuracy, binary pattern based methods are proposed, such as Local Binary Pattern (LBP), Local Derivative Pattern (LDP) and Local Line Binary Pattern (LLBP). However, the rich directional information hidden in the finger vein pattern has not been fully exploited by the existing local patterns. Inspired by the Webber Local Descriptor (WLD), this paper represents a new direction based local descriptor called Local Directional Code (LDC) and applies it to finger vein recognition. In LDC, the local gradient orientation information is coded as an octonary decimal number. Experimental results show that the proposed method using LDC achieves better performance than methods using LLBP. PMID:23202194

Finger vein recognition based on local directional code.

PubMed

Meng, Xianjing; Yang, Gongping; Yin, Yilong; Xiao, Rongyang

2012-11-05

Finger vein patterns are considered as one of the most promising biometric authentication methods for its security and convenience. Most of the current available finger vein recognition methods utilize features from a segmented blood vessel network. As an improperly segmented network may degrade the recognition accuracy, binary pattern based methods are proposed, such as Local Binary Pattern (LBP), Local Derivative Pattern (LDP) and Local Line Binary Pattern (LLBP). However, the rich directional information hidden in the finger vein pattern has not been fully exploited by the existing local patterns. Inspired by the Webber Local Descriptor (WLD), this paper represents a new direction based local descriptor called Local Directional Code (LDC) and applies it to finger vein recognition. In LDC, the local gradient orientation information is coded as an octonary decimal number. Experimental results show that the proposed method using LDC achieves better performance than methods using LLBP.

76 FR 43993 - Notice of Availability for Exclusive, Non-Exclusive, or Partially-Exclusive Licensing of an...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... Agents by Measuring Distinct Pattern in the Levels of Expression of Specific Genes AGENCY: Department of... Measuring Distinct Pattern in the Levels of Expression of Specific Genes,'' issued November 13, 2001. The... determining a difference in the detected amount of protein/gene expression between exposed and unexposed...

The evolution of contact calls in isolated and overlapping populations of two white-eye congeners in East Africa (Aves, Zosterops).

PubMed

Husemann, Martin; Ulrich, Werner; Habel, Jan Christian

2014-06-02

Closely related species often occur in geographic isolation, yet sometimes form contact zones with the potential to hybridize. Pre-zygotic barriers may prevent cross breeding in such contact zones. In East Africa, White-eye birds have evolved into various species, inhabiting different habitat types. Zosterops poliogaster is found in cool and moist cloud forests at higher elevations, whereas Z. abyssinicus is distributed across the dry and hot lowland savannahs. In most areas, these two species occur allopatrically, but in the contact zone where the mountain meets the savannah, the distributions of these species sometimes overlap (parapatry), and in a few areas the two taxa occur sympatrically. Acoustic communication is thought to be an important species recognition mechanism in birds and an effective prezygotic barrier for hybridisation. We recorded contact calls of both the lowland and highland species in (i) distinct populations (allopatry), (ii) along contact zones (parapatry), and (iii) in overlapping populations (sympatry) to test for species and population differentiation. We found significant differences in call characteristics between the highland and lowland species, in addition to call differentiation within species. The highland Z. poliogaster shows a strong call differentiation among local populations, accompanied by comparatively low variability in their contact calls within populations (i.e. a small acoustic space). In contrast, calls of the lowland Z. abyssinicus are not differentiated among local sites but show relatively high variability in calls within single populations. Call patterns in both species show geographic clines in relation to latitude and longitude. Calls from parapatric populations from both species showed greater similarity to the other taxon in comparison to heterospecific populations found in allopatry. However, where the two species occur sympatrically, contact calls of both species are more distinct from each other than in either allopatric or parapatric populations. The contrasting patterns reflect divergent spatial distributions: the highland Z. poliogaster populations are highly disjunct, while Z. abyssinicus lowland populations are interconnected. Higher similarity in contact calls of heterospecific populations might be due to intermixing. In contrast, sympatric populations show reproductive character displacement which leads to strongly divergent call patterns.

Craniofacial divergence by distinct prenatal growth patterns in Fgfr2 mutant mice

PubMed Central

2014-01-01

Background Differences in cranial morphology arise due to changes in fundamental cell processes like migration, proliferation, differentiation and cell death driven by genetic programs. Signaling between fibroblast growth factors (FGFs) and their receptors (FGFRs) affect these processes during head development and mutations in FGFRs result in congenital diseases including FGFR-related craniosynostosis syndromes. Current research in model organisms focuses primarily on how these mutations change cell function local to sutures under the hypothesis that prematurely closing cranial sutures contribute to skull dysmorphogenesis. Though these studies have provided fundamentally important information contributing to the understanding of craniosynostosis conditions, knowledge of changes in cell function local to the sutures leave change in overall three-dimensional cranial morphology largely unexplained. Here we investigate growth of the skull in two inbred mouse models each carrying one of two gain-of-function mutations in FGFR2 on neighboring amino acids (S252W and P253R) that in humans cause Apert syndrome, one of the most severe FGFR-related craniosynostosis syndromes. We examine late embryonic skull development and suture patency in Fgfr2 Apert syndrome mice between embryonic day 17.5 and birth and quantify the effects of these mutations on 3D skull morphology, suture patency and growth. Results We show in mice what studies in humans can only infer: specific cranial growth deviations occur prenatally and worsen with time in organisms carrying these FGFR2 mutations. We demonstrate that: 1) distinct skull morphologies of each mutation group are established by E17.5; 2) cranial suture patency patterns differ between mice carrying these mutations and their unaffected littermates; 3) the prenatal skull grows differently in each mutation group; and 4) unique Fgfr2-related cranial morphologies are exacerbated by late embryonic growth patterns. Conclusions Our analysis of mutation-driven changes in cranial growth provides a previously missing piece of knowledge necessary for explaining variation in emergent cranial morphologies and may ultimately be helpful in managing human cases carrying these same mutations. This information is critical to the understanding of craniofacial development, disease and evolution and may contribute to the evaluation of incipient therapeutic strategies. PMID:24580805

Bending, wrinkling, and folding of thin polymer film/elastomer interfaces

NASA Astrophysics Data System (ADS)

Ebata, Yuri

This work focuses on understanding the buckling deformation mechanisms of bending, wrinkling, and folding that occur on the surfaces and interfaces of polymer systems. We gained fundamental insight into the formation mechanism of these buckled structures for thin glassy films placed on an elastomeric substrate. By taking advantage of geometric confinement, we demonstrated new strategies in controlling wrinkling morphologies. We were able to achieve surfaces with controlled patterned structures which will have a broad impact in optical, adhesive, microelectronics, and microfluidics applications. Wrinkles and strain localized features, such as delaminations and folds, are observed in many natural systems and are useful for a wide range of patterning applications. However, the transition from sinusoidal wrinkles to more complex strain localized structures is not well understood. We investigated the onset of wrinkling and strain localizations under uniaxial strain. We show that careful measurement of feature amplitude allowed not only the determination of wrinkle, fold, or delamination onset, but also allowed clear distinction between each feature. The folds observed in this experiment have an outward morphology from the surface in contrast to folds that form into the plane, as observed in a film floating on a liquid substrate. A critical strain map was constructed, where the critical strain was measured experimentally for wrinkling, folding, and delamination with varying film thickness and modulus. Wrinkle morphologies, i.e. amplitude and wavelength of wrinkles, affect properties such as electron transport in stretchable electronics and adhesion properties of smart surfaces. To gain an understanding of how the wrinkle morphology can be controlled, we introduced a geometrical confinement in the form of rigid boundaries. Upon straining, we found that wrinkles started near the rigid boundaries where maximum local strain occurred and propagated towards the middle as more global strain was applied. In contrast to homogeneous wrinkling with constant amplitude that is observed for an unconfined system, the wrinkling observed here had varying amplitude as a function of distance from the rigid boundaries. We demonstrated that the number of wrinkles can be tuned by controlling the distance between the rigid boundaries. Location of wrinkles was also controlled by introducing local stress distributions via patterning the elastomeric substrate. Two distinct wrinkled regions were achieved on a surface where the film is free-standing over a circular hole pattern and where the film is supported by the substrate. The hoe diameter and applied strain affected the wavelength and amplitude of the free-standing membrane. Using discontinuous dewetting, a one-step fabrication method was developed to selectively deposit a small volume of liquid in patterned microwells and encapsulate it with a polymeric film. The pull-out velocity, a velocity at which the sample is removed from a bath of liquid, was controlled to observe how encapsulation process is affected. The polymeric film was observed to wrinkle at low pull-out velocity due to no encapsulation of liquid; whereas the film bent at medium pull-out velocity due to capillary effect as the liquid evaporated through the film. To quantify the amount of liquid encapsulated, we mixed salt in water and measured the size of the deposited salt crystals. The salt crystal size, and hence the amount of liquid encapsulated, was controlled by varying either the encapsulation velocity or the size of the patterned microwells. In addition, we showed that the deposited salt crystals are protected by the laminated film until the film is removed, providing advantageous control for delivery and release. Yeast cells were also captured in the microwells to show the versatility. This encapsulation method is useful for wide range of applications, such as trapping single cells for biological studies, growing microcrystals for optical and magnetic applications, and single-use sensor technologies.

Contract management in USA hospitals: service duplication and access within local markets.

PubMed

Carey, Kathleen; Dor, Avi

2008-08-01

This paper examines the extent to which hospitals that are under external contract management engage in service duplication, as well as the degree to which the various services they offer contribute to or detract from community access. The study incorporates all USA hospitals using data from the American Hospital Association Annual Survey Database, supplemented by county level measures obtained from the area resource file (ARF). Using data on the 3794 hospitals classified as acute care facilities in 2002, we performed a set of logistic regressions that analyzed whether a hospital offered each of 74 distinct services. For each service (regression), key independent variables measured the number of other hospitals in the local market area that also offered the service. Local area market definitions are the areas circumscribed by the hospital within distances of 10 and 20 miles. Results suggest that contract-managed (CM) hospitals display a more competitive pattern (service duplication) than hospitals in general, but CM hospitals that are the sole provider of services locally are less likely to offer services than traditionally managed sole hospital providers. Contract management does not appear to offer any particular advantages in improving access to hospital services.

Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize.

PubMed

Selinger, D A; Chandler, V L

1999-12-21

The b locus encodes a transcription factor that regulates the expression of genes that produce purple anthocyanin pigment. Different b alleles are expressed in distinct tissues, causing tissue-specific anthocyanin production. Understanding how phenotypic diversity is produced and maintained at the b locus should provide models for how other regulatory genes, including those that influence morphological traits and development, evolve. We have investigated how different levels and patterns of pigmentation have evolved by determining the phenotypic and evolutionary relationships between 18 alleles that represent the diversity of b alleles in Zea mays. Although most of these alleles have few phenotypic differences, five alleles have very distinct tissue-specific patterns of pigmentation. Superimposing the phenotypes on the molecular phylogeny reveals that the alleles with strong and distinctive patterns of expression are closely related to alleles with weak expression, implying that the distinctive patterns have arisen recently. We have identified apparent insertions in three of the five phenotypically distinct alleles, and the fourth has unique upstream restriction fragment length polymorphisms relative to closely related alleles. The insertion in B-Peru has been shown to be responsible for its unique expression and, in the other two alleles, the presence of the insertion correlates with the phenotype. These results suggest that major changes in gene expression are probably the result of large-scale changes in DNA sequence and/or structure most likely mediated by transposable elements.

Concordant Biogeographic Patterns among Multiple Taxonomic Groups in the Mexican Freshwater Biota

PubMed Central

Quiroz-Martínez, Benjamín; Álvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

2014-01-01

In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins. PMID:25136979

Feature and Statistical Model Development in Structural Health Monitoring

NASA Astrophysics Data System (ADS)

Kim, Inho

All structures suffer wear and tear because of impact, excessive load, fatigue, corrosion, etc. in addition to inherent defects during their manufacturing processes and their exposure to various environmental effects. These structural degradations are often imperceptible, but they can severely affect the structural performance of a component, thereby severely decreasing its service life. Although previous studies of Structural Health Monitoring (SHM) have revealed extensive prior knowledge on the parts of SHM processes, such as the operational evaluation, data processing, and feature extraction, few studies have been conducted from a systematical perspective, the statistical model development. The first part of this dissertation, the characteristics of inverse scattering problems, such as ill-posedness and nonlinearity, reviews ultrasonic guided wave-based structural health monitoring problems. The distinctive features and the selection of the domain analysis are investigated by analytically searching the conditions of the uniqueness solutions for ill-posedness and are validated experimentally. Based on the distinctive features, a novel wave packet tracing (WPT) method for damage localization and size quantification is presented. This method involves creating time-space representations of the guided Lamb waves (GLWs), collected at a series of locations, with a spatially dense distribution along paths at pre-selected angles with respect to the direction, normal to the direction of wave propagation. The fringe patterns due to wave dispersion, which depends on the phase velocity, are selected as the primary features that carry information, regarding the wave propagation and scattering. The following part of this dissertation presents a novel damage-localization framework, using a fully automated process. In order to construct the statistical model for autonomous damage localization deep-learning techniques, such as restricted Boltzmann machine and deep belief network, are trained and utilized to interpret nonlinear far-field wave patterns. Next, a novel bridge scour estimation approach that comprises advantages of both empirical and data-driven models is developed. Two field datasets from the literature are used, and a Support Vector Machine (SVM), a machine-learning algorithm, is used to fuse the field data samples and classify the data with physical phenomena. The Fast Non-dominated Sorting Genetic Algorithm (NSGA-II) is evaluated on the model performance objective functions to search for Pareto optimal fronts.

Multiscale Spatial Modeling of Human Exposure from Local Sources to Global Intake.

PubMed

Wannaz, Cedric; Fantke, Peter; Jolliet, Olivier

2018-01-16

Exposure studies, used in human health risk and impact assessments of chemicals, are largely performed locally or regionally. It is usually not known how global impacts resulting from exposure to point source emissions compare to local impacts. To address this problem, we introduce Pangea, an innovative multiscale, spatial multimedia fate and exposure assessment model. We study local to global population exposure associated with emissions from 126 point sources matching locations of waste-to-energy plants across France. Results for three chemicals with distinct physicochemical properties are expressed as the evolution of the population intake fraction through inhalation and ingestion as a function of the distance from sources. For substances with atmospheric half-lives longer than a week, less than 20% of the global population intake through inhalation (median of 126 emission scenarios) can occur within a 100 km radius from the source. This suggests that, by neglecting distant low-level exposure, local assessments might only account for fractions of global cumulative intakes. We also study ∼10 000 emission locations covering France more densely to determine per chemical and exposure route which locations minimize global intakes. Maps of global intake fractions associated with each emission location show clear patterns associated with population and agriculture production densities.

Dissecting DNA damage response pathways by analyzing protein localization and abundance changes during DNA replication stress

PubMed Central

Tkach, Johnny M.; Yimit, Askar; Lee, Anna Y.; Riffle, Michael; Costanzo, Michael; Jaschob, Daniel; Hendry, Jason A.; Ou, Jiongwen; Moffat, Jason; Boone, Charles; Davis, Trisha N.; Nislow, Corey; Brown, Grant W.

2012-01-01

Re-localization of proteins is a hallmark of the DNA damage response. We use high-throughput microscopic screening of the yeast GFP fusion collection to develop a systems-level view of protein re-organization following drug-induced DNA replication stress. Changes in protein localization and abundance reveal drug-specific patterns of functional enrichments. Classification of proteins by sub-cellular destination allows the identification of pathways that respond to replication stress. We analyzed pairwise combinations of GFP fusions and gene deletion mutants to define and order two novel DNA damage responses. In the first, Cmr1 forms subnuclear foci that are regulated by the histone deacetylase Hos2 and are distinct from the typical Rad52 repair foci. In a second example, we find that the checkpoint kinases Mec1/Tel1 and the translation regulator Asc1 regulate P-body formation. This method identifies response pathways that were not detected in genetic and protein interaction screens, and can be readily applied to any form of chemical or genetic stress to reveal cellular response pathways. PMID:22842922

Urban and nomadic isotopic niches reveal dietary connectivities along Central Asia's Silk Roads.

PubMed

Hermes, Taylor R; Frachetti, Michael D; Bullion, Elissa A; Maksudov, Farhod; Mustafokulov, Samariddin; Makarewicz, Cheryl A

2018-03-26

The ancient 'Silk Roads' formed a vast network of trade and exchange that facilitated the movement of commodities and agricultural products across medieval Central Asia via settled urban communities and mobile pastoralists. Considering food consumption patterns as an expression of socio-economic interaction, we analyse human remains for carbon and nitrogen isotopes in order to establish dietary intake, then model isotopic niches to characterize dietary diversity and infer connectivity among communities of urbanites and nomadic pastoralists. The combination of low isotopic variation visible within urban groups with isotopic distinction between urban communities irrespective of local environmental conditions strongly suggests localized food production systems provided primary subsistence rather than agricultural goods exchanged along trade routes. Nomadic communities, in contrast, experienced higher dietary diversity reflecting engagements with a wide assortment of foodstuffs typical for mobile communities. These data indicate tightly bound social connectivity in urban centres pointedly funnelled local food products and homogenized dietary intake within settled communities, whereas open and opportunistic systems of food production and circulation were possible through more mobile lifeways.

Localization of basic fibroblast growth factor binding sites in the chick embryonic neural retina.

PubMed

Cirillo, A; Arruti, C; Courtois, Y; Jeanny, J C

1990-12-01

We have investigated the localization of basic fibroblast growth factor (bFGF) binding sites during the development of the neural retina in the chick embryo. The specificity of the affinity of bFGF for its receptors was assessed by competition experiments with unlabelled growth factor or with heparin, as well as by heparitinase treatment of the samples. Two different types of binding sites were observed in the neural retina by light-microscopic autoradiography. The first type, localized mainly to basement membranes, was highly sensitive to heparitinase digestion and to competition with heparin. It was not developmentally regulated. The second type of binding site, resistant to heparin competition, appeared to be associated with retinal cells from the earliest stages studied (3-day-old embryo, stages 21-22 of Hamburger and Hamilton). Its distribution was found to vary during embryonic development, paralleling layering of the neural retina. Binding of bFGF to the latter sites was observed throughout the retinal neuroepithelium at early stages but displayed a distinct pattern at the time when the inner and outer plexiform layers were formed. During the development of the inner plexiform layer, a banded pattern of bFGF binding was observed. These bands, lying parallel to the vitreal surface, seemed to codistribute with the synaptic bands existing in the inner plexiform layer. The presence of intra-retinal bFGF binding sites whose distribution varies with embryonic development suggests a regulatory mechanism involving differential actions of bFGF on neural retinal cells.

The evolution of sexual size dimorphism in the house finch. II. Population divergence in relation to local selection.

PubMed

Badyaev, A V; Hill, G E; Stoehr, A M; Nolan, P M; McGraw, K J

2000-12-01

Recent colonization of ecologically distinct areas in North America by the house finch (Carpodacus mexicanus) was accompanied by strong population divergence in sexual size dimorphism. Here we examined whether this divergence was produced by population differences in local selection pressures acting on each sex. In a long-term study of recently established populations in Alabama, Michigan, and Montana, we examined three selection episodes for each sex: selection for pairing success, overwinter survival, and within-season fecundity. Populations varied in intensity of these selection episodes, the contribution of each episode to the net selection, and in the targets of selection. Direction and intensity of selection strongly differed between sexes, and different selection episodes often favored opposite changes in morphological traits. In each population, current net selection for sexual dimorphism was highly concordant with observed sexual dimorphism--in each population, selection for dimorphism was the strongest on the most dimorphic traits. Strong directional selection on sexually dimorphic traits, and similar intensities of selection in both sexes, suggest that in each of the recently established populations, both males and females are far from their local fitness optimum, and that sexual dimorphism has arisen from adaptive responses in both sexes. Population differences in patterns of selection on dimorphism, combined with both low levels of ontogenetic integration in heritable sexually dimorphic traits and sexual dimorphism in growth patterns, may account for the close correspondence between dimorphism in selection and observed dimorphism in morphology across house finch populations.

Neural correlates of processing facial identity based on features versus their spacing.

PubMed

Maurer, D; O'Craven, K M; Le Grand, R; Mondloch, C J; Springer, M V; Lewis, T L; Grady, C L

2007-04-08

Adults' expertise in recognizing facial identity involves encoding subtle differences among faces in the shape of individual facial features (featural processing) and in the spacing among features (a type of configural processing called sensitivity to second-order relations). We used fMRI to investigate the neural mechanisms that differentiate these two types of processing. Participants made same/different judgments about pairs of faces that differed only in the shape of the eyes and mouth, with minimal differences in spacing (featural blocks), or pairs of faces that had identical features but differed in the positions of those features (spacing blocks). From a localizer scan with faces, objects, and houses, we identified regions with comparatively more activity for faces, including the fusiform face area (FFA) in the right fusiform gyrus, other extrastriate regions, and prefrontal cortices. Contrasts between the featural and spacing conditions revealed distributed patterns of activity differentiating the two conditions. A region of the right fusiform gyrus (near but not overlapping the localized FFA) showed greater activity during the spacing task, along with multiple areas of right frontal cortex, whereas left prefrontal activity increased for featural processing. These patterns of activity were not related to differences in performance between the two tasks. The results indicate that the processing of facial features is distinct from the processing of second-order relations in faces, and that these functions are mediated by separate and lateralized networks involving the right fusiform gyrus, although the FFA as defined from a localizer scan is not differentially involved.

The effect of feature-based attention on flanker interference processing: An fMRI-constrained source analysis.

PubMed

Siemann, Julia; Herrmann, Manfred; Galashan, Daniela

2018-01-25

The present study examined whether feature-based cueing affects early or late stages of flanker conflict processing using EEG and fMRI. Feature cues either directed participants' attention to the upcoming colour of the target or were neutral. Validity-specific modulations during interference processing were investigated using the N200 event-related potential (ERP) component and BOLD signal differences. Additionally, both data sets were integrated using an fMRI-constrained source analysis. Finally, the results were compared with a previous study in which spatial instead of feature-based cueing was applied to an otherwise identical flanker task. Feature-based and spatial attention recruited a common fronto-parietal network during conflict processing. Irrespective of attention type (feature-based; spatial), this network responded to focussed attention (valid cueing) as well as context updating (invalid cueing), hinting at domain-general mechanisms. However, spatially and non-spatially directed attention also demonstrated domain-specific activation patterns for conflict processing that were observable in distinct EEG and fMRI data patterns as well as in the respective source analyses. Conflict-specific activity in visual brain regions was comparable between both attention types. We assume that the distinction between spatially and non-spatially directed attention types primarily applies to temporal differences (domain-specific dynamics) between signals originating in the same brain regions (domain-general localization).

Seasonal and diurnal variations of ozone at a high-altitude mountain baseline station in East Asia

NASA Astrophysics Data System (ADS)

Ou Yang, Chang-Feng; Lin, Neng-Huei; Sheu, Guey-Rong; Lee, Chung-Te; Wang, Jia-Lin

2012-01-01

Continuous measurements of tropospheric ozone were conducted at the Lulin Atmospheric Background Station (LABS) at an altitude of 2862 m from April 2006 to the end of 2009. Distinct seasonal variations in the ozone concentration were observed at the LABS, with a springtime maximum and a summertime minimum. Based on a backward trajectory analysis, CO data, and ozonesondes, the springtime maximum was most likely caused by the long-range transport of air masses from Southeast Asia, where biomass burning was intense in spring. In contrast, a greater Pacific influence contributed to the summertime minimum. In addition to seasonal variations, a distinct diurnal pattern was also observed at the LABS, with a daytime minimum and a nighttime maximum. The daytime ozone minimum was presumably caused by sinks of dry deposition and NO titration during the up-slope transport of surface air. The higher nighttime values, however, could be the result of air subsidence at night bringing ozone aloft to the LABS. After filtering out the daytime data to remove possible local surface contributions, the average background ozone value for the period of 2006-2009 was approximately 36.6 ppb, increased from 32.3 ppb prior to data filtering, without any changes in the seasonal pattern. By applying HYSPLIT4 model analysis, the origins of the air masses contributing to the background ozone observed at the LABS were investigated.

Activity-Dependent Inhibitory Gating in Molecular Signaling Cascades Induces a Novel Form of Intermediate-Term Synaptic Facilitation in "Aplysia Californica"

ERIC Educational Resources Information Center

Fischbach, Soren; Kopec, Ashley M.; Carew, Thomas J.

2014-01-01

Mechanistically distinct forms of long-lasting plasticity and memory can be induced by a variety of different training patterns. Although several studies have identified distinct molecular pathways that are engaged during these different training patterns, relatively little work has explored potential interactions between pathways when they are…

Dietary patterns in Liberian refugees in Buduburam, Ghana.

PubMed

Ross, Wilhelmenia L; Gallego-Pérez, Daniel F; Lartey, Anna; Sandow, Adam; Pérez-Escamilla, Rafael; Hromi-Fiedler, Amber

2017-10-01

Previous research suggests that acculturation (i.e., exposure and assimilation to local culture) is associated with changes in dietary patterns among immigrants. This study investigates this association in a refugee population using time in refugee settlement as a proxy for acculturation. A cross-sectional survey was conducted among a systematic sample to (a) identify dietary patterns in Liberian refugees and Ghanaians living in or near a refugee settlement, (b) compare adherence to these dietary patterns between groups, and (c) investigate the association between acculturation and dietary patterns in Liberian refugees. Participants were Liberian and Ghanaian women with young children living in the Buduburam refugee settlement or Awutu in Ghana (n = 480; 50% Liberian; mean age 28, SD 6.3, range 16-48 years). Time in settlement was assessed by self-report; food consumption was assessed by food frequency questionnaire. Principal component analysis was used to identify dietary patterns; a generalized linear model was used to test the association of interest. Three distinct dietary patterns emerged: Healthy, Sweets, and Fats. Ghanaians were more adherent to the Healthy pattern than Liberians (p < 0.05). Liberians were more adherent to the Sweets and Fats patterns than Ghanaians (p < 0.05). There were no significant differences in dietary pattern adherence among the Liberians based on time in settlement. Ghanaians living in Awutu were more adherent to the Healthy pattern than Ghanaians who lived in settlement (p < 0.05). Differences in dietary patterns were observed between Liberian refugees and Ghanaians. These differences were not associated with acculturation and may be related to the food environment in the settlement. © 2016 John Wiley & Sons Ltd.

Co-localization patterns of neurotensin receptor 1 and tyrosine hydroxylase in brain regions involved in motivation and social behavior in male European starlings.

PubMed

Merullo, Devin P; Spool, Jeremy A; Zhao, Changjiu; Riters, Lauren V

2018-04-01

Animals communicate in distinct social contexts to convey information specific to those contexts, such as sexual or agonistic motivation. In seasonally-breeding male songbirds, seasonal changes in day length and increases in testosterone stimulate sexually-motivated song directed at females for courtship and reproduction. Dopamine and testosterone may act in the same brain regions to stimulate sexually-motivated singing. The neuropeptide neurotensin, acting at the neurotensin receptor 1 (NTR1), can strongly influence dopamine transmission. The goal of this study was to gain insight into the degree to which seasonal changes in physiology modify interactions between neurotensin and dopamine to adjust context-appropriate communication. Male European starlings were examined in physiological conditions that stimulate season-typical forms of communication: late summer/early fall non-breeding condition (low testosterone; birds sing infrequently), late fall non-breeding condition (low testosterone; birds produce non-sexually motivated song), and spring breeding condition (high testosterone; males produce sexually-motivated song). Double fluorescent immunolabeling was performed to detect co-localization patterns between tyrosine hydroxylase (TH; the rate-limiting enzyme in dopamine synthesis) and NTR1 in brain regions implicated in motivation and song production (the ventral tegmental area, medial preoptic nucleus, periaqueductal gray, and lateral septum). Co-localization between TH and NTR1 was present in the ventral tegmental area for all physiological conditions, and the number of co-localized cells did not differ across conditions. Immunolabeling for TH and NTR1 was also present in the other examined regions, although no co-localization was seen. These results support the hypothesis that interactions between NTR1 and dopamine in the ventral tegmental area may modulate vocalizations, but suggest that testosterone- or photoperiod-induced changes in NTR1/TH co-localization do not underlie seasonally-appropriate adjustment of communication. Copyright © 2018 Elsevier B.V. All rights reserved.

A 15-year climatology of wind pattern impacts on surface ozone in Houston, Texas

NASA Astrophysics Data System (ADS)

Souri, Amir Hossein; Choi, Yunsoo; Li, Xiangshang; Kotsakis, Alexander; Jiang, Xun

2016-06-01

Houston is recognized for its large petrochemical industrial facilities providing abundant radicals for tropospheric ozone formation. Fortunately, maximum daily 8-h average (MDA8) surface ozone concentrations have declined in Houston (- 0.6 ± 0.3 ppbv yr- 1) during the summers (i.e., May to September) of 2000 to 2014, possibly due to the reductions in precursor emissions by effective control policies. However, it is also possible that changes in meteorological variables have affected ozone concentrations. This study focused on the impact of long-term wind patterns which have the highest impact on ozone in Houston. The analysis of long-term wind patterns can benefit surface ozone studies by 1) providing wind patterns that distinctly changed ozone levels, 2) investigating the frequency of patterns and the respective changes and 3) estimating ozone trends in specific wind patterns that local emissions are mostly involved, thus separating emissions impacts from meteorology to some extent. To this end, the 900-hPa flow patterns in summers of 2000 to 2014 were clustered in seven classes (C1-C7) by deploying an unsupervised partitioning method. We confirm the characteristics of the clusters from a backward trajectory analysis, monitoring networks, and a regional chemical transport model simulation. The results indicate that Houston has experienced a statistically significant downward trend (- 0.6 ± 0.4 day yr- 1) of the cluster of weak easterly and northeasterly days (C4), when the highest fraction of ozone exceedances (MDA8 > 70 ppbv) occurred. This suggests that the reduction in ozone precursors was not the sole reason for the decrease in ozone exceedance days (- 1.5 ± 0.6 day yr- 1). Further, to examine the efficiency of control policies intended to reduce the amount of ozone, we estimated the trend of MDA8 ozone in C4 and C5 (weak winds) days when local emissions are primarily responsible for high ambient ozone levels. Both C4 and C5 show a large reduction in the 95th percentile and summertime trends mainly due to effective control strategies. Based on the 5th percentile daytime ozone for C1 (strong southeasterly wind) in coastal sites, this study found that the cleanest air masses that Houston received became more polluted during the summer of 2000-2014 by 1-3 ppbv. Though this study focused on Houston, the analysis method presented could generally be used to estimate ozone trends in other regions where surface ozone is dominantly influenced by both wind patterns and local emissions.

Many local pattern texture features: which is better for image-based multilabel human protein subcellular localization classification?

PubMed

Yang, Fan; Xu, Ying-Ying; Shen, Hong-Bin

2014-01-01

Human protein subcellular location prediction can provide critical knowledge for understanding a protein's function. Since significant progress has been made on digital microscopy, automated image-based protein subcellular location classification is urgently needed. In this paper, we aim to investigate more representative image features that can be effectively used for dealing with the multilabel subcellular image samples. We prepared a large multilabel immunohistochemistry (IHC) image benchmark from the Human Protein Atlas database and tested the performance of different local texture features, including completed local binary pattern, local tetra pattern, and the standard local binary pattern feature. According to our experimental results from binary relevance multilabel machine learning models, the completed local binary pattern, and local tetra pattern are more discriminative for describing IHC images when compared to the traditional local binary pattern descriptor. The combination of these two novel local pattern features and the conventional global texture features is also studied. The enhanced performance of final binary relevance classification model trained on the combined feature space demonstrates that different features are complementary to each other and thus capable of improving the accuracy of classification.

Geographical patterns of human diet derived from stable-isotope analysis of fingernails

USGS Publications Warehouse

Nardoto, G.B.; Silva, S.; Kendall, C.; Ehleringer, J.R.; Chesson, L.A.; Ferraz, E.S.B.; Moreira, M.Z.; Ometto, Jean P. H. B.; Martinelli, L.A.

2006-01-01

Carbon and nitrogen isotope ratios of human fingernails were measured in 490 individuals in the western US and 273 individuals in southeastern Brazil living in urban areas, and 53 individuals living in a moderately isolated area in the central Amazon region of Brazil and consuming mostly locally grown foods. In addition, we measured the carbon and nitrogen isotope ratios of common food items to assess the extent to which these isotopic signatures remain distinct for people eating both omnivorous and vegetarian diets and living in different parts of the world, and the extent to which dietary information can be interpreted from these analyses. Fingernail ??13C values (mean ?? standard deviation) were -15.4 ?? 1.0 and -18.8 ?? 0.8??? and ??15N values were 10.4 ?? 0.7 and 9.4 ?? 0.6??? for southeastern Brazil and western US populations, respectively. Despite opportunities for a "global supermarket" effect to swamp out carbon and nitrogen isotope ratios in these two urbanized regions of the world, differences in the fingernail isotope ratios between southeastern Brazil and western US populations persisted, and appeared to be more associated with regional agricultural and animal production practices. Omnivores and vegetarians from Brazil and the US were isotopically distinct, both within and between regions. In a comparison of fingernails of individuals from an urban city and isolated communities in the Amazonian region, the urban region was similar to southeastern Brazil, whereas individuals from isolated nonurban communities showed distinctive isotopic values consistent with their diets and with the isotopic values of local foods. Although there is a tendency for a "global supermarket" diet, carbon and nitrogen isotopes of human fingernails hold dietary information directly related to both food sources and dietary practices in a region. ?? 2006 Wiley-Liss, Inc.

Geographical patterns of human diet derived from stable-isotope analysis of fingernails.

PubMed

Nardoto, Gabriela B; Silva, Steven; Kendall, Carol; Ehleringer, James R; Chesson, Lesley A; Ferraz, Epaminondas S B; Moreira, Marcelo Z; Ometto, Jean P H B; Martinelli, Luiz A

2006-09-01

Carbon and nitrogen isotope ratios of human fingernails were measured in 490 individuals in the western US and 273 individuals in southeastern Brazil living in urban areas, and 53 individuals living in a moderately isolated area in the central Amazon region of Brazil and consuming mostly locally grown foods. In addition, we measured the carbon and nitrogen isotope ratios of common food items to assess the extent to which these isotopic signatures remain distinct for people eating both omnivorous and vegetarian diets and living in different parts of the world, and the extent to which dietary information can be interpreted from these analyses. Fingernail delta13C values (mean +/- standard deviation) were -15.4 +/- 1.0 and -18.8 +/- 0.8 per thousand and delta15N values were 10.4 +/- 0.7 and 9.4 +/- 0.6 per thousand for southeastern Brazil and western US populations, respectively. Despite opportunities for a "global supermarket" effect to swamp out carbon and nitrogen isotope ratios in these two urbanized regions of the world, differences in the fingernail isotope ratios between southeastern Brazil and western US populations persisted, and appeared to be more associated with regional agricultural and animal production practices. Omnivores and vegetarians from Brazil and the US were isotopically distinct, both within and between regions. In a comparison of fingernails of individuals from an urban city and isolated communities in the Amazonian region, the urban region was similar to southeastern Brazil, whereas individuals from isolated nonurban communities showed distinctive isotopic values consistent with their diets and with the isotopic values of local foods. Although there is a tendency for a "global supermarket" diet, carbon and nitrogen isotopes of human fingernails hold dietary information directly related to both food sources and dietary practices in a region. 2006 Wiley-Liss, Inc.

Regulation of Ras Exchange Factors and Cellular Localization of Ras Activation by Lipid Messengers in T Cells

PubMed Central

Jun, Jesse E.; Rubio, Ignacio; Roose, Jeroen P.

2013-01-01

The Ras-MAPK signaling pathway is highly conserved throughout evolution and is activated downstream of a wide range of receptor stimuli. Ras guanine nucleotide exchange factors (RasGEFs) catalyze GTP loading of Ras and play a pivotal role in regulating receptor-ligand induced Ras activity. In T cells, three families of functionally important RasGEFs are expressed: RasGRF, RasGRP, and Son of Sevenless (SOS)-family GEFs. Early on it was recognized that Ras activation is critical for T cell development and that the RasGEFs play an important role herein. More recent work has revealed that nuances in Ras activation appear to significantly impact T cell development and selection. These nuances include distinct biochemical patterns of analog versus digital Ras activation, differences in cellular localization of Ras activation, and intricate interplays between the RasGEFs during distinct T cell developmental stages as revealed by various new mouse models. In many instances, the exact nature of these nuances in Ras activation or how these may result from fine-tuning of the RasGEFs is not understood. One large group of biomolecules critically involved in the control of RasGEFs functions are lipid second messengers. Multiple, yet distinct lipid products are generated following T cell receptor (TCR) stimulation and bind to different domains in the RasGRP and SOS RasGEFs to facilitate the activation of the membrane-anchored Ras GTPases. In this review we highlight how different lipid-based elements are generated by various enzymes downstream of the TCR and other receptors and how these dynamic and interrelated lipid products may fine-tune Ras activation by RasGEFs in developing T cells. PMID:24027568

Recording, analysis, and interpretation of spreading depolarizations in neurointensive care: Review and recommendations of the COSBID research group.

PubMed

Dreier, Jens P; Fabricius, Martin; Ayata, Cenk; Sakowitz, Oliver W; William Shuttleworth, C; Dohmen, Christian; Graf, Rudolf; Vajkoczy, Peter; Helbok, Raimund; Suzuki, Michiyasu; Schiefecker, Alois J; Major, Sebastian; Winkler, Maren Kl; Kang, Eun-Jeung; Milakara, Denny; Oliveira-Ferreira, Ana I; Reiffurth, Clemens; Revankar, Gajanan S; Sugimoto, Kazutaka; Dengler, Nora F; Hecht, Nils; Foreman, Brandon; Feyen, Bart; Kondziella, Daniel; Friberg, Christian K; Piilgaard, Henning; Rosenthal, Eric S; Westover, M Brandon; Maslarova, Anna; Santos, Edgar; Hertle, Daniel; Sánchez-Porras, Renán; Jewell, Sharon L; Balança, Baptiste; Platz, Johannes; Hinzman, Jason M; Lückl, Janos; Schoknecht, Karl; Schöll, Michael; Drenckhahn, Christoph; Feuerstein, Delphine; Eriksen, Nina; Horst, Viktor; Bretz, Julia S; Jahnke, Paul; Scheel, Michael; Bohner, Georg; Rostrup, Egill; Pakkenberg, Bente; Heinemann, Uwe; Claassen, Jan; Carlson, Andrew P; Kowoll, Christina M; Lublinsky, Svetlana; Chassidim, Yoash; Shelef, Ilan; Friedman, Alon; Brinker, Gerrit; Reiner, Michael; Kirov, Sergei A; Andrew, R David; Farkas, Eszter; Güresir, Erdem; Vatter, Hartmut; Chung, Lee S; Brennan, K C; Lieutaud, Thomas; Marinesco, Stephane; Maas, Andrew Ir; Sahuquillo, Juan; Dahlem, Markus A; Richter, Frank; Herreras, Oscar; Boutelle, Martyn G; Okonkwo, David O; Bullock, M Ross; Witte, Otto W; Martus, Peter; van den Maagdenberg, Arn Mjm; Ferrari, Michel D; Dijkhuizen, Rick M; Shutter, Lori A; Andaluz, Norberto; Schulte, André P; MacVicar, Brian; Watanabe, Tomas; Woitzik, Johannes; Lauritzen, Martin; Strong, Anthony J; Hartings, Jed A

2017-05-01

Spreading depolarizations (SD) are waves of abrupt, near-complete breakdown of neuronal transmembrane ion gradients, are the largest possible pathophysiologic disruption of viable cerebral gray matter, and are a crucial mechanism of lesion development. Spreading depolarizations are increasingly recorded during multimodal neuromonitoring in neurocritical care as a causal biomarker providing a diagnostic summary measure of metabolic failure and excitotoxic injury. Focal ischemia causes spreading depolarization within minutes. Further spreading depolarizations arise for hours to days due to energy supply-demand mismatch in viable tissue. Spreading depolarizations exacerbate neuronal injury through prolonged ionic breakdown and spreading depolarization-related hypoperfusion (spreading ischemia). Local duration of the depolarization indicates local tissue energy status and risk of injury. Regional electrocorticographic monitoring affords even remote detection of injury because spreading depolarizations propagate widely from ischemic or metabolically stressed zones; characteristic patterns, including temporal clusters of spreading depolarizations and persistent depression of spontaneous cortical activity, can be recognized and quantified. Here, we describe the experimental basis for interpreting these patterns and illustrate their translation to human disease. We further provide consensus recommendations for electrocorticographic methods to record, classify, and score spreading depolarizations and associated spreading depressions. These methods offer distinct advantages over other neuromonitoring modalities and allow for future refinement through less invasive and more automated approaches.

Recording, analysis, and interpretation of spreading depolarizations in neurointensive care: Review and recommendations of the COSBID research group

PubMed Central

Fabricius, Martin; Ayata, Cenk; Sakowitz, Oliver W; William Shuttleworth, C; Dohmen, Christian; Graf, Rudolf; Vajkoczy, Peter; Helbok, Raimund; Suzuki, Michiyasu; Schiefecker, Alois J; Major, Sebastian; Winkler, Maren KL; Kang, Eun-Jeung; Milakara, Denny; Oliveira-Ferreira, Ana I; Reiffurth, Clemens; Revankar, Gajanan S; Sugimoto, Kazutaka; Dengler, Nora F; Hecht, Nils; Foreman, Brandon; Feyen, Bart; Kondziella, Daniel; Friberg, Christian K; Piilgaard, Henning; Rosenthal, Eric S; Westover, M Brandon; Maslarova, Anna; Santos, Edgar; Hertle, Daniel; Sánchez-Porras, Renán; Jewell, Sharon L; Balança, Baptiste; Platz, Johannes; Hinzman, Jason M; Lückl, Janos; Schoknecht, Karl; Schöll, Michael; Drenckhahn, Christoph; Feuerstein, Delphine; Eriksen, Nina; Horst, Viktor; Bretz, Julia S; Jahnke, Paul; Scheel, Michael; Bohner, Georg; Rostrup, Egill; Pakkenberg, Bente; Heinemann, Uwe; Claassen, Jan; Carlson, Andrew P; Kowoll, Christina M; Lublinsky, Svetlana; Chassidim, Yoash; Shelef, Ilan; Friedman, Alon; Brinker, Gerrit; Reiner, Michael; Kirov, Sergei A; Andrew, R David; Farkas, Eszter; Güresir, Erdem; Vatter, Hartmut; Chung, Lee S; Brennan, KC; Lieutaud, Thomas; Marinesco, Stephane; Maas, Andrew IR; Sahuquillo, Juan; Dahlem, Markus A; Richter, Frank; Herreras, Oscar; Boutelle, Martyn G; Okonkwo, David O; Bullock, M Ross; Witte, Otto W; Martus, Peter; van den Maagdenberg, Arn MJM; Ferrari, Michel D; Dijkhuizen, Rick M; Shutter, Lori A; Andaluz, Norberto; Schulte, André P; MacVicar, Brian; Watanabe, Tomas; Woitzik, Johannes; Lauritzen, Martin; Strong, Anthony J; Hartings, Jed A

2016-01-01

Spreading depolarizations (SD) are waves of abrupt, near-complete breakdown of neuronal transmembrane ion gradients, are the largest possible pathophysiologic disruption of viable cerebral gray matter, and are a crucial mechanism of lesion development. Spreading depolarizations are increasingly recorded during multimodal neuromonitoring in neurocritical care as a causal biomarker providing a diagnostic summary measure of metabolic failure and excitotoxic injury. Focal ischemia causes spreading depolarization within minutes. Further spreading depolarizations arise for hours to days due to energy supply-demand mismatch in viable tissue. Spreading depolarizations exacerbate neuronal injury through prolonged ionic breakdown and spreading depolarization-related hypoperfusion (spreading ischemia). Local duration of the depolarization indicates local tissue energy status and risk of injury. Regional electrocorticographic monitoring affords even remote detection of injury because spreading depolarizations propagate widely from ischemic or metabolically stressed zones; characteristic patterns, including temporal clusters of spreading depolarizations and persistent depression of spontaneous cortical activity, can be recognized and quantified. Here, we describe the experimental basis for interpreting these patterns and illustrate their translation to human disease. We further provide consensus recommendations for electrocorticographic methods to record, classify, and score spreading depolarizations and associated spreading depressions. These methods offer distinct advantages over other neuromonitoring modalities and allow for future refinement through less invasive and more automated approaches. PMID:27317657

Buffer kinetics shape the spatiotemporal patterns of IP3-evoked Ca2+ signals

PubMed Central

Dargan, Sheila L; Parker, Ian

2003-01-01

Ca2+ liberation through inositol 1,4,5-trisphosphate receptors (IP3Rs) plays a universal role in cell regulation, and specificity of cell signalling is achieved through the spatiotemporal patterning of Ca2+ signals. IP3Rs display Ca2+-induced Ca2+ release (CICR), but are grouped in clusters so that regenerative Ca2+ signals may remain localized to individual clusters, or propagate globally between clusters by successive cycles of Ca2+ diffusion and CICR. We used confocal microscopy and photoreleased IP3 in Xenopus oocytes to study how these properties are modulated by mobile cytosolic Ca2+ buffers. EGTA (a buffer with slow ‘on-rate’) speeded Ca2+ signals and ‘balkanized’ Ca2+ waves by dissociating them into local signals. In contrast, BAPTA (a fast buffer with similar affinity) slowed Ca2+ responses and promoted ‘globalization’ of spatially uniform Ca2+ signals. These actions are likely to arise through differential effects on Ca2+ feedback within and between IP3R clusters, because Ca2+ signals evoked by influx through voltage-gated channels were little affected. We propose that cell-specific expression of Ca2+-binding proteins with distinct kinetics may shape the time course and spatial distribution of IP3-evoked Ca2+ signals for specific physiological roles. PMID:14555715

Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae.

PubMed

Soriano, Ignacio; Morafraile, Esther C; Vázquez, Enrique; Antequera, Francisco; Segurado, Mónica

2014-09-13

Eukaryotic genomes are replicated during S phase according to a temporal program. Several determinants control the timing of origin firing, including the chromatin environment and epigenetic modifications. However, how chromatin structure influences the timing of the activation of specific origins is still poorly understood. By performing high-resolution analysis of genome-wide nucleosome positioning we have identified different chromatin architectures at early and late replication origins. These different patterns are already established in G1 and are tightly correlated with the organization of adjacent transcription units. Moreover, specific early and late nucleosomal patterns are fixed robustly, even in rpd3 mutants in which histone acetylation and origin timing have been significantly altered. Nevertheless, higher histone acetylation levels correlate with the local modulation of chromatin structure, leading to increased origin accessibility. In addition, we conducted parallel analyses of replication and nucleosome dynamics that revealed that chromatin structure at origins is modulated during origin activation. Our results show that early and late replication origins present distinctive nucleosomal configurations, which are preferentially associated to different genomic regions. Our data also reveal that origin structure is dynamic and can be locally modulated by histone deacetylation, as well as by origin activation. These data offer novel insight into the contribution of chromatin structure to origin selection and firing in budding yeast.

Novel localization of peripherin 2, the photoreceptor-specific retinal degeneration slow protein, in retinal pigment epithelium.

PubMed

Uhl, Patrizia B; Amann, Barbara; Hauck, Stefanie M; Deeg, Cornelia A

2015-01-26

Retinal pigment epithelium (RPE) builds the outer blood-retinal barrier of the eye. Since one typical feature of the autoimmune disease, equine recurrent uveitis (ERU), is the breakdown of this barrier, we recently performed comparative analysis of healthy and uveitic RPE. We identified for the first time peripherin 2, which is responsible for visual perception and retina development, to be localized in RPE. The purpose of this study was therefore to validate our findings by characterizing the expression patterns of peripherin 2 in RPE and retina. We also investigated whether peripherin 2 expression changes in ERU and if it is expressed by the RPE itself. Via immunohistochemistry, significant downregulation of peripherin 2 in uveitic RPE compared to the control was detectable, but there was no difference in healthy and uveitic retina. A further interesting finding was the clear distinction between peripherin 2 and the phagocytosis marker, rhodopsin, in healthy RPE. In conclusion, changes in the expression pattern of peripherin 2 selectively affect RPE, but not retina, in ERU. Moreover, peripherin 2 is clearly detectable in healthy RPE due to both phagocytosis and the expression by the RPE cells themselves. Our novel findings are very promising for better understanding the molecular mechanisms taking place on RPE in uveitis.

Differential expression of members of the annexin multigene family in Arabidopsis

NASA Technical Reports Server (NTRS)

Clark, G. B.; Sessions, A.; Eastburn, D. J.; Roux, S. J.

2001-01-01

Although in most plant species no more than two annexin genes have been reported to date, seven annexin homologs have been identified in Arabidopsis, Annexin Arabidopsis 1-7 (AnnAt1--AnnAt7). This establishes that annexins can be a diverse, multigene protein family in a single plant species. Here we compare and analyze these seven annexin gene sequences and present the in situ RNA localization patterns of two of these genes, AnnAt1 and AnnAt2, during different stages of Arabidopsis development. Sequence analysis of AnnAt1--AnnAt7 reveals that they contain the characteristic four structural repeats including the more highly conserved 17-amino acid endonexin fold region found in vertebrate annexins. Alignment comparisons show that there are differences within the repeat regions that may have functional importance. To assess the relative level of expression in various tissues, reverse transcription-PCR was carried out using gene-specific primers for each of the Arabidopsis annexin genes. In addition, northern blot analysis using gene-specific probes indicates differences in AnnAt1 and AnnAt2 expression levels in different tissues. AnnAt1 is expressed in all tissues examined and is most abundant in stems, whereas AnnAt2 is expressed mainly in root tissue and to a lesser extent in stems and flowers. In situ RNA localization demonstrates that these two annexin genes display developmentally regulated tissue-specific and cell-specific expression patterns. These patterns are both distinct and overlapping. The developmental expression patterns for both annexins provide further support for the hypothesis that annexins are involved in the Golgi-mediated secretion of polysaccharides.

The genetics of amphibian decline: population substructure and molecular differentiation in the Yosemite toad, Bufo canorus (Anura, Bufonidae) based on single-strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence data

USGS Publications Warehouse

Shaffer, H. Bradley; Fellers, Gary M.; Magee, Allison; Voss, S. Randal

2000-01-01

We present a comprehensive survey of genetic variation across the range of the narrowly distributed endemic Yosemite toad Bufo canorus, a declining amphibian restricted to the Sierra Nevada of California. Based on 322 bp of mitochondrial cytochrome b sequence data, we found limited support for the monophyly of B. canorus and its closely related congener B. exsul to the exclusion of the widespread western toad B. boreas. However, B. exsul was always phylogenetically nested within B. canorus, suggesting that the latter may not be monophyletic. SSCP (single-strand conformation polymorphism) analysis of 372 individual B. canorus from 28 localities in Yosemite and Kings Canyon National Parks revealed no shared haplotypes among these two regions and lead us to interpret these two parks as distinct management units for B. canorus. Within Yosemite, we found significant genetic substructure both at the level of major drainages and among breeding ponds. Kings Canyon samples show a different pattern, with substantial variation among breeding sites, but no substructure among drainages. Across the range of B. canorus as well as among Yosemite ponds, we found an isolation-by-distance pattern suggestive of a stepping stone model of migration. However, in Kings Canyon we found no hint of such a pattern, suggesting that movement patterns of toads may be quite different in these nearby parklands. Our data imply that management for B. canorus should focus at the individual pond level, and effective management may necessitate reintroductions if local extirpations occur. A brief review of other pond-breeding anurans suggests that highly structured populations are often the case, and thus that our results for B. canorus may be general for other species of frogs and toads.

Numerical studies of the KP line-solitons

NASA Astrophysics Data System (ADS)

Chakravarty, S.; McDowell, T.; Osborne, M.

2017-03-01

The Kadomtsev-Petviashvili (KP) equation admits a class of solitary wave solutions localized along distinct rays in the xy-plane, called the line-solitons, which describe the interaction of shallow water waves on a flat surface. These wave interactions have been observed on long, flat beaches, as well as have been recreated in laboratory experiments. In this paper, the line-solitons are investigated via direct numerical simulations of the KP equation, and the interactions of the evolved solitary wave patterns are studied. The objective is to obtain greater insight into solitary wave interactions in shallow water and to determine the extent the KP equation is a good model in describing these nonlinear interactions.

Response of local vascular volumes to lower body negative pressure stress

NASA Technical Reports Server (NTRS)

Wolthuis, R. A.; Leblanc, A.; Carpentier, W. A.; Bergman, S. A., Jr.

1975-01-01

The present study involved an intravenous injection of radioactive iodinated serum albumin, equilibration of this isotope within the vascular space, and the continuous measurement of isotope activity over selected anatomical areas before, during and following multiple human LBNP tests. Both rate and magnitude of vascular pooling were distinctly different within each of five selected lower body anatomical areas. In the upper body, all areas except the abdomen showed depletions from their resting vascular volumes during LBNP. The presence of uniquely different pooling patterns in the lower body, the apparent stability of abdominal vascular volumes, and a possible decrease in cerebral blood volume during LBNP represent the major findings of this study.

Criticality in Neuronal Networks

NASA Astrophysics Data System (ADS)

Friedman, Nir; Ito, Shinya; Brinkman, Braden A. W.; Shimono, Masanori; Deville, R. E. Lee; Beggs, John M.; Dahmen, Karin A.; Butler, Tom C.

2012-02-01

In recent years, experiments detecting the electrical firing patterns in slices of in vitro brain tissue have been analyzed to suggest the presence of scale invariance and possibly criticality in the brain. Much of the work done however has been limited in two ways: 1) the data collected is from local field potentials that do not represent the firing of individual neurons; 2) the analysis has been primarily limited to histograms. In our work we examine data based on the firing of individual neurons (spike data), and greatly extend the analysis by considering shape collapse and exponents. Our results strongly suggest that the brain operates near a tuned critical point of a highly distinctive universality class.

New insights into the nucleolar localization of a plant RNA virus-encoded protein that acts in both RNA packaging and RNA silencing suppression: involvement of importins alpha and relevance for viral infection.

PubMed

Pérez-Cañamás, Miryam; Hernández, Carmen

2018-05-21

Despite replication of plus strand RNA viruses takes place in the cytoplasm of host cells, different proteins encoded by these infectious agents have been shown to localize in the nucleus, with high accumulation at the nucleolus. In most cases, the molecular determinants and/or biological significance of such subcellular localization remain elusive. Recently, we reported that protein p37 encoded by Pelargonium line pattern virus (family Tombusviridae) acts in both RNA packaging and RNA silencing suppression. Connsistently with these functions, p37 was detected in the cytoplasm of plant cells though it was also present in the nucleus and, particularly, in the nucleolus. Here, we have aimed to gain further insights into factors influencing p37 nucleolar localization and into its potential relevance for viral infection. Besides mapping the protein region containing the nucleolar localization signal, we have found that p37 interacts with distinct members of the importin alpha family -main cellular transporters for nucleo-cytoplasmic traffic of proteins-, and that these interactions are crucial for nucleolar targeting of p37. Impairment of p37 nucleolar localization through down-regulation of importin alpha expression resulted in a reduction of viral accumulation, suggesting that sorting of the protein to the major subnuclear compartment is advantageous for the infection process.

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

PubMed Central

Banaticla-Hilario, Maria Celeste N; van den Berg, Ronald G; Hamilton, Nigel Ruaraidh Sackville; McNally, Kenneth L

2013-01-01

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by FST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (HE = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (HE = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species. PMID:24101993

Dissociation of neural mechanisms underlying orientation processing in humans

PubMed Central

Ling, Sam; Pearson, Joel; Blake, Randolph

2009-01-01

Summary Orientation selectivity is a fundamental, emergent property of neurons in early visual cortex, and discovery of that property [1, 2] dramatically shaped how we conceptualize visual processing [3–6]. However, much remains unknown about the neural substrates of these basic building blocks of perception, and what is known primarily stems from animal physiology studies. To probe the neural concomitants of orientation processing in humans, we employed repetitive transcranial magnetic stimulation (rTMS) to attenuate neural responses evoked by stimuli presented within a local region of the visual field. Previous physiological studies have shown that rTMS can significantly suppress the neuronal spiking activity, hemodynamic responses, and local field potentials within a focused cortical region [7, 8]. By suppressing neural activity with rTMS, we were able to dissociate components of the neural circuitry underlying two distinct aspects of orientation processing: selectivity and contextual effects. Orientation selectivity gauged by masking was unchanged by rTMS, whereas an otherwise robust orientation repulsion illusion was weakened following rTMS. This dissociation implies that orientation processing relies on distinct mechanisms, only one of which was impacted by rTMS. These results are consistent with models positing that orientation selectivity is largely governed by the patterns of convergence of thalamic afferents onto cortical neurons, with intracortical activity then shaping population responses contained within those orientation-selective cortical neurons. PMID:19682905

A new mechanism for spatial pattern formation via lateral and protrusion-mediated lateral signalling

PubMed Central

Hunter, Ginger L.; Baum, Buzz

2016-01-01

Tissue organization and patterning are critical during development when genetically identical cells take on different fates. Lateral signalling plays an important role in this process by helping to generate self-organized spatial patterns in an otherwise uniform collection of cells. Recent data suggest that lateral signalling can be mediated both by junctional contacts between neighbouring cells and via cellular protrusions that allow non-neighbouring cells to interact with one another at a distance. However, it remains unclear precisely how signalling mediated by these distinct types of cell–cell contact can physically contribute to the generation of complex patterns without the assistance of diffusible morphogens or pre-patterns. To explore this question, in this work we develop a model of lateral signalling based on a single receptor/ligand pair as exemplified by Notch and Delta. We show that allowing the signalling kinetics to differ at junctional versus protrusion-mediated contacts, an assumption inspired by recent data which show that the cleavage of Notch in several systems requires both Delta binding and the application of mechanical force, permits individual cells to act to promote both lateral activation and lateral inhibition. Strikingly, under this model, in which Delta can sequester Notch, a variety of patterns resembling those typical of reaction–diffusion systems is observed, together with more unusual patterns that arise when we consider changes in signalling kinetics, and in the length and distribution of protrusions. Importantly, these patterns are self-organizing—so that local interactions drive tissue-scale patterning. Together, these data show that protrusions can, in principle, generate different types of patterns in addition to contributing to long-range signalling and to pattern refinement. PMID:27807273

Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

PubMed

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra--host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern--nearctic and southern--neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance--decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.

Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

PubMed Central

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis. PMID:24086342

The Serotonin Transporter Undergoes Constitutive Internalization and Is Primarily Sorted to Late Endosomes and Lysosomal Degradation*

PubMed Central

Rahbek-Clemmensen, Troels; Bay, Tina; Eriksen, Jacob; Gether, Ulrik; Jørgensen, Trine Nygaard

2014-01-01

The serotonin transporter (SERT) plays a critical role in regulating serotonin signaling by mediating reuptake of serotonin from the extracellular space. The molecular and cellular mechanisms controlling SERT levels in the membrane remain poorly understood. To study trafficking of the surface resident SERT, two functional epitope-tagged variants were generated. Fusion of a FLAG-tagged one-transmembrane segment protein Tac to the SERT N terminus generated a transporter with an extracellular epitope suited for trafficking studies (TacSERT). Likewise, a construct with an extracellular antibody epitope was generated by introducing an HA (hemagglutinin) tag in the extracellular loop 2 of SERT (HA-SERT). By using TacSERT and HA-SERT in antibody-based internalization assays, we show that SERT undergoes constitutive internalization in a dynamin-dependent manner. Confocal images of constitutively internalized SERT demonstrated that SERT primarily co-localized with the late endosomal/lysosomal marker Rab7, whereas little co-localization was observed with the Rab11, a marker of the “long loop” recycling pathway. This sorting pattern was distinct from that of a prototypical recycling membrane protein, the β2-adrenergic receptor. Furthermore, internalized SERT co-localized with the lysosomal marker LysoTracker and not with transferrin. The sorting pattern was further confirmed by visualizing internalization of SERT using the fluorescent cocaine analog JHC1-64 and by reversible and pulse-chase biotinylation assays showing evidence for lysosomal degradation of the internalized transporter. Finally, we found that SERT internalized in response to stimulation with 12-myristate 13-acetate co-localized primarily with Rab7- and LysoTracker-positive compartments. We conclude that SERT is constitutively internalized and that the internalized transporter is sorted mainly to degradation. PMID:24973209

Preservation of the genetic diversity of a local common carp in the agricultural heritage rice–fish system

PubMed Central

Ren, Weizheng; Hu, Liangliang; Guo, Liang; Zhang, Jian; Tang, Lu; Zhang, Entao; Zhang, Jiaen; Luo, Shiming; Tang, Jianjun; Chen, Xin

2018-01-01

We examined how traditional farmers preserve the genetic diversity of a local common carp (Cyprinus carpio), which is locally referred to as “paddy field carp” (PF-carp), in a “globally important agricultural heritage system” (GIAHS), i.e., the 1,200-y-old rice–fish coculture system in Zhejiang Province, China. Our molecular and morphological analysis showed that the PF-carp has changed into a distinct local population with higher genetic diversity and diverse color types. Within this GIAHS region, PF-carps exist as a continuous metapopulation, although three genetic groups could be identified by microsatellite markers. Thousands of small farmer households interdependently obtained fry and parental carps for their own rice–fish production, resulting in a high gene flow and large numbers of parent carps distributing in a mosaic pattern in the region. Landscape genetic analysis indicated that farmers’ connectivity was one of the major factors that shaped this genetic pattern. Population viability analysis further revealed that the numbers of these interconnected small farmer households and their connection intensity affect the carps’ inherent genetic diversity. The practice of mixed culturing of carps with diverse color types helped to preserve a wide range of genetic resources in the paddy field. This widespread traditional practice increases fish yield and resource use, which, in return, encourages famers to continue their practice of selecting and conserving diverse color types of PF-carp. Our results suggested that traditional farmers secure the genetic diversity of PF-carp and its viability over generations in this region through interdependently incubating and mixed-culturing practices within the rice−fish system. PMID:29295926

AUDITORY NUCLEI: DISTINCTIVE RESPONSE PATTERNS TO WHITE NOISE AND TONES IN UNANESTHETIZED CATS.

PubMed

GALIN, D

1964-10-09

Electrical responses to "white" noise and tonal stimuli were recorded from unanesthetized cats with permanently implanted bipolar electrodes. The cochlear nucleus, inferior colliculus, and medial geniculate each showed distinctive patterns of evoked activity. White noise and tones produced qualitatively different types of response. A decrease in activity characterized the response of the inferior colliculus to tonal stimuli.

Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections.

PubMed

Pava, Zuleima; Noviyanti, Rintis; Handayuni, Irene; Trimarsanto, Hidayat; Trianty, Leily; Burdam, Faustina H; Kenangalem, Enny; Utami, Retno A S; Tirta, Yusrifar K; Coutrier, Farah; Poespoprodjo, Jeanne R; Price, Ric N; Marfurt, Jutta; Auburn, Sarah

2017-01-01

Genetic analyses of Plasmodium have potential to inform on transmission dynamics, but few studies have evaluated this on a local spatial scale. We used microsatellite genotyping to characterise the micro-epidemiology of P. vivax and P. falciparum diversity to inform malaria control strategies in Timika, Papua Indonesia. Genotyping was undertaken on 713 sympatric P. falciparum and P. vivax isolates from a cross-sectional household survey and clinical studies conducted in Timika. Standard population genetic measures were applied, and the data was compared to published data from Kalimantan, Bangka, Sumba and West Timor. Higher diversity (HE = 0.847 vs 0.625; p = 0.017) and polyclonality (46.2% vs 16.5%, p<0.001) were observed in P. vivax versus P. falciparum. Distinct P. falciparum substructure was observed, with two subpopulations, K1 and K2. K1 was comprised solely of asymptomatic infections and displayed greater relatedness to isolates from Sumba than to K2, possibly reflecting imported infections. The results demonstrate the greater refractoriness of P. vivax versus P. falciparum to control measures, and risk of distinct parasite subpopulations persisting in the community undetected by passive surveillance. These findings highlight the need for complimentary new surveillance strategies to identify transmission patterns that cannot be detected with traditional malariometric methods.

Different influences on lexical priming for integrative, thematic, and taxonomic relations

PubMed Central

Jones, Lara L.; Golonka, Sabrina

2012-01-01

Word pairs may be integrative (i.e., combination of two concepts into one meaningful entity; e.g., fruit—cake), thematically related (i.e., connected in time and place; e.g., party—cake), and/or taxonomically related (i.e., shared features and category co-members; e.g., muffin—cake). Using participant ratings and computational measures, we demonstrated distinct patterns across measures of similarity and co-occurrence, and familiarity for each relational construct in two different item sets. In a standard lexical decision task (LDT) with various delays between prime and target presentation (SOAs), target RTs and priming magnitudes were consistent across the three relations for both item sets. However, across the SOAs, there were distinct patterns among the three relations on some of the underlying measures influencing target word recognition (LSA, Google, and BEAGLE). These distinct patterns suggest different mechanisms of lexical priming and further demonstrate that integrative relations are distinct from thematic and taxonomic relations. PMID:22798950

Phytogeographic patterns and cryptic diversity in an aposematic toad from NW Argentina.

PubMed

Clemente-Carvalho, Rute B; Vaira, Marcos; King, Laura E; Koscinski, Daria; Bonansea, Maria I; Lougheed, Stephen C

2017-11-01

The Yungas Redbelly Toad, Melanophryniscus rubriventris, is patchily distributed in Argentina, confined to the upland portion (1000-2000m above sea level) of the montane forests of northern and central regions of Salta, and in central-eastern and south-eastern Jujuy. This species is known for its striking aposematic color variation across its geographic distribution, and was once treated as a complex of three subspecies based on distinctive color patterns. Here we assess the geographical genetic variation within M. rubriventris and quantify divergence in color and pattern among individuals sampled from Northwestern Argentina. We compare multi-gene phylogeography of M. rubriventris to patterns of dorsal and ventral coloration to test whether evolutionary affinities predict variation in warning color. Our results reveal two well-supported species lineages: one confined to the extreme northern portion of our sampling area, and the other extending over most of the Argentine portion of the species' range, within which there are two populations. However, these well-supported evolutionary relationships do not mirror the marked variation in warning coloration. This discordance between DNA genealogy and warning color variation may reflect selection brought about by differences in local predation pressures, potentially coupled with effects of sexual selection and thermoregulation. Copyright © 2017 Elsevier Inc. All rights reserved.

Immune networks: multitasking capabilities near saturation

NASA Astrophysics Data System (ADS)

Agliari, E.; Annibale, A.; Barra, A.; Coolen, A. C. C.; Tantari, D.

2013-10-01

Pattern-diluted associative networks were recently introduced as models for the immune system, with nodes representing T-lymphocytes and stored patterns representing signalling protocols between T- and B-lymphocytes. It was shown earlier that in the regime of extreme pattern dilution, a system with NT T-lymphocytes can manage a number N_B={ {O}}(N_T^\\delta ) of B-lymphocytes simultaneously, with δ < 1. Here we study this model in the extensive load regime NB = αNT, with a high degree of pattern dilution, in agreement with immunological findings. We use graph theory and statistical mechanical analysis based on replica methods to show that in the finite-connectivity regime, where each T-lymphocyte interacts with a finite number of B-lymphocytes as NT → ∞, the T-lymphocytes can coordinate effective immune responses to an extensive number of distinct antigen invasions in parallel. As α increases, the system eventually undergoes a second order transition to a phase with clonal cross-talk interference, where the system’s performance degrades gracefully. Mathematically, the model is equivalent to a spin system on a finitely connected graph with many short loops, so one would expect the available analytical methods, which all assume locally tree-like graphs, to fail. Yet it turns out to be solvable. Our results are supported by numerical simulations.

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.

Gaseous templates in ant nests.

PubMed

Cox, M D; Blanchard, G B

2000-05-21

We apply a diffusion model to the atmosphere of ant nests. With particular reference to carbon dioxide (CO2), we explore analytically and numerically the spatial and temporal patterns of brood- or worker-produced gases in nests. The maximum concentration within a typical one-chamber ant nest with approximately 200 ants can reach 12.5 times atmospheric concentration, reaching 95% of equilibrium concentrations within 15 min. Maximum concentration increases with increasing number of ants in the nest (or production rate of the gas), distance between the centre of the nest ants and the nest entrance, entrance length, wall thickness, and with decreasing entrance width, wall permeability and diffusion coefficient. The nest can be divided into three qualitatively distinct regions according to the shape of the gradient: a plateau of high concentration in the back half of the nest; an intermediate region of increasingly steep gradient towards the entrance; and a steep linear gradient in the entrance tunnel. These regions are robust to changes in gas concentrations, but vary with changes in nest architecture. The pattern of diffusing gases contains information about position and orientation relative to gas sources and sinks, and about colony state, including colony size, activity state and aspects of nest architecture. We discuss how this diffusion pattern may act as a "dynamic template", providing local cues which trigger behavioural acts appropriate to colony needs, which in turn may feed back to changes in the gas template. In particular, wall building occurs along lines of similar concentration for a variety of nest geometries; there is surprising convergence between the period of cycles of synchronously active ants and the time taken for CO2 levels to equilibrate; and the qualitatively distinct regions of the "dynamic template" correspond to regions occupied by different groups of ants.

Continental synchronicity of human influenza virus epidemics despite climatic variation.

PubMed

Geoghegan, Jemma L; Saavedra, Aldo F; Duchêne, Sebastián; Sullivan, Sheena; Barr, Ian; Holmes, Edward C

2018-01-01

The factors that determine the pattern and rate of spread of influenza virus at a continental-scale are uncertain. Although recent work suggests that influenza epidemics in the United States exhibit a strong geographical correlation, the spatiotemporal dynamics of influenza in Australia, a country and continent of approximately similar size and climate complexity but with a far smaller population, are not known. Using a unique combination of large-scale laboratory-confirmed influenza surveillance comprising >450,000 entries and genomic sequence data we determined the local-level spatial diffusion of this important human pathogen nationwide in Australia. We used laboratory-confirmed influenza data to characterize the spread of influenza virus across Australia during 2007-2016. The onset of established epidemics varied across seasons, with highly synchronized epidemics coinciding with the emergence of antigenically distinct viruses, particularly during the 2009 A/H1N1 pandemic. The onset of epidemics was largely synchronized between the most populous cities, even those separated by distances of >3000 km and those that experience vastly diverse climates. In addition, by analyzing global phylogeographic patterns we show that the synchronized dissemination of influenza across Australian cities involved multiple introductions from the global influenza population, coupled with strong domestic connectivity, rather than through the distinct radial patterns of geographic dispersal that are driven by work-flow transmission as observed in the United States. In addition, by comparing the spatial structure of influenza A and B, we found that these viruses tended to occupy different geographic regions, and peak in different seasons, perhaps indicative of moderate cross-protective immunity or viral interference effects. The highly synchronized outbreaks of influenza virus at a continental-scale revealed here highlight the importance of coordinated public health responses in the event of the emergence of a novel, human-to-human transmissible, virus.

Early Ethanol and Water Consumption: Accumulating Experience Differentially Regulates Drinking Pattern and Bout Parameters in Male Alcohol Preferring (P) vs. Wistar and Sprague Dawley Rats

PubMed Central

Azarov, Alexey V.; Woodward, Donald J.

2013-01-01

Alcohol-preferring (P) rats develop high ethanol intake over several weeks of water/10% ethanol (10E) choice drinking. However, it is not yet clear precisely what components of drinking behavior undergo modification to achieve higher intake. Our concurrent report compared precisely measured daily intake in P vs. non-selected Wistar and Sprague Dawley (SD) rats. Here we analyze their drinking patterns and bouts to clarify microbehavioral components that are common to rats of different origin, vs. features that are unique to each. Under sole-fluid conditions P, Wistar and SD rats all consumed water at a high initial rate followed by a slow maintenance phase, but 10E - in a distinctly different step-like pattern of evenly distributed bouts. During choice period, 10E vs. water patterns for P rat appeared as an overlap of sole-fluid patterns. The SD rat choice patterns resembled sole-fluid patterns but were less regular. Choice patterns in Wistar differed from both P and SD rats, by consisting of intermixed small frequent episodes of drinking both 10E and water. Wistar and SD rats increased choice ethanol intake by elevating the number of bouts. A key finding was that P rat increased choice ethanol intake through a gradual increase of the bout size and duration, but kept bout number constant. This supports the hypothesis that genetic selection modifies microbehavioral machinery controlling drinking bout initiation, duration, and other pattern features. Precision analysis of drinking patterns and bouts allows differentiation between genetic lines, and provides a venue for study of localized circuit and transmitter influences mediating mesolimbic control over ethanol consumption. PMID:24095931

Rapid Processing of a Global Feature in the ON Visual Pathways of Behaving Monkeys.

PubMed

Huang, Jun; Yang, Yan; Zhou, Ke; Zhao, Xudong; Zhou, Quan; Zhu, Hong; Yang, Yingshan; Zhang, Chunming; Zhou, Yifeng; Zhou, Wu

2017-01-01

Visual objects are recognized by their features. Whereas, some features are based on simple components (i.e., local features, such as orientation of line segments), some features are based on the whole object (i.e., global features, such as an object having a hole in it). Over the past five decades, behavioral, physiological, anatomical, and computational studies have established a general model of vision, which starts from extracting local features in the lower visual pathways followed by a feature integration process that extracts global features in the higher visual pathways. This local-to-global model is successful in providing a unified account for a vast sets of perception experiments, but it fails to account for a set of experiments showing human visual systems' superior sensitivity to global features. Understanding the neural mechanisms underlying the "global-first" process will offer critical insights into new models of vision. The goal of the present study was to establish a non-human primate model of rapid processing of global features for elucidating the neural mechanisms underlying differential processing of global and local features. Monkeys were trained to make a saccade to a target in the black background, which was different from the distractors (white circle) in color (e.g., red circle target), local features (e.g., white square target), a global feature (e.g., white ring with a hole target) or their combinations (e.g., red square target). Contrary to the predictions of the prevailing local-to-global model, we found that (1) detecting a distinction or a change in the global feature was faster than detecting a distinction or a change in color or local features; (2) detecting a distinction in color was facilitated by a distinction in the global feature, but not in the local features; and (3) detecting the hole was interfered by the local features of the hole (e.g., white ring with a squared hole). These results suggest that monkey ON visual systems have a subsystem that is more sensitive to distinctions in the global feature than local features. They also provide the behavioral constraints for identifying the underlying neural substrates.

Mosquito politics: local vector control policies and the spread of West Nile Virus in the Chicago region.

PubMed

Tedesco, Carmen; Ruiz, Marilyn; McLafferty, Sara

2010-11-01

Differences in mosquito control practices at the local level involve the interplay of place, scale and politics. During the Chicago West Nile Virus (WNV) outbreak of 2002, mosquito abatement districts represent distinct suburban clusters of human WNV cases, independent of characteristics of the local population, housing and physical environment. We examine how the contrasting actions of four districts reveal a distinct local politics of mosquito control that may have contributed to local-scale geographic differences in WNV incidence. This politics is rooted in political, economic and philosophical differences within and between administrative boundaries. Copyright © 2010 Elsevier Ltd. All rights reserved.

Dengue and Dengue Hemorrhagic Fever, Brazil, 1981–2002

PubMed Central

Martelli, Celina Maria Turchi; Coelho, Giovanini Evelim; Simplício, Ana Cristina da Rocha; Hatch, Douglas L.

2005-01-01

In the last 5 years, Brazil has accounted for ≈70% of reported dengue fever cases in the Americas. We analyzed trends of dengue and dengue hemorrhagic fever (DHF) from the early 1980s to 2002 by using surveillance data from the Brazilian Ministry of Health. Two distinct epidemiologic patterns for dengue were observed: localized epidemics (1986–1993), and endemic and epidemic virus circulation countrywide (1994–2002). Currently, serotypes 1, 2, and 3 cocirculate in 22 of 27 states. Dengue and DHF affected mainly adults; however, an increase in occurrence of DHF among children has been recently detected in northern Brazil, which suggests a shift in the occurrence of severe disease to younger age groups. In 2002, hospitalizations increased, which points out the change in disease severity compared to that seen in the 1990s. We describe the epidemiology of dengue in Brazil, characterizing the changing patterns of it and DHF during the last 20 years. PMID:15705322

Multilayer block copolymer meshes by orthogonal self-assembly

PubMed Central

Tavakkoli K. G., Amir; Nicaise, Samuel M.; Gadelrab, Karim R.; Alexander-Katz, Alfredo; Ross, Caroline A.; Berggren, Karl K.

2016-01-01

Continued scaling-down of lithographic-pattern feature sizes has brought templated self-assembly of block copolymers (BCPs) into the forefront of nanofabrication research. Technologies now exist that facilitate significant control over otherwise unorganized assembly of BCP microdomains to form both long-range and locally complex monolayer patterns. In contrast, the extension of this control into multilayers or 3D structures of BCP microdomains remains limited, despite the possible technological applications in next-generation devices. Here, we develop and analyse an orthogonal self-assembly method in which multiple layers of distinct-molecular-weight BCPs naturally produce nanomesh structures of cylindrical microdomains without requiring layer-by-layer alignment or high-resolution lithographic templating. The mechanisms for orthogonal self-assembly are investigated with both experiment and simulation, and we determine that the control over height and chemical preference of templates are critical process parameters. The method is employed to produce nanomeshes with the shapes of circles and Y-intersections, and is extended to produce three layers of orthogonally oriented cylinders. PMID:26796218

Solute mixing regulates heterogeneity of mineral precipitation in porous media: Effect of Solute Mixing on Precipitation

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

Cil, Mehmet B.; Xie, Minwei; Packman, Aaron I.

Synchrotron X-ray microtomography was used to track the spatiotemporal evolution of mineral precipitation and the consequent alteration of the pore structure. Column experiments were conducted by injecting CaCl2 and NaHCO3 solutions into granular porous media either as a premixed supersaturated solution (external mixing) or as separate solutions that mixed within the specimen (internal mixing). The two mixing modes produced distinct mineral growth patterns. While internal mixing promoted transverse heterogeneity with precipitation at the mixing zone, external mixing favored relatively homogeneous precipitation along the flow direction. The impact of precipitation on pore water flow and permeability was assessed via 3-D flowmore » simulations, which indicated anisotropic permeability evolution for both mixing modes. Under both mixing modes, precipitation decreased the median pore size and increased the skewness of the pore size distribution. Such similar pore-scale evolution patterns suggest that the clogging of individual pores depends primarily on local supersaturation state and pore geometry.« less

Notochord-derived Shh concentrates in close association with the apically positioned basal body in neural target cells and forms a dynamic gradient during neural patterning.

PubMed

Chamberlain, Chester E; Jeong, Juhee; Guo, Chaoshe; Allen, Benjamin L; McMahon, Andrew P

2008-03-01

Sonic hedgehog (Shh) ligand secreted by the notochord induces distinct ventral cell identities in the adjacent neural tube by a concentration-dependent mechanism. To study this process, we genetically engineered mice that produce bioactive, fluorescently labeled Shh from the endogenous locus. We show that Shh ligand concentrates in close association with the apically positioned basal body of neural target cells, forming a dynamic, punctate gradient in the ventral neural tube. Both ligand lipidation and target field response influence the gradient profile, but not the ability of Shh to concentrate around the basal body. Further, subcellular analysis suggests that Shh from the notochord might traffic into the neural target field by means of an apical-to-basal-oriented microtubule scaffold. This study, in which we directly observe, measure, localize and modify notochord-derived Shh ligand in the context of neural patterning, provides several new insights into mechanisms of Shh morphogen action.

Pattern-induced anchoring transitions in nematic liquid crystals

NASA Astrophysics Data System (ADS)

Rojas-Gómez, Óscar A.; Romero-Enrique, José M.; Silvestre, Nuno M.; Telo da Gama, Margarida M.

2017-02-01

In this paper we revisit the problem of a nematic liquid crystal in contact with patterned substrates. The substrate is modelled as a periodic array of parallel infinite grooves of well-defined cross-section sculpted on a chemically homogeneous substrate which favours local homeotropic anchoring of the nematic. We consider three cases: a sawtooth, a crenellated and a sinusoidal substrate. We analyse this problem within the modified Frank-Oseen formalism. We argue that, for substrate periodicities much larger than the extrapolation length, the existence of different nematic textures with distinct far-field orientations, as well as the anchoring transitions between them, are associated with the presence of topological defects either on or close to the substrate. For the sawtooth and sinusoidal cases, we observe a homeotropic to planar anchoring transition as the substrate roughness increases. On the other hand, a homeotropic to oblique anchoring transition is observed for crenellated substrates. In this case, the anchoring phase diagram shows a complex dependence on the substrate roughness and substrate anchoring strength.

Broadscale postseismic gravity change following the 2011 Tohoku-Oki earthquake and implication for deformation by viscoelastic relaxation and afterslip.

PubMed

Han, Shin-Chan; Sauber, Jeanne; Pollitz, Fred

2014-08-28

The analysis of GRACE gravity data revealed postseismic gravity increase by 6 μGal over a 500 km scale within a couple of years after the 2011 Tohoku-Oki earthquake, which is nearly 40-50% of the coseismic gravity change. It originates mostly from changes in the isotropic component corresponding to the M rr moment tensor element. The exponential decay with rapid change in a year and gradual change afterward is a characteristic temporal pattern. Both viscoelastic relaxation and afterslip models produce reasonable agreement with the GRACE free-air gravity observation, while their Bouguer gravity patterns and seafloor vertical deformations are distinctly different. The postseismic gravity variation is best modeled by the biviscous relaxation with a transient and steady state viscosity of 10 18 and 10 19  Pa s, respectively, for the asthenosphere. Our calculated higher-resolution viscoelastic relaxation model, underlying the partially ruptured elastic lithosphere, yields the localized postseismic subsidence above the hypocenter reported from the GPS-acoustic seafloor surveying.

Broadscale postseismic gravity change following the 2011 Tohoku-Oki earthquake and implication for deformation by viscoelastic relaxation and afterslip

PubMed Central

Han, Shin-Chan; Sauber, Jeanne; Pollitz, Fred

2014-01-01

The analysis of GRACE gravity data revealed postseismic gravity increase by 6 μGal over a 500 km scale within a couple of years after the 2011 Tohoku-Oki earthquake, which is nearly 40–50% of the coseismic gravity change. It originates mostly from changes in the isotropic component corresponding to the Mrr moment tensor element. The exponential decay with rapid change in a year and gradual change afterward is a characteristic temporal pattern. Both viscoelastic relaxation and afterslip models produce reasonable agreement with the GRACE free-air gravity observation, while their Bouguer gravity patterns and seafloor vertical deformations are distinctly different. The postseismic gravity variation is best modeled by the biviscous relaxation with a transient and steady state viscosity of 1018 and 1019 Pa s, respectively, for the asthenosphere. Our calculated higher-resolution viscoelastic relaxation model, underlying the partially ruptured elastic lithosphere, yields the localized postseismic subsidence above the hypocenter reported from the GPS-acoustic seafloor surveying. PMID:25821272

Positive Selection Drives the Evolution of rhino, a Member of the Heterochromatin Protein 1 Family in Drosophila

PubMed Central

Vermaak, Danielle; Henikoff, Steven; Malik, Harmit S

2005-01-01

Heterochromatin comprises a significant component of many eukaryotic genomes. In comparison to euchromatin, heterochromatin is gene poor, transposon rich, and late replicating. It serves many important biological roles, from gene silencing to accurate chromosome segregation, yet little is known about the evolutionary constraints that shape heterochromatin. A complementary approach to the traditional one of directly studying heterochromatic DNA sequence is to study the evolution of proteins that bind and define heterochromatin. One of the best markers for heterochromatin is the heterochromatin protein 1 (HP1), which is an essential, nonhistone chromosomal protein. Here we investigate the molecular evolution of five HP1 paralogs present in Drosophila melanogaster. Three of these paralogs have ubiquitous expression patterns in adult Drosophila tissues, whereas HP1D/rhino and HP1E are expressed predominantly in ovaries and testes respectively. The HP1 paralogs also have distinct localization preferences in Drosophila cells. Thus, Rhino localizes to the heterochromatic compartment in Drosophila tissue culture cells, but in a pattern distinct from HP1A and lysine-9 dimethylated H3. Using molecular evolution and population genetic analyses, we find that rhino has been subject to positive selection in all three domains of the protein: the N-terminal chromo domain, the C-terminal chromo-shadow domain, and the hinge region that connects these two modules. Maximum likelihood analysis of rhino sequences from 20 species of Drosophila reveals that a small number of residues of the chromo and shadow domains have been subject to repeated positive selection. The rapid and positive selection of rhino is highly unusual for a gene encoding a chromosomal protein and suggests that rhino is involved in a genetic conflict that affects the germline, belying the notion that heterochromatin is simply a passive recipient of “junk DNA” in eukaryotic genomes. PMID:16103923

Bringing Together Evolution on Serpentine and Polyploidy: Spatiotemporal History of the Diploid-Tetraploid Complex of Knautia arvensis (Dipsacaceae)

PubMed Central

Kolář, Filip; Fér, Tomáš; Štech, Milan; Trávníček, Pavel; Dušková, Eva; Schönswetter, Peter; Suda, Jan

2012-01-01

Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb Knautia arvensis (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of K. arvensis allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary ‘dead-ends’ but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes K. arvensis a unique system for addressing general questions of polyploid research. PMID:22792207

Within-Host Evolution of Simian Arteriviruses in Crab-Eating Macaques

PubMed Central

Moncla, Louise H.; Weiler, Andrea M.; Barry, Gabrielle; Weinfurter, Jason T.; Dinis, Jorge M.; Charlier, Olivia; Lauck, Michael; Bailey, Adam L.; Wahl-Jensen, Victoria; Nelson, Chase W.; Johnson, Joshua C.; Caì, Yíngyún; Goldberg, Tony L.; O'Connor, David H.; Jahrling, Peter B.

2016-01-01

ABSTRACT Simian arteriviruses are a diverse clade of viruses infecting captive and wild nonhuman primates. We recently reported that Kibale red colobus virus 1 (KRCV-1) causes a mild and self-limiting disease in experimentally infected crab-eating macaques, while simian hemorrhagic fever virus (SHFV) causes lethal viral hemorrhagic fever. Here we characterize how these viruses evolved during replication in cell culture and in experimentally infected macaques. During passage in cell culture, 68 substitutions that were localized in open reading frames (ORFs) likely associated with host cell entry and exit became fixed in the KRCV-1 genome. However, we did not detect any strong signatures of selection during replication in macaques. We uncovered patterns of evolution that were distinct from those observed in surveys of wild red colobus monkeys, suggesting that these species may exert different adaptive challenges for KRCV-1. During SHFV infection, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome. Overall, our data suggest that patterns of evolution differ markedly among simian arteriviruses and among host species. IMPORTANCE Certain RNA viruses can cross species barriers and cause disease in new hosts. Simian arteriviruses are a diverse group of related viruses that infect captive and wild nonhuman primates, with associated disease severity ranging from apparently asymptomatic infections to severe, viral hemorrhagic fevers. We infected nonhuman primate cell cultures and then crab-eating macaques with either simian hemorrhagic fever virus (SHFV) or Kibale red colobus virus 1 (KRCV-1) and assessed within-host viral evolution. We found that KRCV-1 quickly acquired a large number of substitutions in its genome during replication in cell culture but that evolution in macaques was limited. In contrast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins. These patterns suggest that in addition to diverse pathogenic phenotypes, these viruses may also exhibit distinct patterns of within-host evolution both in vitro and in vivo. PMID:27974564

French-Dutch Bilinguals Do Not Maintain Obligatory Semantic Distinctions: Evidence from Placement Verbs

ERIC Educational Resources Information Center

Alferink, Inge; Gullberg, Marianne

2014-01-01

It is often said that bilinguals are not the sum of two monolinguals but that bilingual systems represent a third pattern. This study explores the exact nature of this pattern. We ask whether there is evidence of a merged system when one language makes an obligatory distinction that the other one does not, namely in the case of placement verbs in…

The role of predators in maintaining the geographic organization of aposematic signals.

PubMed

Chouteau, Mathieu; Angers, Bernard

2011-12-01

Selective predation of aposematic signals is expected to promote phenotypic uniformity. But while these signals may be uniform within a population, numerous species display impressive variations in warning signals among adjacent populations. Predators from different localities who learn to avoid distinct signals while performing intense selection on others are thus expected to maintain such a geographic organization. We tested this assumption by placing clay frog models, representing distinct color morphs of the Peruvian poison dart frog Ranitomeya imitator and a nonconspicuous frog, reciprocally between adjacent localities. In each locality, avian predators were able to discriminate between warning signals; the adjacent exotic morph experienced up to four times more attacks than the local one and two times more than the nonconspicuous phenotype. Moreover, predation attempts on the exotic morph quickly decreased to almost nil, suggesting rapid learning. This experiment offers direct evidence for the existence of different predator communities performing localized homogenizing selection on distinct aposematic signals.

Hydroclimatic variability in the Lake Mondsee region and its relationships with large-scale climate anomaly patterns

NASA Astrophysics Data System (ADS)

Rimbu, Norel; Ionita, Monica; Swierczynski, Tina; Brauer, Achim; Kämpf, Lucas; Czymzik, Markus

2017-04-01

Flood triggered detrital layers in varved sediments of Lake Mondsee, located at the northern fringe of the European Alps (47°48'N,13°23'E), provide an important archive of regional hydroclimatic variability during the mid- to late Holocene. To improve the interpretation of the flood layer record in terms of large-scale climate variability, we investigate the relationships between observational hydrological records from the region, like the Mondsee lake level, the runoff of the lake's main inflow Griesler Ache, with observed precipitation and global climate patterns. The lake level shows a strong positive linear trend during the observational period in all seasons. Additionally, lake level presents important interannual to multidecadal variations. These variations are associated with distinct seasonal atmospheric circulation patterns. A pronounced anomalous anticyclonic center over the Iberian Peninsula is associated with high lake levels values during winter. This center moves southwestward during spring, summer and autumn. In the same time, a cyclonic anomaly center is recorded over central and western Europe. This anomalous circulation extends southwestward from winter to autumn. Similar atmospheric circulation patterns are associated with river runoff and precipitation variability from the region. High lake levels are associated with positive local precipitation anomalies in all seasons as well as with negative local temperature anomalies during spring, summer and autumn. A correlation analysis reveals that lake level, runoff and precipitation variability is related to large-scale sea surface temperature anomaly patterns in all seasons suggesting a possible impact of large-scale climatic modes, like the North Atlantic Oscillation and Atlantic Multidecadal Oscillation on hydroclimatic variability in the Lake Mondsee region. The results presented in this study can be used for a more robust interpretation of the long flood layer record from Lake Mondsee sediments in terms of regional and large-scale climate variability during the past.

Teenage Drinking, Symbolic Capital and Distinction

ERIC Educational Resources Information Center

Jarvinen, Margaretha; Gundelach, Peter

2007-01-01

This article analyses alcohol-related lifestyles among Danish teenagers. Building on Bourdieu's reasoning on symbolic capital and distinction, we analyse three interrelated themes. First, we show that alcohol-related variables (drinking patterns, drinking debut, experience of intoxication, etc.) can be used to identify some very distinctive life…

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.

The use of satellite tags to redefine movement patterns of spiny dogfish (Squalus acanthias) along the U.S. east coast: implications for fisheries management.

PubMed

Carlson, Amy E; Hoffmayer, Eric R; Tribuzio, Cindy A; Sulikowski, James A

2014-01-01

Spiny dogfish (Squalus acanthias) are assumed to be a highly migratory species, making habitual north-south migrations throughout their northwestern Atlantic United States (U.S.) range. Also assumed to be a benthic species, spiny dogfish stock structure is estimated through Northeast Fisheries Science Center (NEFSC) bottom-trawl surveys. Recent anomalies in population trends, including a recent four-fold increase in estimated spawning stock biomass, suggest alternative movement patterns could exist for this shark species. To obtain a better understanding of the horizontal and vertical movement dynamics of this species, Microwave Telemetry pop-up satellite archival X-Tags were attached to forty adult spiny dogfish at the northern (Gulf of Maine) and southern (North Carolina) extents of their core U.S. geographic range. Reconstructed geolocation tracks ranging in lengths from two to 12 months suggest that the seasonal migration patterns appear to be local in nature to each respective northern and southern deployment site, differing from previously published migration paradigms. Differences in distance and direction traveled between seasonal geolocations possibly indicate separate migratory patterns between groups. Kernel utilization distribution models also suggest strong separate core home ranges. Significant differences in seasonal temperature and depths between the two regions further substantiate the possibility of separate regional movement patterns between the two groups. Vertical utilization also suggests distinct diel patterns and that this species may not utilize the benthos as previously thought, potentially decreasing availability to benthic gear.

The Use of Satellite Tags to Redefine Movement Patterns of Spiny Dogfish (Squalus acanthias) along the U.S. East Coast: Implications for Fisheries Management

PubMed Central

Carlson, Amy E.; Hoffmayer, Eric R.; Tribuzio, Cindy A.; Sulikowski, James A.

2014-01-01

Spiny dogfish (Squalus acanthias) are assumed to be a highly migratory species, making habitual north-south migrations throughout their northwestern Atlantic United States (U.S.) range. Also assumed to be a benthic species, spiny dogfish stock structure is estimated through Northeast Fisheries Science Center (NEFSC) bottom-trawl surveys. Recent anomalies in population trends, including a recent four-fold increase in estimated spawning stock biomass, suggest alternative movement patterns could exist for this shark species. To obtain a better understanding of the horizontal and vertical movement dynamics of this species, Microwave Telemetry pop-up satellite archival X-Tags were attached to forty adult spiny dogfish at the northern (Gulf of Maine) and southern (North Carolina) extents of their core U.S. geographic range. Reconstructed geolocation tracks ranging in lengths from two to 12 months suggest that the seasonal migration patterns appear to be local in nature to each respective northern and southern deployment site, differing from previously published migration paradigms. Differences in distance and direction traveled between seasonal geolocations possibly indicate separate migratory patterns between groups. Kernel utilization distribution models also suggest strong separate core home ranges. Significant differences in seasonal temperature and depths between the two regions further substantiate the possibility of separate regional movement patterns between the two groups. Vertical utilization also suggests distinct diel patterns and that this species may not utilize the benthos as previously thought, potentially decreasing availability to benthic gear. PMID:25068584

A Bayesian Model of Category-Specific Emotional Brain Responses

PubMed Central

Wager, Tor D.; Kang, Jian; Johnson, Timothy D.; Nichols, Thomas E.; Satpute, Ajay B.; Barrett, Lisa Feldman

2015-01-01

Understanding emotion is critical for a science of healthy and disordered brain function, but the neurophysiological basis of emotional experience is still poorly understood. We analyzed human brain activity patterns from 148 studies of emotion categories (2159 total participants) using a novel hierarchical Bayesian model. The model allowed us to classify which of five categories—fear, anger, disgust, sadness, or happiness—is engaged by a study with 66% accuracy (43-86% across categories). Analyses of the activity patterns encoded in the model revealed that each emotion category is associated with unique, prototypical patterns of activity across multiple brain systems including the cortex, thalamus, amygdala, and other structures. The results indicate that emotion categories are not contained within any one region or system, but are represented as configurations across multiple brain networks. The model provides a precise summary of the prototypical patterns for each emotion category, and demonstrates that a sufficient characterization of emotion categories relies on (a) differential patterns of involvement in neocortical systems that differ between humans and other species, and (b) distinctive patterns of cortical-subcortical interactions. Thus, these findings are incompatible with several contemporary theories of emotion, including those that emphasize emotion-dedicated brain systems and those that propose emotion is localized primarily in subcortical activity. They are consistent with componential and constructionist views, which propose that emotions are differentiated by a combination of perceptual, mnemonic, prospective, and motivational elements. Such brain-based models of emotion provide a foundation for new translational and clinical approaches. PMID:25853490

From intentions to actions: Neural oscillations encode motor processes through phase, amplitude and phase-amplitude coupling.

PubMed

Combrisson, Etienne; Perrone-Bertolotti, Marcela; Soto, Juan Lp; Alamian, Golnoush; Kahane, Philippe; Lachaux, Jean-Philippe; Guillot, Aymeric; Jerbi, Karim

2017-02-15

Goal-directed motor behavior is associated with changes in patterns of rhythmic neuronal activity across widely distributed brain areas. In particular, movement initiation and execution are mediated by patterns of synchronization and desynchronization that occur concurrently across distinct frequency bands and across multiple motor cortical areas. To date, motor-related local oscillatory modulations have been predominantly examined by quantifying increases or suppressions in spectral power. However, beyond signal power, spectral properties such as phase and phase-amplitude coupling (PAC) have also been shown to carry information with regards to the oscillatory dynamics underlying motor processes. Yet, the distinct functional roles of phase, amplitude and PAC across the planning and execution of goal-directed motor behavior remain largely elusive. Here, we address this question with unprecedented resolution thanks to multi-site intracerebral EEG recordings in human subjects while they performed a delayed motor task. To compare the roles of phase, amplitude and PAC, we monitored intracranial brain signals from 748 sites across six medically intractable epilepsy patients at movement execution, and during the delay period where motor intention is present but execution is withheld. In particular, we used a machine-learning framework to identify the key contributions of various neuronal responses. We found a high degree of overlap between brain network patterns observed during planning and those present during execution. Prominent amplitude increases in the delta (2-4Hz) and high gamma (60-200Hz) bands were observed during both planning and execution. In contrast, motor alpha (8-13Hz) and beta (13-30Hz) power were suppressed during execution, but enhanced during the delay period. Interestingly, single-trial classification revealed that low-frequency phase information, rather than spectral power change, was the most discriminant feature in dissociating action from intention. Additionally, despite providing weaker decoding, PAC features led to statistically significant classification of motor states, particularly in anterior cingulate cortex and premotor brain areas. These results advance our understanding of the distinct and partly overlapping involvement of phase, amplitude and the coupling between them, in the neuronal mechanisms underlying motor intentions and executions. Copyright © 2016 Elsevier Inc. All rights reserved.

Component deficits of visual neglect: "Magnetic" attraction of attention vs. impaired spatial working memory.

PubMed

Toba, Monica N; Rabuffetti, Marco; Duret, Christophe; Pradat-Diehl, Pascale; Gainotti, Guido; Bartolomeo, Paolo

2018-01-31

Visual neglect is a disabling consequence of right hemisphere damage, whereby patients fail to detect left-sided objects. Its precise mechanisms are debated, but there is some consensus that distinct component deficits may variously associate and interact in different patients. Here we used a touch-screen based procedure to study two putative component deficits of neglect, rightward "magnetic" attraction of attention and impaired spatial working memory, in a group of 47 right brain-damaged patients, of whom 33 had signs of left neglect. Patients performed a visual search task on three distinct conditions, whereby touched targets could (1) be tagged, (2) disappear or (3) show no change. Magnetic attraction of attention was defined as more left neglect on the tag condition than on the disappear condition, where right-sided disappeared targets could not capture patients' attention. Impaired spatial working memory should instead produce more neglect on the no change condition, where no external cue indicated that a target had already been explored, than on the tag condition. Using a specifically developed analysis algorithm, we identified significant differences of performance between the critical conditions. Neglect patients as a group performed better on the disappear condition than on the no change condition and also better in the tag condition comparing with the no change condition. No difference was found between the tag condition and the disappear condition. Some of our neglect patients had dissociated patterns of performance, with predominant magnetic attraction or impaired spatial working memory. Anatomical results issued from both grey matter analysis and fiber tracking were consistent with the typical patterns of fronto-parietal and occipito-frontal disconnection in neglect, but did not identify lesional patterns specifically associated with one or another deficit, thus suggesting the possible co-localization of attentional and working memory processes in fronto-parietal networks. These findings give support to the hypothesis of the co-occurrence of distinct cognitive deficits in visual neglect and stress the necessity of multi-component models of visuospatial disorders. Copyright © 2017 Elsevier Ltd. All rights reserved.

Immunohistochemical differentiation of atypical hyperplasia vs. carcinoma in situ of the breast.

PubMed

Masood, S; Sim, S J; Lu, L

1992-01-01

The distinction between atypical hyperplasia and carcinoma in situ in breast lesions can be difficult. The identification of myoepithelial cell layers may be helpful in establishing a diagnosis of proliferative breast disease vs. intraepithelial neoplasia. We reviewed pathologic material on 20 cases of atypical hyperplasia and 29 cases of carcinoma in situ. Immunohistochemical stains were employed against muscle-specific actin, S-100 protein, and cytokeratin to identify myoepithelial cells and to recognize different staining patterns. In atypical hyperplasia, muscle-specific actin staining identified myoepithelial cells in fine branching fibrovascular layers or as scattered cells between other proliferating cells. This pattern was absent in carcinoma in situ. S-100 protein showed more positive staining in atypical hyperplasia than in carcinoma in situ with patterns distinct from muscle-specific actin. Immunostaining for cytokeratin demonstrated distinctly different patterns between the two lesions. This study suggests that muscle-specific actin, S-100 protein, and cytokeratin in combination may assist in distinguishing proliferative breast disease with atypia from carcinoma in situ.

Geographic and temporal patterns of variation in total mercury concentrations in blood of harlequin ducks and blue mussels from Alaska

USGS Publications Warehouse

Savoy, Lucas; Flint, Paul L.; Zwiefelhofer, Denny; Brant, Heather; Perkins, Christopher R.; Taylor, Robert J.; Lane, Oksana P.; Hall, Jefferson S.; Evers, David C.; Schamber, Jason

2017-01-01

We compared total mercury (Hg) concentrations in whole blood of harlequin ducks (Histrionicus histrionicus) sampled within and among two geographically distinct locations and across three years in southwest Alaska. Blue mussels were collected to assess correlation between Hg concentrations in locally available forage and birds. Mercury concentrations in harlequin duck blood were significantly higher at Unalaska Island (0.31 ± 0.19 mean ± SD, μg/g blood) than Kodiak Island (0.04 ± 0.02 mean ± SD, μg/g blood). We found no evidence for annual variation in blood Hg concentration between years at Unalaska Island. However, blood Hg concentration did vary among specific sampling locations (i.e., bays) at Unalaska Island. Findings from this study demonstrate harlequin ducks are exposed to environmental sources of Hg, and whole blood Hg concentrations are associated with their local food source.

Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages

PubMed Central

Eichenfield, Dawn Z; Troutman, Ty Dale; Link, Verena M; Lam, Michael T; Cho, Han; Gosselin, David; Spann, Nathanael J; Lesch, Hanna P; Tao, Jenhan; Muto, Jun; Gallo, Richard L; Evans, Ronald M; Glass, Christopher K

2016-01-01

Although macrophages can be polarized to distinct phenotypes in vitro with individual ligands, in vivo they encounter multiple signals that control their varied functions in homeostasis, immunity, and disease. Here, we identify roles of Rev-erb nuclear receptors in regulating responses of mouse macrophages to complex tissue damage signals and wound repair. Rather than reinforcing a specific program of macrophage polarization, Rev-erbs repress subsets of genes that are activated by TLR ligands, IL4, TGFβ, and damage-associated molecular patterns (DAMPS). Unexpectedly, a complex damage signal promotes co-localization of NF-κB, Smad3, and Nrf2 at Rev-erb-sensitive enhancers and drives expression of genes characteristic of multiple polarization states in the same cells. Rev-erb-sensitive enhancers thereby integrate multiple damage-activated signaling pathways to promote a wound repair phenotype. DOI: http://dx.doi.org/10.7554/eLife.13024.001 PMID:27462873

A biomechanical model of agonist-initiated contraction in the asthmatic airway.

PubMed

Brook, B S; Peel, S E; Hall, I P; Politi, A Z; Sneyd, J; Bai, Y; Sanderson, M J; Jensen, O E

2010-01-31

This paper presents a modelling framework in which the local stress environment of airway smooth muscle (ASM) cells may be predicted and cellular responses to local stress may be investigated. We consider an elastic axisymmetric model of a layer of connective tissue and circumferential ASM fibres embedded in parenchymal tissue and model the active contractile force generated by ASM via a stress acting along the fibres. A constitutive law is proposed that accounts for active and passive material properties as well as the proportion of muscle to connective tissue. The model predicts significantly different contractile responses depending on the proportion of muscle to connective tissue in the remodelled airway. We find that radial and hoop-stress distributions in remodelled muscle layers are highly heterogenous with distinct regions of compression and tension. Such patterns of stress are likely to have important implications, from a mechano-transduction perspective, on contractility, short-term cytoskeletal adaptation and long-term airway remodelling in asthma. Copyright 2009 Elsevier B.V. All rights reserved.

The informational architecture of the cell.

PubMed

Walker, Sara Imari; Kim, Hyunju; Davies, Paul C W

2016-03-13

We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for regulation of the cell cycle of the fission yeast Schizosaccharomyces pombe. We compare calculated values of local and global information measures for the fission yeast cell cycle to the same measures as applied to two different classes of random networks: Erdös-Rényi and scale-free. We report patterns in local information processing and storage that do indeed distinguish biological from random, associated with control nodes that regulate the function of the fission yeast cell-cycle network. Conversely, we find that integrated information, which serves as a global measure of 'emergent' information processing, does not differ from random for the case presented. We discuss implications for our understanding of the informational architecture of the fission yeast cell-cycle network in particular, and more generally for illuminating any distinctive physics that may be operative in life. © 2016 The Author(s).

Mesoscale monitoring of the soil freeze/thaw boundary from orbital microwave radiometry

NASA Technical Reports Server (NTRS)

Dobson, Craig; Ulaby, Fawwaz T.; Zuerndorfer, Brian; England, Anthony W.

1990-01-01

A technique was developed for mapping the spatial extent of frozen soils from the spectral characteristics of the 10.7 to 37 GHz radiobrightness. Through computational models for the spectral radiobrightness of diurnally heated freesing soils, a distinctive radiobrightness signature was identified for frozen soils, and the signature was cast as a discriminant for unsupervised classification. In addition to large area images, local area spatial averages of radiobrightness were calculated for each radiobrightness channel at 7 meteorologic sites within the test region. Local area averages at the meteorologic sites were used to define the preliminary boundaries in the Freeze Indicator discriminate. Freeze Indicator images based upon Nimbus 7, Scanning Multichannel Microwave Radiometer (SMMR) data effectively map temporal variations in the freeze/thaw pattern for the northern Great Plains at the time scale of days. Diurnal thermal gradients have a small but measurable effect upon the SMMR spectral gradient. Scale-space filtering can be used to improve the spatial resolution of a freeze/thaw classified image.

New chondrichthyan fin spines from the Pedra de Fogo Formation, Brazil

NASA Astrophysics Data System (ADS)

Figueroa, Rodrigo T.; Gallo, Valéria

2017-07-01

The Pedra de Fogo Formation is located at the northeast region of Brazil and possesses a diverse palaeobiota mainly composed by plants and vertebrate remains of Lower Permian age (Cisuralian). The palaeoichthyofauna includes several chondrichthyans (e.g. Sphenacanthus maranhensis, Taquaralodus albuquerquei, Itapyrodus punctatus and Anisopleurodontis pricei) but also include osteichthyans as the 'palaeoniscoid' Brazilichthys macrognathus and several actinopterygian and sarcopterygian remains. This variety of fish taxa of both marine and freshwater affinities is important for understanding taxonomical diversity and distribution of vertebrates from Western Gondwana. Here, specimens collected at the Pastos Bons locality, near Nova Iorque at State of Maranhão, are described as two new species for known genera, Sphenacanthus ignis sp. nov. and Bythiacanthus lopesi sp. nov., also a new genus and a new species Rubencanthus diplotuberculatus gen. et sp. nov. that exhibit a distinct pattern of ornamentation from all previously known Palaeozoic chondrichthyans. These new records highlight the importance of more palaeontological studies for the Pedra de Fogo Formation and enlarge the variety of chondrichthyan for the locality.

The N-terminal domain of Slack determines the formation and trafficking of Slick/Slack heteromeric sodium-activated potassium channels.

PubMed

Chen, Haijun; Kronengold, Jack; Yan, Yangyang; Gazula, Valeswara-Rao; Brown, Maile R; Ma, Liqun; Ferreira, Gonzalo; Yang, Youshan; Bhattacharjee, Arin; Sigworth, Fred J; Salkoff, Larry; Kaczmarek, Leonard K

2009-04-29

Potassium channels activated by intracellular Na(+) ions (K(Na)) play several distinct roles in regulating the firing patterns of neurons, and, at the single channel level, their properties are quite diverse. Two known genes, Slick and Slack, encode K(Na) channels. We have now found that Slick and Slack subunits coassemble to form heteromeric channels that differ from the homomers in their unitary conductance, kinetic behavior, subcellular localization, and response to activation of protein kinase C. Heteromer formation requires the N-terminal domain of Slack-B, one of the alternative splice variants of the Slack channel. This cytoplasmic N-terminal domain of Slack-B also facilitates the localization of heteromeric K(Na) channels to the plasma membrane. Immunocytochemical studies indicate that Slick and Slack-B subunits are coexpressed in many central neurons. Our findings provide a molecular explanation for some of the diversity in reported properties of neuronal K(Na) channels.

Genetic evaluation of the evolutionary distinctness of a federally endangered butterfly, Lange's Metalmark.

PubMed

Proshek, Benjamin; Dupuis, Julian R; Engberg, Anna; Davenport, Ken; Opler, Paul A; Powell, Jerry A; Sperling, Felix A H

2015-04-25

The Mormon Metalmark (Apodemia mormo) species complex occurs as isolated and phenotypically variable colonies in dryland areas across western North America. Lange's Metalmark, A. m. langei, one of the 17 subspecies taxonomically recognized in the complex, is federally listed under the U.S. Endangered Species Act of 1973. Metalmark taxa have traditionally been described based on phenotypic and ecological characteristics, and it is unknown how well this nomenclature reflects their genetic and evolutionary distinctiveness. Genetic variation in six microsatellite loci and mitochondrial cytochrome oxidase subunit I sequence was used to assess the population structure of the A. mormo species complex across 69 localities, and to evaluate A. m. langei's qualifications as an Evolutionarily Significant Unit. We discovered substantial genetic divergence within the species complex, especially across the Continental Divide, with population genetic structure corresponding more closely with geographic proximity and local isolation than with taxonomic divisions originally based on wing color and pattern characters. Lange's Metalmark was as genetically divergent as several other locally isolated populations in California, and even the unique phenotype that warranted subspecific and conservation status is reminiscent of the morphological variation found in some other populations. This study is the first genetic treatment of the A. mormo complex across western North America and potentially provides a foundation for reassessing the taxonomy of the group. Furthermore, these results illustrate the utility of molecular markers to aid in demarcation of biological units below the species level. From a conservation point of view, Apodemia mormo langei's diagnostic taxonomic characteristics may, by themselves, not support its evolutionary significance, which has implications for its formal listing as an Endangered Species.

Plant roots use a patterning mechanism to position lateral root branches toward available water.

PubMed

Bao, Yun; Aggarwal, Pooja; Robbins, Neil E; Sturrock, Craig J; Thompson, Mark C; Tan, Han Qi; Tham, Cliff; Duan, Lina; Rodriguez, Pedro L; Vernoux, Teva; Mooney, Sacha J; Bennett, Malcolm J; Dinneny, José R

2014-06-24

The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth; however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydropatterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of tryptophan aminotransferase of Arabidopsis 1 and PIN-formed 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root.

Vesicle Docking Is a Key Target of Local PI(4,5)P2 Metabolism in the Secretory Pathway of INS-1 Cells.

PubMed

Ji, Chen; Fan, Fan; Lou, Xuelin

2017-08-08

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 ) signaling is transient and spatially confined in live cells. How this pattern of signaling regulates transmitter release and hormone secretion has not been addressed. We devised an optogenetic approach to control PI(4,5)P 2 levels in time and space in insulin-secreting cells. Combining this approach with total internal reflection fluorescence microscopy, we examined individual vesicle-trafficking steps. Unlike long-term PI(4,5)P 2 perturbations, rapid and cell-wide PI(4,5)P 2 reduction in the plasma membrane (PM) strongly inhibits secretion and intracellular Ca 2+ concentration ([Ca 2+ ] i ) responses, but not sytaxin1a clustering. Interestingly, local PI(4,5)P 2 reduction selectively at vesicle docking sites causes remarkable vesicle undocking from the PM without affecting [Ca 2+ ] i . These results highlight a key role of local PI(4,5)P 2 in vesicle tethering and docking, coordinated with its role in priming and fusion. Thus, different spatiotemporal PI(4,5)P 2 signaling regulates distinct steps of vesicle trafficking, and vesicle docking may be a key target of local PI(4,5)P 2 signaling in vivo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Excitons in Core-Shell Nanowires with Polygonal Cross Sections.

PubMed

Sitek, Anna; Urbaneja Torres, Miguel; Torfason, Kristinn; Gudmundsson, Vidar; Bertoni, Andrea; Manolescu, Andrei

2018-04-11

The distinctive prismatic geometry of semiconductor core-shell nanowires leads to complex localization patterns of carriers. Here, we describe the formation of optically active in-gap excitonic states induced by the interplay between localization of carriers in the corners and their mutual Coulomb interaction. To compute the energy spectra and configurations of excitons created in the conductive shell, we use a multielectron numerical approach based on the exact solution of the multiparticle Hamiltonian for electrons in the valence and conduction bands, which includes the Coulomb interaction in a nonperturbative manner. We expose the formation of well-separated quasidegenerate levels, and focus on the implications of the electron localization in the corners or on the sides of triangular, square, and hexagonal cross sections. We obtain excitonic in-gap states associated with symmetrically distributed electrons in the spin singlet configuration. They acquire large contributions due to Coulomb interaction, and thus are shifted to much higher energies than other states corresponding to the conduction electron and the vacancy localized in the same corner. We compare the results of the multielectron method with those of an electron-hole model, and we show that the latter does not reproduce the singlet excitonic states. We also obtain the exciton lifetime and explain selection rules which govern the recombination process.

Impact of wall hydrophobicity on condensation flow and heat transfer in silicon microchannels

NASA Astrophysics Data System (ADS)

Fang, Chen; Steinbrenner, Julie E.; Wang, Fu-Min; Goodson, Kenneth E.

2010-04-01

While microchannel condensation has been the subject of several recent studies, the critical impact of wall hydrophobicity on the microchannel condensation flow has received very little attention. The paper experimentally studies steam condensation in a silicon microchannel 286 µm in hydraulic diameter with three different wall hydrophobicities. It is found that the channel surface wettability has a significant impact on the flow pattern, pressure drop and heat transfer characteristic. Spatial flow pattern transition is observed in both hydrophobic and hydrophilic channels. In the hydrophobic channel, the transition from dropwise/slugwise flow to plug flow is induced by the slug instability. In the hydrophilic channel, the flow transition is characterized by the periodic bubble detachment, a process in which pressure evolution is found important. Local temperature measurement is conducted and heat flux distribution in the microchannel is reconstructed. For the same inlet vapor flux and temperature, the hydrophobic microchannel yields higher heat transfer rate and pressure drop compared to the hydrophilic channel. The difference is attributed to the distinction in flow pattern and heat transfer mechanism dictated by the channel hydrophobicity. This study highlights the importance of the channel hydrophobicity control for the optimization of the microchannel condenser.

Hyaluronic acid gel distribution pattern in periocular area with high-resolution ultrasound imaging.

PubMed

Goh, Alice S; Kohn, Jocelyne C; Rootman, Daniel B; Lin, Joseph L; Goldberg, Robert A

2014-05-01

High-resolution ultrasound (HRUS) is a useful tool in defining anatomic and dynamic soft tissue relationships in the periocular area. It also allows visualization of hyaluronic acid (HA) gel within the soft tissue. The authors investigate the difference in the distribution pattern between 2 HA fillers in the periocular tissue using HRUS. The charts of 10 patients who underwent periocular injection using HA gel filler and were subsequently examined with HRUS were reviewed. Half of the patients (n = 5) were treated with Restylane-L (Medicis Aesthetics, Inc, Scottsdale, Arizona) and the remaining 5 with Belotero Balance (Merz Aesthetics, Inc, San Mateo, California). Ultrasonographic evaluation (Logiq p6; GE Healthcare, Waukesha, Washington) was performed before and immediately after HA filler injection. The HA appears as a hypoechoic image within the soft tissue plane on HRUS. Restylane-L filler formed a localized hypoechoic image within the tissue, with some spread into bubbles or pearl-like configuration. Belotero Balance spread more widely into the tissue plane and diffused into an elongated or spindle-shaped hypoechoic image. Our preliminary data suggest that HA gel fillers with differing production technologies show distinct spread and distribution patterns in the periocular tissues on HRUS examination.

The Ndst Gene Family in Zebrafish: Role of Ndst1b in Pharyngeal Arch Formation

PubMed Central

Haitina, Tatjana; Habicher, Judith; Ledin, Johan; Kjellén, Lena

2015-01-01

Heparan sulfate (HS) proteoglycans are ubiquitous components of the extracellular matrix and plasma membrane of metazoans. The sulfation pattern of the HS glycosaminoglycan chain is characteristic for each tissue and changes during development. The glucosaminyl N-deacetylase/N-sulfotransferase (NDST) enzymes catalyze N-deacetylation and N-sulfation during HS biosynthesis and have a key role in designing the sulfation pattern. We here report on the presence of five NDST genes in zebrafish. Zebrafish ndst1a, ndst1b, ndst2a and ndst2b represent duplicated mammalian orthologues of NDST1 and NDST2 that arose through teleost specific genome duplication. Interestingly, the single zebrafish orthologue ndst3, is equally similar to tetrapod Ndst3 and Ndst4. It is likely that a local duplication in the common ancestor of lobe-finned fish and tetrapods gave rise to these two genes. All zebrafish Ndst genes showed distinct but partially overlapping expression patterns during embryonic development. Morpholino knockdown of ndst1b resulted in delayed development, craniofacial cartilage abnormalities, shortened body and pectoral fin length, resembling some of the features of the Ndst1 mouse knockout. PMID:25767878

A microcosm of musical expression: II. Quantitative analysis of pianists' dynamics in the initial measures of Chopin's Etude in E major.

PubMed

Repp, B H

1999-03-01

Patterns of expressive dynamics were measured in bars 1-5 of 115 commercially recorded performances of Chopin's Etude in E major, op. 10, No. 3. The grand average pattern (or dynamic profile) was representative of many performances and highly similar to the average dynamic profile of a group of advanced student performances, which suggests a widely shared central norm of expressive dynamics. The individual dynamic profiles were subjected to principal components analysis, which yielded Varimax-rotated components, each representing a different, nonstandard dynamic profile associated with a small subset of performances. Most performances had dynamic patterns resembling a mixture of several components, and no clustering of of performances into distinct groups was apparent. Some weak relationships of dynamic profiles with sociocultural variables were found, most notably a tendency of female pianists to exhibit a greater dynamic range in the melody. Within the melody, there were no significant relationships between expressive timing [Repp, J. Acoust. Soc. Am. 104, 1085-1100 (1998)] and expressive dynamics. These two important dimensions seemed to be controlled independently at this local level and thus offer the artist many degrees of freedom in giving a melody expressive shape.

Patterning of sympathetic nerve activity in response to vestibular stimulation

NASA Technical Reports Server (NTRS)

Kerman, I. A.; McAllen, R. M.; Yates, B. J.

2000-01-01

Growing evidence suggests a role for the vestibular system in regulation of autonomic outflow during postural adjustments. In the present paper we review evidence for the patterning of sympathetic nerve activity elicited by vestibular stimulation. In response to electrical activation of vestibular afferents, firing of sympathetic nerves located throughout the body is altered. However, activity of the renal nerve is most sensitive to vestibular inputs. In contrast, high-intensity simultaneous activation of cutaneous and muscle inputs elicits equivalent changes in firing of the renal, superior mesenteric and lumbar colonic nerves. Responses of muscle vasoconstrictor (MVC) efferents to vestibular stimulation are either inhibitory (Type I) or are comprised of a combination of excitation and inhibition (Type II). Interestingly, single MVC units located in the hindlimb exhibited predominantly Type I responses while those located in the forelimb and face exhibited Type II responses. Furthermore, brachial and femoral arterial blood flows were dissociated in response to vestibular stimulation, such that brachial vascular resistance increased while femoral resistance decreased. These studies demonstrate that vestibulosympathetic reflexes are patterned according to both the anatomical location and innervation target of a particular sympathetic nerve, and can lead to distinct changes in local blood flow.

Cell migration without a lamellipodium: translation of actin dynamics into cell movement mediated by tropomyosin.

PubMed

Gupton, Stephanie L; Anderson, Karen L; Kole, Thomas P; Fischer, Robert S; Ponti, Aaron; Hitchcock-DeGregori, Sarah E; Danuser, Gaudenz; Fowler, Velia M; Wirtz, Denis; Hanein, Dorit; Waterman-Storer, Clare M

2005-02-14

The actin cytoskeleton is locally regulated for functional specializations for cell motility. Using quantitative fluorescent speckle microscopy (qFSM) of migrating epithelial cells, we previously defined two distinct F-actin networks based on their F-actin-binding proteins and distinct patterns of F-actin turnover and movement. The lamellipodium consists of a treadmilling F-actin array with rapid polymerization-dependent retrograde flow and contains high concentrations of Arp2/3 and ADF/cofilin, whereas the lamella exhibits spatially random punctae of F-actin assembly and disassembly with slow myosin-mediated retrograde flow and contains myosin II and tropomyosin (TM). In this paper, we microinjected skeletal muscle alphaTM into epithelial cells, and using qFSM, electron microscopy, and immunolocalization show that this inhibits functional lamellipodium formation. Cells with inhibited lamellipodia exhibit persistent leading edge protrusion and rapid cell migration. Inhibition of endogenous long TM isoforms alters protrusion persistence. Thus, cells can migrate with inhibited lamellipodia, and we suggest that TM is a major regulator of F-actin functional specialization in migrating cells.

Multipotent versus differentiated cell fate selection in the developing Drosophila airways

PubMed Central

Matsuda, Ryo; Hosono, Chie; Samakovlis, Christos; Saigo, Kaoru

2015-01-01

Developmental potentials of cells are tightly controlled at multiple levels. The embryonic Drosophila airway tree is roughly subdivided into two types of cells with distinct developmental potentials: a proximally located group of multipotent adult precursor cells (P-fate) and a distally located population of more differentiated cells (D-fate). We show that the GATA-family transcription factor (TF) Grain promotes the P-fate and the POU-homeobox TF Ventral veinless (Vvl/Drifter/U-turned) stimulates the D-fate. Hedgehog and receptor tyrosine kinase (RTK) signaling cooperate with Vvl to drive the D-fate at the expense of the P-fate while negative regulators of either of these signaling pathways ensure P-fate specification. Local concentrations of Decapentaplegic/BMP, Wingless/Wnt, and Hedgehog signals differentially regulate the expression of D-factors and P-factors to transform an equipotent primordial field into a concentric pattern of radially different morphogenetic potentials, which gradually gives rise to the distal-proximal organization of distinct cell types in the mature airway. DOI: http://dx.doi.org/10.7554/eLife.09646.001 PMID:26633813

High-latitude distributions of plasma waves and spatial irregularities from DE 2 alternating current electric field observations

NASA Technical Reports Server (NTRS)

Heppner, J. P.; Liebrecht, M. C.; Maynard, N. C.; Pfaff, R. F.

1993-01-01

The high-latitude spatial distributions of average signal intensities in 12 frequency channels between 4 Hz and 512 kHz as measured by the ac electric field spectrometers on the DE-2 spacecraft are analyzed for 18 mo of measurements. In MLT-INL (magnetic local time-invariant latitude) there are three distinct distributions that can be identified with 4-512 Hz signals from spatial irregularities and Alfven waves, 256-Hz to 4.1-kHz signals from ELF hiss, and 4.1-64 kHz signals from VLF auroral hiss, respectively. Overlap between ELF hiss and spatial irregularity signals occurs in the 256-512 Hz band. VLF hiss signals extend downward in frequency into the 1.0-4.1 kHz band and upward into the frequency range 128-512 kHz. The distinctly different spatial distribution patterns for the three bands, 4-256 Hz, 512-1204 Hz, and 4.1-64 kHz, indicate a lack of any causal relationships between VLF hiss, ELF hiss, and lower-frequency signals from spatial irregularities and Alfven waves.

Task 1, Fractal characteristics of drainage patterns observed in the Appalachian Valley and Ridge and Plateau provinces

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

Wilson, T.; Dominic, J.; Halverson, J.

1996-04-10

Drainage patterns observed in the Appalachian Valley and Ridge and Plateau provinces exhibit distinctly different patterns. The patterns appear to be controlled by varying influences of local structural and lithologic variability. Drainage patterns in the Valley and Ridge study area can be classified as a combination of dendritic and trellis arrangements. The patterns vary over short distances in both the strike and dip directions. In the Granny Creek area of the Appalachian Plateau drainage patterns are predominantly dendritic. The possibility that these drainage patterns have fractal characteristics was evaluated by box-counting. Results obtained from box counting do not yield amore » well defined fractal regime in either areas. In the Valley and Ridge a space-filling, or random regime (D=2) is observed for boxes with side-lengths of 300 meters and greater. Below 300 meters, large changes in D occur between consecutively smaller box sizes. From side lengths of 300 to 150m, 150 to 75m, and 75 to 38m, D is measured at 1.77, 1.39, and 1.08 respectively. For box sizes less than 38m the fractal dimension is 1 or less. While the l0g-log response of the box counting data is nonlinear and does not define a fractal regime, the curves offer the possibility of characterizing non-fractal patterns. The rate at which D drops outside the random regime correlates to drainage density. D in areas with a smaller density of drainage segments fell toward saturation (D=1) more abruptly. The break-away point from the random regime and the transition to the saturated regime may provide useful information about the relative lengths of stream segments.« less

Effects of Noncovalent Platinum Drug–Protein Interactions on Drug Efficacy: Use of Fluorescent Conjugates as Probes for Drug Metabolism

PubMed Central

Benedetti, Brad T.; Peterson, Erica J.; Kabolizadeh, Peyman; Martínez, Alberto; Kipping, Ralph; Farrell, Nicholas P.

2012-01-01

The overall efficacy of platinum based drugs is limited by metabolic deactivation through covalent drug–protein binding. In this study the factors affecting cytotoxicity in the presence of glutathione, human serum albumin (HSA) and whole serum binding with cisplatin, BBR3464, and TriplatinNC, a “noncovalent” derivative of BBR3464, were investigated. Upon treatment with buthionine sulfoximine (BSO), to reduce cellular glutathione levels, cisplatin and BBR3464-induced apoptosis was augmented whereas TriplatinNC-induced cytotoxicity was unaltered. Treatment of A2780 ovarian carcinoma cells with HSA-bound cisplatin (cisplatin/HSA) and cisplatin preincubated with whole serum showed dramatic decreases in cytotoxicity, cellular accumulation, and DNA adduct formation compared to treatment with cisplatin alone. Similar effects are seen with BBR3464. In contrast, TriplatinNC, the HSAbound derivative (TriplatinNC/HSA), and TriplatinNC pretreated with whole serum retained identical cytotoxic profiles and equal levels of cellular accumulation at all time points. Confocal microscopy of both TriplatinNC-NBD, a fluorescent derivative of TriplatinNC, and TriplatinNC-NBD/HSA showed nuclear/nucleolar localization patterns, distinctly different from the lysosomal localization pattern seen with HSA. Cisplatin-NBD, a fluorescent derivative of cisplatin, was shown to accumulate in the nucleus and throughout the cytoplasmwhile the localization of cisplatin-NBD/HSA was limited to lysosomal regions of the cytoplasm. The results suggest that TriplatinNCcan avoid high levels of metabolic deactivation currently seen with clinical platinum chemotherapeutics, and therefore retain a unique cytotoxic profile after cellular administration. PMID:21548575

Cyclic lipopeptides from Bacillus subtilis activate distinct patterns of defence responses in grapevine.

PubMed

Farace, Giovanni; Fernandez, Olivier; Jacquens, Lucile; Coutte, François; Krier, François; Jacques, Philippe; Clément, Christophe; Barka, Essaid Ait; Jacquard, Cédric; Dorey, Stéphan

2015-02-01

Non-self-recognition of microorganisms partly relies on the perception of microbe-associated molecular patterns (MAMPs) and leads to the activation of an innate immune response. Bacillus subtilis produces three main families of cyclic lipopeptides (LPs), namely surfactins, iturins and fengycins. Although LPs are involved in induced systemic resistance (ISR) activation, little is known about defence responses induced by these molecules and their involvement in local resistance to fungi. Here, we showed that purified surfactin, mycosubtilin (iturin family) and plipastatin (fengycin family) are perceived by grapevine plant cells. Although surfactin and mycosubtilin stimulated grapevine innate immune responses, they differentially activated early signalling pathways and defence gene expression. By contrast, plipastatin perception by grapevine cells only resulted in early signalling activation. Gene expression analysis suggested that mycosubtilin activated salicylic acid (SA) and jasmonic acid (JA) signalling pathways, whereas surfactin mainly induced an SA-regulated response. Although mycosubtilin and plipastatin displayed direct antifungal activity, only surfactin and mycosubtilin treatments resulted in a local long-lasting enhanced tolerance to the necrotrophic fungus Botrytis cinerea in grapevine leaves. Moreover, challenge with specific strains overproducing surfactin and mycosubtilin led to a slightly enhanced stimulation of the defence response compared with the LP-non-producing strain of B. subtilis. Altogether, our results provide the first comprehensive view of the involvement of LPs from B. subtilis in grapevine plant defence and local resistance against the necrotrophic pathogen Bo. cinerea. Moreover, this work is the first to highlight the ability of mycosubtilin to trigger an immune response in plants. © 2014 BSPP AND JOHN WILEY & SONS LTD.

Is there a geometric module for spatial orientation? Insights from a rodent navigation model.

PubMed

Sheynikhovich, Denis; Chavarriaga, Ricardo; Strösslin, Thomas; Arleo, Angelo; Gerstner, Wulfram

2009-07-01

Modern psychological theories of spatial cognition postulate the existence of a geometric module for reorientation. This concept is derived from experimental data showing that in rectangular arenas with distinct landmarks in the corners, disoriented rats often make diagonal errors, suggesting their preference for the geometric (arena shape) over the nongeometric (landmarks) cues. Moreover, sensitivity of hippocampal cell firing to changes in the environment layout was taken in support of the geometric module hypothesis. Using a computational model of rat navigation, the authors proposed and tested the alternative hypothesis that the influence of spatial geometry on both behavioral and neuronal levels can be explained by the properties of visual features that constitute local views of the environment. Their modeling results suggest that the pattern of diagonal errors observed in reorientation tasks can be understood by the analysis of sensory information processing that underlies the navigation strategy employed to solve the task. In particular, 2 navigation strategies were considered: (a) a place-based locale strategy that relies on a model of grid and place cells and (b) a stimulus-response taxon strategy that involves direct association of local views with action choices. The authors showed that the application of the 2 strategies in the reorientation tasks results in different patterns of diagonal errors, consistent with behavioral data. These results argue against the geometric module hypothesis by providing a simpler and biologically more plausible explanation for the related experimental data. Moreover, the same model also describes behavioral results in different types of water-maze tasks. Copyright (c) 2009 APA, all rights reserved.

Suggested Mechanisms of Tracheal Occlusion Mediated Accelerated Fetal Lung Growth: A Case for Heterogeneous Topological Zones

PubMed Central

Marwan, Ahmed I.; Shabeka, Uladzimir; Dobrinskikh, Evgenia

2018-01-01

In this article, we report an up-to-date summary on tracheal occlusion (TO) as an approach to drive accelerated lung growth and strive to review the different maternal- and fetal-derived local and systemic signals and mechanisms that may play a significant biological role in lung growth and formation of heterogeneous topological zones following TO. Pulmonary hypoplasia is a condition whereby branching morphogenesis and embryonic pulmonary vascular development are globally affected and is classically seen in congenital diaphragmatic hernia. TO is an innovative approach aimed at driving accelerated lung growth in the most severe forms of diaphragmatic hernia and has been shown to result in improved neonatal outcomes. Currently, most research on mechanisms of TO-induced lung growth is focused on mechanical forces and is viewed from the perspective of homogeneous changes within the lung. We suggest that the key principle in understanding changes in fetal lungs after TO is taking into account formation of unique variable topological zones. Following TO, fetal lungs might temporarily look like a dynamically changing topologic mosaic with varying proliferation rates, dissimilar scale of vasculogenesis, diverse patterns of lung tissue damage, variable metabolic landscape, and different structures. The reasons for this dynamic topological mosaic pattern may include distinct degree of increased hydrostatic pressure in different parts of the lung, dissimilar degree of tissue stress/damage and responses to this damage, and incomparable patterns of altered lung zones with variable response to systemic maternal and fetal factors, among others. The local interaction between these factors and their accompanying processes in addition to the potential role of other systemic factors might lead to formation of a common vector of biological response unique to each zone. The study of the interaction between various networks formed after TO (action of mechanical forces, activation of mucosal mast cells, production and secretion of damage-associated molecular pattern substances, low-grade local pulmonary inflammation, and cardiac contraction-induced periodic agitation of lung tissue, among others) will bring us closer to an appreciation of the biological phenomenon of topological heterogeneity within the fetal lungs. PMID:29376042

Rapid tsunami models and earthquake source parameters: Far-field and local applications

USGS Publications Warehouse

Geist, E.L.

2005-01-01

Rapid tsunami models have recently been developed to forecast far-field tsunami amplitudes from initial earthquake information (magnitude and hypocenter). Earthquake source parameters that directly affect tsunami generation as used in rapid tsunami models are examined, with particular attention to local versus far-field application of those models. First, validity of the assumption that the focal mechanism and type of faulting for tsunamigenic earthquakes is similar in a given region can be evaluated by measuring the seismic consistency of past events. Second, the assumption that slip occurs uniformly over an area of rupture will most often underestimate the amplitude and leading-wave steepness of the local tsunami. Third, sometimes large magnitude earthquakes will exhibit a high degree of spatial heterogeneity such that tsunami sources will be composed of distinct sub-events that can cause constructive and destructive interference in the wavefield away from the source. Using a stochastic source model, it is demonstrated that local tsunami amplitudes vary by as much as a factor of two or more, depending on the local bathymetry. If other earthquake source parameters such as focal depth or shear modulus are varied in addition to the slip distribution patterns, even greater uncertainty in local tsunami amplitude is expected for earthquakes of similar magnitude. Because of the short amount of time available to issue local warnings and because of the high degree of uncertainty associated with local, model-based forecasts as suggested by this study, direct wave height observations and a strong public education and preparedness program are critical for those regions near suspected tsunami sources.

Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague

PubMed Central

Vogler, Amy J.; Andrianaivoarimanana, Voahangy; Telfer, Sandra; Hall, Carina M.; Sahl, Jason W.; Hepp, Crystal M.; Centner, Heather; Andersen, Genevieve; Birdsell, Dawn N.; Rahalison, Lila; Nottingham, Roxanne; Keim, Paul; Rajerison, Minoarisoa

2017-01-01

Background Yersinia pestis appears to be maintained in multiple, geographically separate, and phylogenetically distinct subpopulations within the highlands of Madagascar. However, the dynamics of these locally differentiated subpopulations through time are mostly unknown. To address that gap and further inform our understanding of plague epidemiology, we investigated the phylogeography of Y. pestis in Madagascar over an 18 year period. Methodology/Principal findings We generated whole genome sequences for 31 strains and discovered new SNPs that we used in conjunction with previously identified SNPs and variable-number tandem repeats (VNTRs) to genotype 773 Malagasy Y. pestis samples from 1995 to 2012. We mapped the locations where samples were obtained on a fine geographic scale to examine phylogeographic patterns through time. We identified 18 geographically separate and phylogenetically distinct subpopulations that display spatial and temporal stability, persisting in the same locations over a period of almost two decades. We found that geographic areas with higher levels of topographical relief are associated with greater levels of phylogenetic diversity and that sampling frequency can vary considerably among subpopulations and from year to year. We also found evidence of various Y. pestis dispersal events, including over long distances, but no evidence that any dispersal events resulted in successful establishment of a transferred genotype in a new location during the examined time period. Conclusions/Significance Our analysis suggests that persistent endemic cycles of Y. pestis transmission within local areas are responsible for the long term maintenance of plague in Madagascar, rather than repeated episodes of wide scale epidemic spread. Landscape likely plays a role in maintaining Y. pestis subpopulations in Madagascar, with increased topographical relief associated with increased levels of localized differentiation. Local ecological factors likely affect the dynamics of individual subpopulations and the associated likelihood of observing human plague cases in a given year in a particular location. PMID:28873412

Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague.

PubMed

Vogler, Amy J; Andrianaivoarimanana, Voahangy; Telfer, Sandra; Hall, Carina M; Sahl, Jason W; Hepp, Crystal M; Centner, Heather; Andersen, Genevieve; Birdsell, Dawn N; Rahalison, Lila; Nottingham, Roxanne; Keim, Paul; Wagner, David M; Rajerison, Minoarisoa

2017-09-01

Yersinia pestis appears to be maintained in multiple, geographically separate, and phylogenetically distinct subpopulations within the highlands of Madagascar. However, the dynamics of these locally differentiated subpopulations through time are mostly unknown. To address that gap and further inform our understanding of plague epidemiology, we investigated the phylogeography of Y. pestis in Madagascar over an 18 year period. We generated whole genome sequences for 31 strains and discovered new SNPs that we used in conjunction with previously identified SNPs and variable-number tandem repeats (VNTRs) to genotype 773 Malagasy Y. pestis samples from 1995 to 2012. We mapped the locations where samples were obtained on a fine geographic scale to examine phylogeographic patterns through time. We identified 18 geographically separate and phylogenetically distinct subpopulations that display spatial and temporal stability, persisting in the same locations over a period of almost two decades. We found that geographic areas with higher levels of topographical relief are associated with greater levels of phylogenetic diversity and that sampling frequency can vary considerably among subpopulations and from year to year. We also found evidence of various Y. pestis dispersal events, including over long distances, but no evidence that any dispersal events resulted in successful establishment of a transferred genotype in a new location during the examined time period. Our analysis suggests that persistent endemic cycles of Y. pestis transmission within local areas are responsible for the long term maintenance of plague in Madagascar, rather than repeated episodes of wide scale epidemic spread. Landscape likely plays a role in maintaining Y. pestis subpopulations in Madagascar, with increased topographical relief associated with increased levels of localized differentiation. Local ecological factors likely affect the dynamics of individual subpopulations and the associated likelihood of observing human plague cases in a given year in a particular location.

BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms.

PubMed

Esteves, Francisco F; Springhorn, Alexander; Kague, Erika; Taylor, Erika; Pyrowolakis, George; Fisher, Shannon; Bier, Ethan

2014-09-01

In a broad variety of bilaterian species the trunk central nervous system (CNS) derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of "neural identity" gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs) act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs) that control localized expression of the Drosophila msh and zebrafish (Danio rerio) msxB in the dorsal central nervous system (CNS). Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages.

BMPs Regulate msx Gene Expression in the Dorsal Neuroectoderm of Drosophila and Vertebrates by Distinct Mechanisms

PubMed Central

Esteves, Francisco F.; Taylor, Erika; Pyrowolakis, George; Fisher, Shannon; Bier, Ethan

2014-01-01

In a broad variety of bilaterian species the trunk central nervous system (CNS) derives from three primary rows of neuroblasts. The fates of these neural progenitor cells are determined in part by three conserved transcription factors: vnd/nkx2.2, ind/gsh and msh/msx in Drosophila melanogaster/vertebrates, which are expressed in corresponding non-overlapping patterns along the dorsal-ventral axis. While this conserved suite of “neural identity” gene expression strongly suggests a common ancestral origin for the patterning systems, it is unclear whether the original regulatory mechanisms establishing these patterns have been similarly conserved during evolution. In Drosophila, genetic evidence suggests that Bone Morphogenetic Proteins (BMPs) act in a dosage-dependent fashion to repress expression of neural identity genes. BMPs also play a dose-dependent role in patterning the dorsal and lateral regions of the vertebrate CNS, however, the mechanism by which they achieve such patterning has not yet been clearly established. In this report, we examine the mechanisms by which BMPs act on cis-regulatory modules (CRMs) that control localized expression of the Drosophila msh and zebrafish (Danio rerio) msxB in the dorsal central nervous system (CNS). Our analysis suggests that BMPs act differently in these organisms to regulate similar patterns of gene expression in the neuroectoderm: repressing msh expression in Drosophila, while activating msxB expression in the zebrafish. These findings suggest that the mechanisms by which the BMP gradient patterns the dorsal neuroectoderm have reversed since the divergence of these two ancient lineages. PMID:25210771

More distinct food intake patterns among women than men in northern Sweden: a population-based survey.

PubMed

Winkvist, Anna; Hörnell, Agneta; Hallmans, Göran; Lindahl, Bernt; Weinehall, Lars; Johansson, Ingegerd

2009-02-19

The need to promote a healthy diet to curb the current obesity epidemic has today been recognized by most countries. A prerequisite for planning and evaluating interventions on dietary intake is the existence of valid information on long-term average dietary intake in a population. Few large, population-based studies of dietary intake have been carried out in Sweden. The largest to date is the Västerbotten Intervention Program (VIP), which was initiated in 1985, with data collection still ongoing. This paper reports on the first comprehensive analyses of the dietary data and presents dietary intake patterns among over 60,000 women and men in northern Sweden during 1992-2005. Between 1992 and 2005, 71,367 inhabitants in Västerbotten county aged 30, 40, 50, and 60 years visited their local health care center as part of the VIP. Participants of VIP filled in an 84- or 64-item food frequency questionnaire (FFQ) and provided sociodemographic information. Complete and realistic information on consumption frequency was provided by 62,531 individuals. Food intake patterns were analyzed using K-means cluster analyses. The mean daily energy intake was 6,83 (+/- 1,77) MJ among women and 8,71 (+/- 2,26) MJ among men. More than half of both women and men were classified as Low Energy Reporters (defined as individuals reporting a food intake level below the lower 95% confidence interval limit of the physical activity level). Larger variation in frequency of daily intake was seen among women than among men for most food groups. Among women, four dietary clusters were identified, labeled "Fruit and vegetables", "High fat", "Coffee and sandwich", and "Tea and ice cream". Among men, three dietary clusters were identified, labeled "Fruit and vegetables", "High fat", and "Tea, soda and cookies". More distinct food intake patterns were seen among women than men in this study in northern Sweden. Due to large proportions of Low Energy Reporters, our results on dietary intake may not be suitable for comparisons with recommended intake levels. However, the results on food intake patterns should still be valid and useful as a basis for targeting interventions to groups most in need.

Scaling biodiversity responses to hydrological regimes.

PubMed

Rolls, Robert J; Heino, Jani; Ryder, Darren S; Chessman, Bruce C; Growns, Ivor O; Thompson, Ross M; Gido, Keith B

2018-05-01

Of all ecosystems, freshwaters support the most dynamic and highly concentrated biodiversity on Earth. These attributes of freshwater biodiversity along with increasing demand for water mean that these systems serve as significant models to understand drivers of global biodiversity change. Freshwater biodiversity changes are often attributed to hydrological alteration by water-resource development and climate change owing to the role of the hydrological regime of rivers, wetlands and floodplains affecting patterns of biodiversity. However, a major gap remains in conceptualising how the hydrological regime determines patterns in biodiversity's multiple spatial components and facets (taxonomic, functional and phylogenetic). We synthesised primary evidence of freshwater biodiversity responses to natural hydrological regimes to determine how distinct ecohydrological mechanisms affect freshwater biodiversity at local, landscape and regional spatial scales. Hydrological connectivity influences local and landscape biodiversity, yet responses vary depending on spatial scale. Biodiversity at local scales is generally positively associated with increasing connectivity whereas landscape-scale biodiversity is greater with increasing fragmentation among locations. The effects of hydrological disturbance on freshwater biodiversity are variable at separate spatial scales and depend on disturbance frequency and history and organism characteristics. The role of hydrology in determining habitat for freshwater biodiversity also depends on spatial scaling. At local scales, persistence, stability and size of habitat each contribute to patterns of freshwater biodiversity yet the responses are variable across the organism groups that constitute overall freshwater biodiversity. We present a conceptual model to unite the effects of different ecohydrological mechanisms on freshwater biodiversity across spatial scales, and develop four principles for applying a multi-scaled understanding of freshwater biodiversity responses to hydrological regimes. The protection and restoration of freshwater biodiversity is both a fundamental justification and a central goal of environmental water allocation worldwide. Clearer integration of concepts of spatial scaling in the context of understanding impacts of hydrological regimes on biodiversity will increase uptake of evidence into environmental flow implementation, identify suitable biodiversity targets responsive to hydrological change or restoration, and identify and manage risks of environmental flows contributing to biodiversity decline. © 2017 Cambridge Philosophical Society.

Ecology and evolution of rabies virus in Europe.

PubMed

Bourhy, H; Kissi, B; Audry, L; Smreczak, M; Sadkowska-Todys, M; Kulonen, K; Tordo, N; Zmudzinski, J F; Holmes, E C

1999-10-01

The evolution of rabies viruses of predominantly European origin was studied by comparing nucleotide sequences of the nucleoprotein and glycoprotein genes, and by typing isolates using RFLP. Phylogenetic analysis of the gene sequence data revealed a number of distinct groups, each associated with a particular geographical area. Such a pattern suggests that rabies virus has spread westwards and southwards across Europe during this century, but that physical barriers such as the Vistula river in Poland have enabled localized evolution. During this dispersal process, two species jumps took place - one into red foxes and another into raccoon dogs, although it is unclear whether virus strains are preferentially adapted to particular animal species or whether ecological forces explain the occurrence of the phylogenetic groups.

Surface compositions across Pluto and Charon.

PubMed

Grundy, W M; Binzel, R P; Buratti, B J; Cook, J C; Cruikshank, D P; Dalle Ore, C M; Earle, A M; Ennico, K; Howett, C J A; Lunsford, A W; Olkin, C B; Parker, A H; Philippe, S; Protopapa, S; Quirico, E; Reuter, D C; Schmitt, B; Singer, K N; Verbiscer, A J; Beyer, R A; Buie, M W; Cheng, A F; Jennings, D E; Linscott, I R; Parker, J Wm; Schenk, P M; Spencer, J R; Stansberry, J A; Stern, S A; Throop, H B; Tsang, C C C; Weaver, H A; Weigle, G E; Young, L A

2016-03-18

The New Horizons spacecraft mapped colors and infrared spectra across the encounter hemispheres of Pluto and Charon. The volatile methane, carbon monoxide, and nitrogen ices that dominate Pluto's surface have complicated spatial distributions resulting from sublimation, condensation, and glacial flow acting over seasonal and geological time scales. Pluto's water ice "bedrock" was also mapped, with isolated outcrops occurring in a variety of settings. Pluto's surface exhibits complex regional color diversity associated with its distinct provinces. Charon's color pattern is simpler, dominated by neutral low latitudes and a reddish northern polar region. Charon's near-infrared spectra reveal highly localized areas with strong ammonia absorption tied to small craters with relatively fresh-appearing impact ejecta. Copyright © 2016, American Association for the Advancement of Science.

Patterns of productive activity engagement as a longitudinal predictor of depressive symptoms among older adults in urban China.

PubMed

Liu, Huiying; Lou, Vivian W Q

2017-11-01

Using two waves of panel data from the China Health and Retirement Longitudinal Study, this study prospectively assessed whether four distinct patterns of productive activity engagement would predict depressive symptoms among older adults in urban China two years later. A sample of urban residents aged 60 or above at Wave 1 and who were interviewed in both waves (N = 2398) was used. Latent class analysis (LCA) was conducted to identify distinct patterns of productive activity engagement that occurred within the Wave 1 data. Next, the generalized estimating equations were used to assess whether identified patterns predicted the levels of depressive symptoms measured at Wave 2. Our use of LCA confirmed the existence of four distinct patterns of productive activity engagement among the study sample: Informal Helper/Carer, Working-Caring Engager, Civic Contributor, and Low/Spousal Carer. All of these three patterns exhibited significantly lower levels of depressive symptoms than that of Low/Spousal Carer two years later. Our use of individual-based categorization of productive engagement better captured the reality of older adults performing various productive activities than summative scales of productive activities did and, therefore, provided a more valid clarification of differential well-being outcomes among older adults.

Genetic mosaic in a marine species flock.

PubMed

McCartney, Michael A; Acevedo, Jenny; Heredia, Christine; Rico, Ciro; Quenoville, Brice; Bermingham, Eldredge; McMillan, W Owen

2003-11-01

We used molecular approaches to study the status of speciation in coral reef fishes known as hamlets (Serranidae: Hypoplectrus). Several hamlet morphospecies coexist on Caribbean reefs, and mate assortatively with respect to their strikingly distinct colour patterns. We provide evidence that, genetically, the hamlets display characteristics common in species flocks on land and in freshwaters. Substitutions within two mitochondrial DNA (mtDNA) protein-coding genes place hamlets within a monophyletic group relative to members of two related genera (Serranus and Diplectrum), and establish that the hamlet radiation must have been very recent. mtDNA distances separating hamlet morphospecies were slight (0.6 +/- 0.04%), yielding a coalescent estimate for the age of the hamlet flock of approximately 430 000 years. Morphospecies did not sort into distinct mtDNA haplotype phylogroups, and alleles at five hypervariable microsatellite loci were shared broadly across species boundaries. None the less, molecular variation was not distributed at random. Analyses of mtDNA haplotype frequencies and nested clades in haplotype networks revealed significant genetic differences between geographical regions and among colour morphospecies. We also observed significant microsatellite differentiation between geographical regions and in Puerto Rico, among colour morphospecies; the latter providing evidence for reproductive isolation between colour morphospecies at this locale. In our Panama collection, however, colour morphospecies were mostly genetically indistinguishable. This mosaic pattern of DNA differentiation implies a complex interaction between population history, mating behaviour and geography and suggests that porous boundaries separate species in this flock of brilliantly coloured coral reef fishes.

Geospatial tools for landscape character assessment in Cyprus

NASA Astrophysics Data System (ADS)

Symons, N. P.; Vogiatzakis, I. N.; Griffiths, G. H.; Warnock, S.; Vassou, V.; Zomeni, M.; Trigkas, V.

2013-08-01

The development of Landscape Typologies in Europe relies upon advances in geospatial tools and increasing availability of digital datasets. Landscape Character Assessment (LCA) is a technique used to classify, describe and understand the combined physical, ecological and cultural characteristics of a landscape. LCA uses a range of data sources to identify and describe areas of common character and can operate at a range of scales i.e.national and regional and local. The paper describes the steps taken to develop an island wide landscape typology for Cyprus, based on the use of GIS and remote sensing tools. The methodology involved integrating physiographical, ecological and cultural information about the Cypriot landscape. Datasets on the cultural attributes (e.g. settlement and field patterns) were not available, so they were created de novo based on information from topographical maps (for settlement dispersion and density) and medium resolution satellite imagery from Google Earth, from which a number of distinctive field patterns could be distinguished. The mapping work is carried out on two levels using a hierarchical approach. The first level at a 1:100, 000 scale has been completed resulting in a map with 17 distinct landscape types. The second level is under way with the view of producing a more detailed landscape typology at 1:50, 000 scale which will incorporate the cultural aspects of the island. This is the first time that such a typology has been produced for Cyprus and it is expected to provide an invaluable tool for landscape planning and management.

Emotion word processing: does mood make a difference?

PubMed

Sereno, Sara C; Scott, Graham G; Yao, Bo; Thaden, Elske J; O'Donnell, Patrick J

2015-01-01

Visual emotion word processing has been in the focus of recent psycholinguistic research. In general, emotion words provoke differential responses in comparison to neutral words. However, words are typically processed within a context rather than in isolation. For instance, how does one's inner emotional state influence the comprehension of emotion words? To address this question, the current study examined lexical decision responses to emotionally positive, negative, and neutral words as a function of induced mood as well as their word frequency. Mood was manipulated by exposing participants to different types of music. Participants were randomly assigned to one of three conditions-no music, positive music, and negative music. Participants' moods were assessed during the experiment to confirm the mood induction manipulation. Reaction time results confirmed prior demonstrations of an interaction between a word's emotionality and its frequency. Results also showed a significant interaction between participant mood and word emotionality. However, the pattern of results was not consistent with mood-congruency effects. Although positive and negative mood facilitated responses overall in comparison to the control group, neither positive nor negative mood appeared to additionally facilitate responses to mood-congruent words. Instead, the pattern of findings seemed to be the consequence of attentional effects arising from induced mood. Positive mood broadens attention to a global level, eliminating the category distinction of positive-negative valence but leaving the high-low arousal dimension intact. In contrast, negative mood narrows attention to a local level, enhancing within-category distinctions, in particular, for negative words, resulting in less effective facilitation.

Geographic Mosaic of Plant Evolution: Extrafloral Nectary Variation Mediated by Ant and Herbivore Assemblages

PubMed Central

Nogueira, Anselmo; Rey, Pedro J.; Alcántara, Julio M.; Feitosa, Rodrigo M.; Lohmann, Lúcia G.

2015-01-01

Herbivory is an ecological process that is known to generate different patterns of selection on defensive plant traits across populations. Studies on this topic could greatly benefit from the general framework of the Geographic Mosaic Theory of Coevolution (GMT). Here, we hypothesize that herbivory represents a strong pressure for extrafloral nectary (EFN) bearing plants, with differences in herbivore and ant visitor assemblages leading to different evolutionary pressures among localities and ultimately to differences in EFN abundance and function. In this study, we investigate this hypothesis by analyzing 10 populations of Anemopaegma album (30 individuals per population) distributed through ca. 600 km of Neotropical savanna and covering most of the geographic range of this plant species. A common garden experiment revealed a phenotypic differentiation in EFN abundance, in which field and experimental plants showed a similar pattern of EFN variation among populations. We also did not find significant correlations between EFN traits and ant abundance, herbivory and plant performance across localities. Instead, a more complex pattern of ant–EFN variation, a geographic mosaic, emerged throughout the geographical range of A. album. We modeled the functional relationship between EFNs and ant traits across ant species and extended this phenotypic interface to characterize local situations of phenotypic matching and mismatching at the population level. Two distinct types of phenotypic matching emerged throughout populations: (1) a population with smaller ants (Crematogaster crinosa) matched with low abundance of EFNs; and (2) seven populations with bigger ants (Camponotus species) matched with higher EFN abundances. Three matched populations showed the highest plant performance and narrower variance of EFN abundance, representing potential plant evolutionary hotspots. Cases of mismatched and matched populations with the lowest performance were associated with abundant and highly detrimental herbivores. Our findings provide insights on the ecology and evolution of plant–ant guarding systems, and suggest new directions to research on facultative mutualistic interactions at wide geographic scales. PMID:25885221

Expression Patterns and Subcellular Localization of Carbonic Anhydrases Are Developmentally Regulated during Tooth Formation

PubMed Central

Reibring, Claes-Göran; El Shahawy, Maha; Hallberg, Kristina; Kannius-Janson, Marie; Nilsson, Jeanette; Parkkila, Seppo; Sly, William S.; Waheed, Abdul; Linde, Anders; Gritli-Linde, Amel

2014-01-01

Carbonic anhydrases (CAs) play fundamental roles in several physiological events, and emerging evidence points at their involvement in an array of disorders, including cancer. The expression of CAs in the different cells of teeth is unknown, let alone their expression patterns during odontogenesis. As a first step towards understanding the role of CAs during odontogenesis, we used immunohistochemistry, histochemistry and in situ hybridization to reveal hitherto unknown dynamic distribution patterns of eight CAs in mice. The most salient findings include expression of CAII/Car2 not only in maturation-stage ameloblasts (MA) but also in the papillary layer, dental papilla mesenchyme, odontoblasts and the epithelial rests of Malassez. We uncovered that the latter form lace-like networks around incisors; hitherto these have been known to occur only in molars. All CAs studied were produced by MA, however CAIV, CAIX and CARPXI proteins were distinctly enriched in the ruffled membrane of the ruffled MA but exhibited a homogeneous distribution in smooth-ended MA. While CAIV, CAVI/Car6, CAIX, CARPXI and CAXIV were produced by all odontoblasts, CAIII distribution displayed a striking asymmetry, in that it was virtually confined to odontoblasts in the root of molars and root analog of incisors. Remarkably, from initiation until near completion of odontogenesis and in several other tissues, CAXIII localized mainly in intracellular punctae/vesicles that we show to overlap with LAMP-1- and LAMP-2-positive vesicles, suggesting that CAXIII localizes within lysosomes. We showed that expression of CAs in developing teeth is not confined to cells involved in biomineralization, pointing at their participation in other biological events. Finally, we uncovered novel sites of CA expression, including the developing brain and eye, the olfactory epithelium, melanoblasts, tongue, notochord, nucleus pulposus and sebaceous glands. Our study provides important information for future single or multiple gene targeting strategies aiming at deciphering the function of CAs during odontogenesis. PMID:24789143

Neurogenic and myogenic motor patterns of rabbit proximal, mid, and distal colon.

PubMed

Dinning, P G; Costa, M; Brookes, S J; Spencer, N J

2012-07-01

The rabbit colon consists of four distinct regions. The motility of each region is controlled by myogenic and neurogenic mechanisms. Associating these mechanisms with specific motor patterns throughout all regions of the colon has not previously been achieved. Three sections of the colon (the proximal, mid, and distal colon) were removed from euthanized rabbits. The proximal colon consists of a triply teniated region and a single tenia region. Spatio-temporal maps were constructed from video recordings of colonic wall diameter, with associated intraluminal pressure recorded from the aboral end. Hexamethonium (100 μM) and tetrodotoxin (TTX; 0.6 μM) were used to inhibit neural activity. Four distinct patterns of motility were detected: 1 myogenic and 3 neurogenic. The myogenic activity consisted of circular muscle (CM) contractions (ripples) that occurred throughout the colon and propagated in both antegrade (anal) and retrograde (oral) directions. The neural activity of the proximal colon consisted of slowly (0.1 mm/s) propagating colonic migrating motor complexes, which were abolished by hexamethonium. These complexes were observed in the region of the proximal colon with a single band of tenia. In the distal colon, tetrodotoxin-sensitive, thus neurally mediated, but hexamethonium-resistant, peristaltic (anal) and antiperistaltic (oral) contractions were identified. The distinct patterns of neurogenic and myogenic motor activity recorded from isolated rabbit colon are specific to each anatomically distinct region. The regional specificity motor pattern is likely to facilitate orderly transit of colonic content from semi-liquid to solid composition of feces.

EEG functional connectivity, axon delays and white matter disease.

PubMed

Nunez, Paul L; Srinivasan, Ramesh; Fields, R Douglas

2015-01-01

Both structural and functional brain connectivities are closely linked to white matter disease. We discuss several such links of potential interest to neurologists, neurosurgeons, radiologists, and non-clinical neuroscientists. Treatment of brains as genuine complex systems suggests major emphasis on the multi-scale nature of brain connectivity and dynamic behavior. Cross-scale interactions of local, regional, and global networks are apparently responsible for much of EEG's oscillatory behaviors. Finite axon propagation speed, often assumed to be infinite in local network models, is central to our conceptual framework. Myelin controls axon speed, and the synchrony of impulse traffic between distant cortical regions appears to be critical for optimal mental performance and learning. Several experiments suggest that axon conduction speed is plastic, thereby altering the regional and global white matter connections that facilitate binding of remote local networks. Combined EEG and high resolution EEG can provide distinct multi-scale estimates of functional connectivity in both healthy and diseased brains with measures like frequency and phase spectra, covariance, and coherence. White matter disease may profoundly disrupt normal EEG coherence patterns, but currently these kinds of studies are rare in scientific labs and essentially missing from clinical environments. Copyright © 2014 International Federation of Clinical Neurophysiology. All rights reserved.

Functional metabolomics as a tool to analyze Mediator function and structure in plants.

PubMed

Davoine, Celine; Abreu, Ilka N; Khajeh, Khalil; Blomberg, Jeanette; Kidd, Brendan N; Kazan, Kemal; Schenk, Peer M; Gerber, Lorenz; Nilsson, Ove; Moritz, Thomas; Björklund, Stefan

2017-01-01

Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast. Based on these results, we suggest localization of previously unassigned plant Mediator subunits to specific modules. We also describe novel roles for individual subunits in development, and demonstrate changes in gene expression patterns and specific metabolite levels in med18 and med25, which can explain their phenotypes. We find that med18 displays levels of phytoalexins normally found in wild type plants only after exposure to pathogens. Our results indicate that different Mediator subunits are involved in specific signaling pathways that control developmental processes and tolerance to pathogen infections.

Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1.

PubMed

Kronholm, Ilkka; Picó, F Xavier; Alonso-Blanco, Carlos; Goudet, Jérôme; de Meaux, Juliette

2012-07-01

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation. © 2012 The Author(s).

Evolution of the vestibulo-ocular system

NASA Technical Reports Server (NTRS)

Fritzsch, B.

1998-01-01

The evolutionary and developmental changes in the eye muscle innervation, the inner ear, and the vestibulo-ocular reflex are examined. Three eye muscle patterns, based on the innervation by distinct ocular motoneurons populations, can be identified: a lamprey, an elasmobranch, and a bony fish/tetrapod pattern. Four distinct patterns of variation in the vestibular system are described: a hagfish pattern, a lamprey pattern, an elasmobranch pattern, and a bony fish/tetrapod pattern. Developmental data suggest an influence of the hindbrain on ear pattern formation, thus potentially allowing a concomitant change of eye muscle innervation and ear variation. The connections between the ear and the vestibular nuclei and between the vestibular nuclei and ocular motoneurons are reviewed, and the role of neurotrophins for pattern specification is discussed. Three patterns are recognized in central projections: a hagfish pattern, a lamprey pattern, and a pattern for jawed vertebrates. Second-order connections show both similarities and differences between distantly related species such as lampreys and mammals. For example, elasmobranchs lack an internuclear system, which is at best poorly developed in lampreys. It is suggested that the vestibulo-ocular system shows only a limited degree of variation because of the pronounced functional constraints imposed on it.

Comprehensive Expression Map of Transcription Regulators in the Adult Zebrafish Telencephalon Reveals Distinct Neurogenic Niches

PubMed Central

Diotel, Nicolas; Rodriguez Viales, Rebecca; Armant, Olivier; März, Martin; Ferg, Marco; Rastegar, Sepand; Strähle, Uwe

2015-01-01

The zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression. The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. J. Comp. Neurol. 523:1202–1221, 2015. © 2015 Wiley Periodicals, Inc. PMID:25556858

Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches.

PubMed

Diotel, Nicolas; Rodriguez Viales, Rebecca; Armant, Olivier; März, Martin; Ferg, Marco; Rastegar, Sepand; Strähle, Uwe

2015-06-01

The zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression. The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. © 2015 Wiley Periodicals, Inc.

Monorchiids (Platyhelminthes: Digenea) of chaetodontid fishes (Perciformes): biogeographical patterns in the tropical Indo-West Pacific.

PubMed

McNamara, M K A; Adlard, R D; Bray, R A; Sasal, P; Cribb, T H

2012-06-01

Species richness and biogeography of the monorchiid genus Hurleytrematoides was studied by the examination of 2834 individuals of 45 species of Chaetodontidae at six major sites in the tropical Indo-West Pacific: Heron Island, Lizard Island, Ningaloo (Western Australia), Palau, New Caledonia and Moorea (French Polynesia). In total, 18 species were distributed among six sites; descriptions are provided for eight new species: H. boucheti n. sp., H. combesi n. sp., H. deblocki n. sp., H. dollfusi n. sp., H. euzeti n. sp., H. kulbickii n. sp., H. pasteuri n. sp., and H. planesi n. sp. Overall richness ranged from zero to five Hurleytrematoides species per chaetodontid species. Seven Hurleytrematoides species were found at only one locality and eleven were found at multiple localities. Only one species, H. morandi, was found at all localities. Individual localities had between six (Moorea) and 10 (Heron Island) species; we attribute Moorea's depauperate parasite fauna to its isolation and distance from the Indo-Philippine centre of biological diversity. Using cluster analysis of 18 species of Hurleytrematoides and 45 species of chaetodontids sampled in the Indo-West Pacific, we show that the localities on the Great Barrier Reef (Heron Island and Lizard Island) and New Caledonia have the most similar chaetodontid and parasite fauna of any locality pairs. Cluster analysis results also show that the similarity of the chaetodontid assemblages at five of the six localities is relatively high and that Ningaloo has the most distinct fauna. Similarity values based on sharing of species of Hurleytrematoides are generally lower than those for their hosts; Moorea, Ningaloo and Palau all have low similarity to New Caledonia and Great Barrier Reef sites. We attribute these distinctions to the differential dispersal capability of the fish and their parasites. Chaetodontids have long-lived mobile pelagic larvae, the dispersal of which would be most affected by prominent biogeographical barriers, such as that between the Indian and Pacific Oceans. In contrast, monorchiids have no obvious dispersal stage, and vast distances have the capacity to act as effective barriers to dispersal. We conclude that the present distributions of species of Hurleytrematoides in the Indo-Pacific are driven by historical opportunity and capacity to disperse, and that some disjunct distributions are sculpted by stochasticity. Copyright © 2011. Published by Elsevier Ireland Ltd.

Pattern Laser Annealing by a Pulsed Laser

NASA Astrophysics Data System (ADS)

Komiya, Yoshio; Hoh, Koichiro; Murakami, Koichi; Takahashi, Tetsuo; Tarui, Yasuo

1981-10-01

Preliminary experiments with contact-type pattern laser annealing were made for local polycrystallization of a-Si, local evaporation of a-Si and local formation of Ni-Si alloy. These experiments showed that the mask patterns can be replicated as annealed regions with a resolution of a few microns on substrates. To overcome shortcomings due to the contact type pattern annealing, a projection type reduction pattern laser annealing system is proposed for resistless low temperature pattern forming processes.

Local sparse bump hunting reveals molecular heterogeneity of colon tumors‡

PubMed Central

Dazard, Jean-Eudes; Rao, J. Sunil; Markowitz, Sanford

2013-01-01

The question of molecular heterogeneity and of tumoral phenotype in cancer remains unresolved. To understand the underlying molecular basis of this phenomenon, we analyzed genome-wide expression data of colon cancer metastasis samples, as these tumors are the most advanced and hence would be anticipated to be the most likely heterogeneous group of tumors, potentially exhibiting the maximum amount of genetic heterogeneity. Casting a statistical net around such a complex problem proves difficult because of the high dimensionality and multi-collinearity of the gene expression space, combined with the fact that genes act in concert with one another and that not all genes surveyed might be involved. We devise a strategy to identify distinct subgroups of samples and determine the genetic/molecular signature that defines them. This involves use of the local sparse bump hunting algorithm, which provides a much more optimal and biologically faithful transformed space within which to search for bumps. In addition, thanks to the variable selection feature of the algorithm, we derived a novel sparse gene expression signature, which appears to divide all colon cancer patients into two populations: a population whose expression pattern can be molecularly encompassed within the bump and an outlier population that cannot be. Although all patients within any given stage of the disease, including the metastatic group, appear clinically homogeneous, our procedure revealed two subgroups in each stage with distinct genetic/molecular profiles. We also discuss implications of such a finding in terms of early detection, diagnosis and prognosis. PMID:22052459

Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome.

PubMed

Cheng, Lixin; Leung, Kwong-Sak

2018-05-16

Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncRNAs. MoonFinder is a statistical algorithm identifying moonlighting lncRNAs without a priori knowledge through the integration of protein interactome, RNA-protein interactions, and functional annotation of proteins. We identify 155 moonlighting lncRNA candidates and uncover that they are a distinct class of lncRNAs characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncRNAs tend to have shorter but more exons and the moonlighting lncRNAs have a variable localization pattern with a high chance of residing in the cytoplasmic compartment in comparison to the other lncRNAs. Moreover, moonlighting lncRNAs and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases. The code implementing MoonFinder is supplied as an R package in the supplementary material. lxcheng@cse.cuhk.edu.hk or ksleung@cse.cuhk.edu.hk. Supplementary data are available at Bioinformatics online.

Pinhole Micro-SPECT/CT for Noninvasive Monitoring and Quantitation of Oncolytic Virus Dispersion and Percent Infection in Solid Tumors

PubMed Central

Penheiter, Alan R.; Griesmann, Guy E.; Federspiel, Mark J.; Dingli, David; Russell, Stephen J.; Carlson, Stephanie K.

2011-01-01

The purpose of our study was to validate the ability of pinhole micro-single-photon emission computed tomography/computed tomography (SPECT/CT) to 1) accurately resolve the intratumoral dispersion pattern and 2) quantify the infection percentage in solid tumors of an oncolytic measles virus encoding the human sodium iodide symporter (MV-NIS). NIS RNA level and dispersion pattern were determined in control and MV-NIS infected BxPC-3 pancreatic tumor cells and mouse xenografts using quantitative, real-time, reverse transcriptase, polymerase chain reaction, autoradiography, and immunohistochemistry (IHC). Mice with BxPC-3 xenografts were imaged with 123I or 99TcO4 micro-SPECT/CT. Tumor dimensions and radionuclide localization were determined with imaging software. Linear regression and correlation analyses were performed to determine the relationship between tumor infection percentage and radionuclide uptake (% injected dose per gram) above background and a highly significant correlation was observed (r2 = 0.947). A detection threshold of 1.5-fold above the control tumor uptake (background) yielded a sensitivity of 2.7% MV-NIS infected tumor cells. We reliably resolved multiple distinct intratumoral zones of infection from noninfected regions. Pinhole micro-SPECT/CT imaging using the NIS reporter demonstrated precise localization and quantitation of oncolytic MV-NIS infection and can replace more time-consuming and expensive analyses (eg, autoradiography and IHC) that require animal sacrifice. PMID:21753796

From shape to cells: mouse models reveal mechanisms altering palate development in Apert syndrome

PubMed Central

Martínez-Abadías, Neus; Holmes, Greg; Pankratz, Talia; Wang, Yingli; Zhou, Xueyan; Jabs, Ethylin Wang; Richtsmeier, Joan T.

2013-01-01

SUMMARY Apert syndrome is a congenital disorder characterized by severe skull malformations and caused by one of two missense mutations, S252W and P253R, on fibroblast growth factor receptor 2 (FGFR2). The molecular bases underlying differential Apert syndrome phenotypes are still poorly understood and it is unclear why cleft palate is more frequent in patients carrying the S252W mutation. Taking advantage of Apert syndrome mouse models, we performed a novel combination of morphometric, histological and immunohistochemical analyses to precisely quantify distinct palatal phenotypes in Fgfr2+/S252W and Fgfr2+/P253R mice. We localized regions of differentially altered FGF signaling and assessed local cell patterns to establish a baseline for understanding the differential effects of these two Fgfr2 mutations. Palatal suture scoring and comparative 3D shape analysis from high resolution μCT images of 120 newborn mouse skulls showed that Fgfr2+/S252W mice display relatively more severe palate dysmorphologies, with contracted and more separated palatal shelves, a greater tendency to fuse the maxillary-palatine sutures and aberrant development of the inter-premaxillary suture. These palatal defects are associated with suture-specific patterns of abnormal cellular proliferation, differentiation and apoptosis. The posterior region of the developing palate emerges as a potential target for therapeutic strategies in clinical management of cleft palate in Apert syndrome patients. PMID:23519026

Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

PubMed Central

Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

2014-01-01

Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

Energy-selective Neutron Imaging for Three-dimensional Non-destructive Probing of Crystalline Structures

NASA Astrophysics Data System (ADS)

Peetermans, S.; Bopp, M.; Vontobel, P.; Lehmann, E. H.

Common neutron imaging uses the full polychromatic neutron beam spectrum to reveal the material distribution in a non-destructive way. Performing it with a reduced energy band, i.e. energy-selective neutron imaging, allows access to local variation in sample crystallographic properties. Two sample categories can be discerned with different energy responses. Polycrystalline materials have an energy-dependent cross-section featuring Bragg edges. Energy-selective neutron imaging can be used to distinguish be- tween crystallographic phases, increase material sensitivity or penetration, improve quantification etc. An example of the latter is shown by the examination of copper discs prior to machining them into linear accelerator cavity structures. The cross-section of single crystals features distinct Bragg peaks. Based on their pattern, one can determine the orientation of the crystal, as in a Laue pattern, but with the tremendous advantage that the operation can be performed for each pixel, yielding crystal orientation maps at high spatial resolution. A wholly different method to investigate such samples is also introduced: neutron diffraction imaging. It is based on projections formed by neutrons diffracted from the crystal lattice out of the direct beam. The position of these projections on the detector gives information on the crystal orientation. The projection itself can be used to reconstruct the crystal shape. A three-dimensional mapping of local Bragg reflectivity or a grain orientation mapping can thus be obtained.

Distinct Patterns of IFITM-Mediated Restriction of Filoviruses, SARS Coronavirus, and Influenza A Virus

DTIC Science & Technology

2011-01-06

identified viral restriction factors that inhibit infection mediated by the influenza A virus ( IAV ) hemagglutinin (HA) protein. Here we show that IFITM...observations, interferon-b specifically restricted filovirus and IAV entry processes. IFITM proteins also inhibited replication of infectious MARV and EBOV...We observed distinct patterns of IFITM-mediated restriction: compared with IAV , the entry processes of MARV and EBOV were less restricted by IFITM3

Distinct Chemical Contrast in Adhesion Force Images of Hydrophobic-Hydrophilic Patterned Surfaces Using Multiwalled Carbon Nanotube Probe Tips

NASA Astrophysics Data System (ADS)

Azehara, Hiroaki; Kasanuma, Yuka; Ide, Koichiro; Hidaka, Kishio; Tokumoto, Hiroshi

2008-05-01

In this paper, we describe a fabrication procedure for large-diameter carbon nanotube probe tips (CNT tips) for atomic force microscopy, the tip-end chemistry of the CNT tips, and their advantage drawn from the study of adhesion force imaging in an ambient atmosphere on a patterned hydrophobic and hydrophilic self-assembled monolayer, which has been prepared by a microcontact printing method. Force titration measurements in phosphate buffer solutions reveal that the CNT tip has retained carboxyl groups at its end. In adhesion force imaging, a distinct chemical contrast is obtained for the patterned surfaces as compared to a case using a silicon nitride tip. The origin of the distinct contrast is discussed in terms of the tip-end chemistry featured by carboxyl groups and a possible weakening of capillary forces of water caused at around the tip-sample interface because of the intrinsically hydrophobic nature of CNTs.

Psychological profiling of offender characteristics from crime behaviors in serial rape offences.

PubMed

Kocsis, Richard N; Cooksey, Ray W; Irwin, Harvey J

2002-04-01

Criminal psychological profiling has progressively been incorporated into police procedures despite a dearth of empirical research. Indeed, in the study of serial violent crimes for the purpose of psychological profiling, very few original, quantitative, academically reviewed studies actually exist. This article reports on the analysis of 62 incidents of serial sexual assault. The statistical procedure of multidimensional scaling was employed in the analysis of this data, which in turn produced a five-cluster model of serial rapist behavior. First, a central cluster of behaviors were identified that represent common behaviors to all patterns of serial rape. Second, four distinct outlying patterns were identified as demonstrating distinct offence styles, these being assigned the following descriptive labels brutality, intercourse, chaotic, and ritual. Furthermore, analysis of these patterns also identified distinct offender characteristics that allow for the use of empirically robust offender profiles in future serial rape investigations.

Young Children’s Affective Responses to Another’s Distress: Dynamic and Physiological Features

PubMed Central

Fink, Elian; Heathers, James A. J.; de Rosnay, Marc

2015-01-01

Two descriptive studies set out a new approach for exploring the dynamic features of children’s affective responses (sadness and interest-worry) to another’s distress. In two samples (N study1 = 75; N study2 = 114), Kindergarten children were shown a video-vignette depicting another child in distress and the temporal pattern of spontaneous expressions were examined across the unfolding vignette. Results showed, in both study 1 and 2, that sadness and interest-worry had distinct patterns of elicitation across the events of the vignette narrative and there was little co-occurrence of these affects within a given child. Temporal heart rate changes (study 2) were closely aligned to the events of the vignette and, furthermore, affective responses corresponded to distinctive physiological response profiles. The implications of distinct temporal patterns of elicitation for the meaning of sadness and interest-worry are discussed within the framework of emotion regulation and empathy. PMID:25874952

Neural Activity Patterns in the Human Brain Reflect Tactile Stickiness Perception.

PubMed

Kim, Junsuk; Yeon, Jiwon; Ryu, Jaekyun; Park, Jang-Yeon; Chung, Soon-Cheol; Kim, Sung-Phil

2017-01-01

Our previous human fMRI study found brain activations correlated with tactile stickiness perception using the uni-variate general linear model (GLM) (Yeon et al., 2017). Here, we conducted an in-depth investigation on neural correlates of sticky sensations by employing a multivoxel pattern analysis (MVPA) on the same dataset. In particular, we statistically compared multi-variate neural activities in response to the three groups of sticky stimuli: A supra-threshold group including a set of sticky stimuli that evoked vivid sticky perception; an infra-threshold group including another set of sticky stimuli that barely evoked sticky perception; and a sham group including acrylic stimuli with no physically sticky property. Searchlight MVPAs were performed to search for local activity patterns carrying neural information of stickiness perception. Similar to the uni-variate GLM results, significant multi-variate neural activity patterns were identified in postcentral gyrus, subcortical (basal ganglia and thalamus), and insula areas (insula and adjacent areas). Moreover, MVPAs revealed that activity patterns in posterior parietal cortex discriminated the perceptual intensities of stickiness, which was not present in the uni-variate analysis. Next, we applied a principal component analysis (PCA) to the voxel response patterns within identified clusters so as to find low-dimensional neural representations of stickiness intensities. Follow-up clustering analyses clearly showed separate neural grouping configurations between the Supra- and Infra-threshold groups. Interestingly, this neural categorization was in line with the perceptual grouping pattern obtained from the psychophysical data. Our findings thus suggest that different stickiness intensities would elicit distinct neural activity patterns in the human brain and may provide a neural basis for the perception and categorization of tactile stickiness.

Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

NASA Astrophysics Data System (ADS)

Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

2018-04-01

The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

Neural Activity Patterns in the Human Brain Reflect Tactile Stickiness Perception

PubMed Central

Kim, Junsuk; Yeon, Jiwon; Ryu, Jaekyun; Park, Jang-Yeon; Chung, Soon-Cheol; Kim, Sung-Phil

2017-01-01

Our previous human fMRI study found brain activations correlated with tactile stickiness perception using the uni-variate general linear model (GLM) (Yeon et al., 2017). Here, we conducted an in-depth investigation on neural correlates of sticky sensations by employing a multivoxel pattern analysis (MVPA) on the same dataset. In particular, we statistically compared multi-variate neural activities in response to the three groups of sticky stimuli: A supra-threshold group including a set of sticky stimuli that evoked vivid sticky perception; an infra-threshold group including another set of sticky stimuli that barely evoked sticky perception; and a sham group including acrylic stimuli with no physically sticky property. Searchlight MVPAs were performed to search for local activity patterns carrying neural information of stickiness perception. Similar to the uni-variate GLM results, significant multi-variate neural activity patterns were identified in postcentral gyrus, subcortical (basal ganglia and thalamus), and insula areas (insula and adjacent areas). Moreover, MVPAs revealed that activity patterns in posterior parietal cortex discriminated the perceptual intensities of stickiness, which was not present in the uni-variate analysis. Next, we applied a principal component analysis (PCA) to the voxel response patterns within identified clusters so as to find low-dimensional neural representations of stickiness intensities. Follow-up clustering analyses clearly showed separate neural grouping configurations between the Supra- and Infra-threshold groups. Interestingly, this neural categorization was in line with the perceptual grouping pattern obtained from the psychophysical data. Our findings thus suggest that different stickiness intensities would elicit distinct neural activity patterns in the human brain and may provide a neural basis for the perception and categorization of tactile stickiness. PMID:28936171

Caspase-2 Is Localized at the Golgi Complex and Cleaves Golgin-160 during Apoptosis

PubMed Central

Mancini, Marie; Machamer, Carolyn E.; Roy, Sophie; Nicholson, Donald W.; Thornberry, Nancy A.; Casciola-Rosen, Livia A.; Rosen, Antony

2000-01-01

Caspases are an extended family of cysteine proteases that play critical roles in apoptosis. Animals deficient in caspases-2 or -3, which share very similar tetrapeptide cleavage specificities, exhibit very different phenotypes, suggesting that the unique features of individual caspases may account for distinct regulation and specialized functions. Recent studies demonstrate that unique apoptotic stimuli are transduced by distinct proteolytic pathways, with multiple components of the proteolytic machinery clustering at distinct subcellular sites. We demonstrate here that, in addition to its nuclear distribution, caspase-2 is localized to the Golgi complex, where it cleaves golgin-160 at a unique site not susceptible to cleavage by other caspases with very similar tetrapeptide specificities. Early cleavage at this site precedes cleavage at distal sites by other caspases. Prevention of cleavage at the unique caspase-2 site delays disintegration of the Golgi complex after delivery of a pro-apoptotic signal. We propose that the Golgi complex, like mitochondria, senses and integrates unique local conditions, and transduces pro-apoptotic signals through local caspases, which regulate local effectors. PMID:10791974

Comparison of genomes of malignant catarrhal fever-associated herpesviruses by restriction endonuclease analysis.

PubMed

Shih, L M; Zee, Y C; Castro, A E

1989-01-01

The restriction endonuclease DNA cleavage patterns of eight isolates of malignant catarrhal fever-associated herpesviruses were examined using the restriction endonucleases HindIII and EcoRI. The eight viruses could be assigned to two distinct groups. Virus isolates from a blue wildebeest, a sika deer and an ibex had restriction endonuclease DNA cleavage patterns that were in general similar to each other. The restriction pattern of these three viruses was distinct from the other five. Of these five, four were isolated from a greater kudu, a white tailed wildebeest, a white bearded wildebeest, and a cape hartebeest. The fifth isolate C500, was isolated from a domestic cow with malignant catarrhal fever. These five viruses had similar DNA cleavage patterns.

Compassion: An Evolutionary Analysis and Empirical Review

PubMed Central

Goetz, Jennifer L.; Keltner, Dacher; Simon-Thomas, Emiliana

2010-01-01

What is compassion? And how did it evolve? In this review, we integrate three evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering, distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization, and a phenomenological experience and physiological response that orients the individual to social approach. This response profile of compassion differs from those of distress, sadness, and love, suggesting that compassion is indeed a distinct emotion. We conclude by considering how compassion shapes moral judgment and action, how it varies across different cultures, and how it may engage specific patterns of neural activation, as well as emerging directions of research. PMID:20438142

Emerging European winter precipitation pattern linked to atmospheric circulation changes over the North Atlantic region in recent decades

NASA Astrophysics Data System (ADS)

Ummenhofer, Caroline C.; Seo, Hyodae; Kwon, Young-Oh; Parfitt, Rhys; Brands, Swen; Joyce, Terrence M.

2017-08-01

Dominant European winter precipitation patterns over the past century, along with their associated extratropical North Atlantic circulation changes, are evaluated using cluster analysis. Contrary to the four regimes traditionally identified based on daily wintertime atmospheric circulation patterns, five distinct seasonal precipitation regimes are detected here. Recurrent precipitation patterns in each regime are linked to changes in atmospheric blocking, storm track, and sea surface temperatures across the North Atlantic region. Multidecadal variability in the frequency of the precipitation patterns reveals more (fewer) winters with wet conditions in northern (southern) Europe in recent decades and an emerging distinct pattern of enhanced wintertime precipitation over the northern British Isles. This pattern has become unusually common since the 1980s and is associated with changes in moisture transport and more frequent atmospheric river events. The observed precipitation changes post-1950 coincide with changes in storm track activity over the central/eastern North Atlantic toward the northern British Isles.

Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq.

PubMed

Shi, Junchao; Chen, Qi; Li, Xin; Zheng, Xiudeng; Zhang, Ying; Qiao, Jie; Tang, Fuchou; Tao, Yi; Zhou, Qi; Duan, Enkui

2015-10-15

During mammalian pre-implantation embryo development, when the first asymmetry emerges and how it develops to direct distinct cell fates remain longstanding questions. Here, by analyzing single-blastomere transcriptome data from mouse and human pre-implantation embryos, we revealed that the initial blastomere-to-blastomere biases emerge as early as the first embryonic cleavage division, following a binomial distribution pattern. The subsequent zygotic transcriptional activation further elevated overall blastomere-to-blastomere biases during the two- to 16-cell embryo stages. The trends of transcriptional asymmetry fell into two distinct patterns: for some genes, the extent of asymmetry was minimized between blastomeres (monostable pattern), whereas other genes, including those known to be lineage specifiers, showed ever-increasing asymmetry between blastomeres (bistable pattern), supposedly controlled by negative or positive feedbacks. Moreover, our analysis supports a scenario in which opposing lineage specifiers within an early blastomere constantly compete with each other based on their relative ratio, forming an inclined 'lineage strength' that pushes the blastomere onto a predisposed, yet flexible, lineage track before morphological distinction. © 2015. Published by The Company of Biologists Ltd.

Double activity imaging reveals distinct cellular targets of haloperidol, clozapine and dopamine D(3) receptor selective RGH-1756.

PubMed

Kovács, K J; Csejtei, M; Laszlovszky, I

2001-03-01

Acute administration of typical (haloperidol) and atypical (clozapine) antipsychotics results in distinct and overlapping regions of immediate-early gene expression in the rat brain. RGH-1756 is a recently developed atypical antipsychotic with high affinity to dopamine D(3) receptors that results in a unique pattern of c-Fos induction. A single injection of either antipsychotic results in c-fos mRNA expression that peaks around 30 min after drug administration, while the maximum of c-Fos protein induction is seen 2 h after challenge. The transient and distinct temporal inducibility of c-fos mRNA and c-Fos protein was exploited to reveal and compare cellular targets of different antipsychotic drugs by concomitant localization of c-fos mRNA and c-Fos immunoreactivity in brain sections of rats that were timely challenged with two different antipsychotics. Double activity imaging revealed that haloperidol, clozapine and RGH-1756 share cellular targets in the nucleus accumbens, where 40% of all labeled neurons displayed both c-fos mRNA and c-Fos protein. Haloperidol activates cells in the caudate putamen, while clozapine-responsive, single labeled neurons were dominant in the prefrontal cortex and major island of Calleja. RGH-1756 targets haloperidol-sensitive cells in the caudate putamen, but cells that are activated by clozapine and RGH-1756 in the major island of Calleja are different.

Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections

PubMed Central

Pava, Zuleima; Noviyanti, Rintis; Handayuni, Irene; Trimarsanto, Hidayat; Trianty, Leily; Burdam, Faustina H.; Kenangalem, Enny; Utami, Retno A. S.; Tirta, Yusrifar K.; Coutrier, Farah; Poespoprodjo, Jeanne R.; Price, Ric N.; Marfurt, Jutta

2017-01-01

Background Genetic analyses of Plasmodium have potential to inform on transmission dynamics, but few studies have evaluated this on a local spatial scale. We used microsatellite genotyping to characterise the micro-epidemiology of P. vivax and P. falciparum diversity to inform malaria control strategies in Timika, Papua Indonesia. Methods Genotyping was undertaken on 713 sympatric P. falciparum and P. vivax isolates from a cross-sectional household survey and clinical studies conducted in Timika. Standard population genetic measures were applied, and the data was compared to published data from Kalimantan, Bangka, Sumba and West Timor. Results Higher diversity (HE = 0.847 vs 0.625; p = 0.017) and polyclonality (46.2% vs 16.5%, p<0.001) were observed in P. vivax versus P. falciparum. Distinct P. falciparum substructure was observed, with two subpopulations, K1 and K2. K1 was comprised solely of asymptomatic infections and displayed greater relatedness to isolates from Sumba than to K2, possibly reflecting imported infections. Conclusions The results demonstrate the greater refractoriness of P. vivax versus P. falciparum to control measures, and risk of distinct parasite subpopulations persisting in the community undetected by passive surveillance. These findings highlight the need for complimentary new surveillance strategies to identify transmission patterns that cannot be detected with traditional malariometric methods. PMID:28498860

Functional transformations of odor inputs in the mouse olfactory bulb.

PubMed

Adam, Yoav; Livneh, Yoav; Miyamichi, Kazunari; Groysman, Maya; Luo, Liqun; Mizrahi, Adi

2014-01-01

Sensory inputs from the nasal epithelium to the olfactory bulb (OB) are organized as a discrete map in the glomerular layer (GL). This map is then modulated by distinct types of local neurons and transmitted to higher brain areas via mitral and tufted cells. Little is known about the functional organization of the circuits downstream of glomeruli. We used in vivo two-photon calcium imaging for large scale functional mapping of distinct neuronal populations in the mouse OB, at single cell resolution. Specifically, we imaged odor responses of mitral cells (MCs), tufted cells (TCs) and glomerular interneurons (GL-INs). Mitral cells population activity was heterogeneous and only mildly correlated with the olfactory receptor neuron (ORN) inputs, supporting the view that discrete input maps undergo significant transformations at the output level of the OB. In contrast, population activity profiles of TCs were dense, and highly correlated with the odor inputs in both space and time. Glomerular interneurons were also highly correlated with the ORN inputs, but showed higher activation thresholds suggesting that these neurons are driven by strongly activated glomeruli. Temporally, upon persistent odor exposure, TCs quickly adapted. In contrast, both MCs and GL-INs showed diverse temporal response patterns, suggesting that GL-INs could contribute to the transformations MCs undergo at slow time scales. Our data suggest that sensory odor maps are transformed by TCs and MCs in different ways forming two distinct and parallel information streams.

Multigene Phylogeography of Bactrocera caudata (Insecta: Tephritidae): Distinct Genetic Lineages in Northern and Southern Hemispheres

PubMed Central

Yong, Hoi-Sen; Lim, Phaik-Eem; Tan, Ji; Song, Sze-Looi; Suana, I Wayan; Eamsobhana, Praphathip

2015-01-01

Bactrocera caudata is a pest of pumpkin flower. Specimens of B. caudata from the northern hemisphere (mainland Asia) and southern hemisphere (Indonesia) were analysed using the partial DNA sequences of the nuclear 28S rRNA and internal transcribed spacer region 2 (ITS-2) genes, and the mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and 16S rRNA genes. The COI, COII, 16S rDNA and concatenated COI+COII+16S and COI+COII+16S+28S+ITS-2 nucleotide sequences revealed that B. caudata from the northern hemisphere (Peninsular Malaysia, East Malaysia, Thailand) was distinctly different from the southern hemisphere (Indonesia: Java, Bali and Lombok), without common haplotype between them. Phylogenetic analysis revealed two distinct clades (northern and southern hemispheres), indicating distinct genetic lineage. The uncorrected ‘p’ distance for the concatenated COI+COII+16S nucleotide sequences between the taxa from the northern and southern hemispheres (‘p’ = 4.46-4.94%) was several folds higher than the ‘p’ distance for the taxa in the northern hemisphere (‘p’ = 0.00-0.77%) and the southern hemisphere (‘p’ = 0.00%). This distinct difference was also reflected by concatenated COI+COII+16S+28S+ITS-2 nucleotide sequences with an uncorrected 'p' distance of 2.34-2.69% between the taxa of northern and southern hemispheres. In accordance with the type locality the Indonesian taxa belong to the nominal species. Thus the taxa from the northern hemisphere, if they were to constitute a cryptic species of the B. caudata species complex based on molecular data, need to be formally described as a new species. The Thailand and Malaysian B. caudata populations in the northern hemisphere showed distinct genetic structure and phylogeographic pattern. PMID:26090853

The MYB23 Gene Provides a Positive Feedback Loop for Cell Fate Specification in the Arabidopsis Root Epidermis[C][W

PubMed Central

Kang, Yeon Hee; Kirik, Victor; Hulskamp, Martin; Nam, Kyoung Hee; Hagely, Katherine; Lee, Myeong Min; Schiefelbein, John

2009-01-01

The specification of cell fates during development requires precise regulatory mechanisms to ensure robust cell type patterns. Theoretical models of pattern formation suggest that a combination of negative and positive feedback mechanisms are necessary for efficient specification of distinct fates in a field of differentiating cells. Here, we examine the role of the R2R3-MYB transcription factor gene, AtMYB23 (MYB23), in the establishment of the root epidermal cell type pattern in Arabidopsis thaliana. MYB23 is closely related to, and is positively regulated by, the WEREWOLF (WER) MYB gene during root epidermis development. Furthermore, MYB23 is able to substitute for the function of WER and to induce its own expression when controlled by WER regulatory sequences. We also show that the MYB23 protein binds to its own promoter, suggesting a MYB23 positive feedback loop. The localization of MYB23 transcripts and MYB23-green fluorescent protein (GFP) fusion protein, as well as the effect of a chimeric MYB23-SRDX repressor construct, links MYB23 function to the developing non-hair cell type. Using mutational analyses, we find that MYB23 is necessary for precise establishment of the root epidermal pattern, particularly under conditions that compromise the cell specification process. These results suggest that MYB23 participates in a positive feedback loop to reinforce cell fate decisions and ensure robust establishment of the cell type pattern in the Arabidopsis root epidermis. PMID:19395683

The MYB23 gene provides a positive feedback loop for cell fate specification in the Arabidopsis root epidermis.

PubMed

Kang, Yeon Hee; Kirik, Victor; Hulskamp, Martin; Nam, Kyoung Hee; Hagely, Katherine; Lee, Myeong Min; Schiefelbein, John

2009-04-01

The specification of cell fates during development requires precise regulatory mechanisms to ensure robust cell type patterns. Theoretical models of pattern formation suggest that a combination of negative and positive feedback mechanisms are necessary for efficient specification of distinct fates in a field of differentiating cells. Here, we examine the role of the R2R3-MYB transcription factor gene, AtMYB23 (MYB23), in the establishment of the root epidermal cell type pattern in Arabidopsis thaliana. MYB23 is closely related to, and is positively regulated by, the WEREWOLF (WER) MYB gene during root epidermis development. Furthermore, MYB23 is able to substitute for the function of WER and to induce its own expression when controlled by WER regulatory sequences. We also show that the MYB23 protein binds to its own promoter, suggesting a MYB23 positive feedback loop. The localization of MYB23 transcripts and MYB23-green fluorescent protein (GFP) fusion protein, as well as the effect of a chimeric MYB23-SRDX repressor construct, links MYB23 function to the developing non-hair cell type. Using mutational analyses, we find that MYB23 is necessary for precise establishment of the root epidermal pattern, particularly under conditions that compromise the cell specification process. These results suggest that MYB23 participates in a positive feedback loop to reinforce cell fate decisions and ensure robust establishment of the cell type pattern in the Arabidopsis root epidermis.

Altered Actin Centripetal Retrograde Flow in Physically Restricted Immunological Synapses

PubMed Central

Yu, Cheng-han; Wu, Hung-Jen; Kaizuka, Yoshihisa; Vale, Ronald D.; Groves, Jay T.

2010-01-01

Antigen recognition by T cells involves large scale spatial reorganization of numerous receptor, adhesion, and costimulatory proteins within the T cell-antigen presenting cell (APC) junction. The resulting patterns can be distinctive, and are collectively known as the immunological synapse. Dynamical assembly of cytoskeletal network is believed to play an important role in driving these assembly processes. In one experimental strategy, the APC is replaced with a synthetic supported membrane. An advantage of this configuration is that solid structures patterned onto the underlying substrate can guide immunological synapse assembly into altered patterns. Here, we use mobile anti-CD3ε on the spatial-partitioned supported bilayer to ligate and trigger T cell receptor (TCR) in live Jurkat T cells. Simultaneous tracking of both TCR clusters and GFP-actin speckles reveals their dynamic association and individual flow patterns. Actin retrograde flow directs the inward transport of TCR clusters. Flow-based particle tracking algorithms allow us to investigate the velocity distribution of actin flow field across the whole synapse, and centripetal velocity of actin flow decreases as it moves toward the center of synapse. Localized actin flow analysis reveals that, while there is no influence on actin motion from substrate patterns directly, velocity differences of actin are observed over physically trapped TCR clusters. Actin flow regains its velocity immediately after passing through confined TCR clusters. These observations are consistent with a dynamic and dissipative coupling between TCR clusters and viscoelastic actin network. PMID:20686692

Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

PubMed

Luo, Shitao; Zhang, Fengming; Ruan, Yingfei; Li, Jie; Zhang, Zheng; Sun, Yan; Deng, Shixiong; Peng, Rui

2018-06-01

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis. These results suggest that bowtie structure may be a common property of TRNs of plants, and distinct variation patterns of genes in bowtie structures of TRNs during biological processes may reflect distinct functions. Overall, our study provides an insight into the molecular mechanisms underlying photomorphogenesis and heat shock, and emphasizes the necessity to investigate the strong connectivity structures while studying TRNs. Copyright © 2018 Elsevier B.V. All rights reserved.

Competitive aggregation dynamics using phase wave signals.

PubMed

Sakaguchi, Hidetsugu; Maeyama, Satomi

2014-10-21

Coupled equations of the phase equation and the equation of cell concentration n are proposed for competitive aggregation dynamics of slime mold in two dimensions. Phase waves are used as tactic signals of aggregation in this model. Several aggregation clusters are formed initially, and target patterns appear around the localized aggregation clusters. Owing to the competition among target patterns, the number of the localized aggregation clusters decreases, and finally one dominant localized pattern survives. If the phase equation is replaced with the complex Ginzburg-Landau equation, several spiral patterns appear, and n is localized near the center of the spiral patterns. After the competition among spiral patterns, one dominant spiral survives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sequencing of Local Therapy Affects the Pattern of Treatment Failure and Survival in Children With Atypical Teratoid Rhabdoid Tumors of the Central Nervous System

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

Pai Panandiker, Atmaram S., E-mail: atmaram.pai-panandiker@stjude.org; Merchant, Thomas E.; Beltran, Chris

Purpose: To assess the pattern of treatment failure associated with current therapeutic paradigms for childhood atypical teratoid rhabdoid tumors (AT/RT). Methods and Materials: Pediatric patients with AT/RT of the central nervous system treated at our institution between 1987 and 2007 were retrospectively evaluated. Overall survival (OS), progression-free survival, and cumulative incidence of local failure were correlated with age, sex, tumor location, extent of disease, and extent of surgical resection. Radiotherapy (RT) sequencing, chemotherapy, dose, timing, and volume administered after resection were also evaluated. Results: Thirty-one patients at a median age of 2.3 years at diagnosis (range, 0.45-16.87 years) were enrolledmore » into protocols that included risk- and age-stratified RT. Craniospinal irradiation with focal tumor bed boost (median dose, 54 Gy) was administered to 18 patients. Gross total resection was achieved in 16. Ten patients presented with metastases at diagnosis. RT was delayed more than 3 months in 20 patients and between 1 and 3 months in 4; 7 patients received immediate postoperative irradiation preceding high-dose alkylator-based chemotherapy. At a median follow-up of 48 months, the cumulative incidence of local treatment failure was 37.5% {+-} 9%; progression-free survival was 33.2% {+-} 10%; and OS was 53.5% {+-} 10%. Children receiving delayed RT ({>=}1 month postoperatively) were more likely to experience local failure (hazard ratio [HR] 1.23, p = 0.007); the development of distant metastases before RT increased the risk of progression (HR 3.49, p = 0.006); and any evidence of disease progressionbefore RT decreased OS (HR 20.78, p = 0.004). Disease progression occurred in 52% (11/21) of children with initially localized tumors who underwent gross total resection, and the progression rate increased proportionally with increasing delay from surgery to RT. Conclusions: Delayed RT is associated with a higher rate of local and metastatic disease progression in children with AT/RT. Current treatment regimens for pediatric patients with AT/RT are distinctly age stratified; novel protocols investigating RT volumes and sequencing are needed.« less

Isolation by environmental distance in mobile marine species: molecular ecology of franciscana dolphins at their southern range.

PubMed

Mendez, Martin; Rosenbaum, Howard C; Subramaniam, Ajit; Yackulic, Charles; Bordino, Pablo

2010-06-01

The assessment of population structure is a valuable tool for studying the ecology of endangered species and drafting conservation strategies. As we enhance our understanding about the structuring of natural populations, it becomes important that we also understand the processes behind these patterns. However, there are few rigorous assessments of the influence of environmental factors on genetic patterns in mobile marine species. Given their dispersal capabilities and localized habitat preferences, coastal cetaceans are adequate study species for evaluating environmental effects on marine population structure. The franciscana dolphin, a rare coastal cetacean endemic to the Western South Atlantic, was studied to examine these issues. We analysed genetic data from the mitochondrial DNA and 12 microsatellite markers for 275 franciscana samples utilizing frequency-based, maximum-likelihood and Bayesian algorithms to assess population structure and migration patterns. This information was combined with 10 years of remote sensing environmental data (chlorophyll concentration, water turbidity and surface temperature). Our analyses show the occurrence of genetically isolated populations within Argentina, in areas that are environmentally distinct. Combined evidence of genetic and environmental structure suggests that isolation by distance and a process here termed isolation by environmental distance can explain the observed correlations. Our approach elucidated important ecological and conservation aspects of franciscana dolphins, and has the potential to increase our understanding of ecological processes influencing genetic patterns in other marine species.

Synoptic evolution of Atmospheric River landfalls in Northern California and the pre-conditioning of their characteristics by the climate state

NASA Astrophysics Data System (ADS)

Gershunov, A.; Guirguis, K.; Shulgina, T.; Clemesha, R.; Ralph, M.

2017-12-01

Atmospheric Rivers (ARs) contribute the lion's share of water resources for California, but can also cause flooding and draw heavily on emergency resources of state and local governments. Comprehensive probabilistic tools relating landfalling ARs to pre-existing weather/climate conditions could be useful for subseasonal forecasting, emergency preparedness and water resource management. We examine ARs targeting the Northern California coast using long-term observations of synoptic-scale circulation, high-resolution precipitation, and a seven-decade-long catalog of AR landfalls to quantify distinct orientations of landfalling ARs. Using a probabilistic approach to relate these historic events to precursor weather patterns, we identify synoptic circulation patterns that precede AR landfalls at various lead times in the range of 0-30 days. Examination of the evolution of these precursor patterns reveals subtle but important differences in the atmospheric states that lead to AR landfalls versus those that don't. Synoptic precursors can also differentiate between orientations of ARs at landfall, which produce rather different precipitation patterns over the region's complex topography. Moreover, low-frequency climate forcing appears to modulate the likelihood of AR landfalls, as well as their preferred orientations. These results provide a link between seasonal and subseasonal timescales and suggest a new approach toward extended-range prediction of land-falling atmospheric rivers and their related precipitation.

A Systematic Review of Global Drivers of Ant Elevational Diversity

PubMed Central

Szewczyk, Tim; McCain, Christy M.

2016-01-01

Ant diversity shows a variety of patterns across elevational gradients, though the patterns and drivers have not been evaluated comprehensively. In this systematic review and reanalysis, we use published data on ant elevational diversity to detail the observed patterns and to test the predictions and interactions of four major diversity hypotheses: thermal energy, the mid-domain effect, area, and the elevational climate model. Of sixty-seven published datasets from the literature, only those with standardized, comprehensive sampling were used. Datasets included both local and regional ant diversity and spanned 80° in latitude across six biogeographical provinces. We used a combination of simulations, linear regressions, and non-parametric statistics to test multiple quantitative predictions of each hypothesis. We used an environmentally and geometrically constrained model as well as multiple regression to test their interactions. Ant diversity showed three distinct patterns across elevations: most common were hump-shaped mid-elevation peaks in diversity, followed by low-elevation plateaus and monotonic decreases in the number of ant species. The elevational climate model, which proposes that temperature and precipitation jointly drive diversity, and area were partially supported as independent drivers. Thermal energy and the mid-domain effect were not supported as primary drivers of ant diversity globally. The interaction models supported the influence of multiple drivers, though not a consistent set. In contrast to many vertebrate taxa, global ant elevational diversity patterns appear more complex, with the best environmental model contingent on precipitation levels. Differences in ecology and natural history among taxa may be crucial to the processes influencing broad-scale diversity patterns. PMID:27175999

Root Water Uptake and Soil Moisture Pattern Dynamics - Capturing Connections, Controls and Causalities

NASA Astrophysics Data System (ADS)

Blume, T.; Heidbuechel, I.; Hassler, S. K.; Simard, S.; Guntner, A.; Stewart, R. D.; Weiler, M.

2015-12-01

We hypothesize that there is a shift in controls on landscape scale soil moisture patterns when plants become active during the growing season. Especially during the summer soil moisture patterns are not only controlled by soils, topography and related abiotic site characteristics but also by root water uptake. Root water uptake influences soil moisture patterns both in the lateral and vertical direction. Plant water uptake from different soil depths is estimated based on diurnal fluctuations in soil moisture content and was investigated with a unique setup of 46 field sites in Luxemburg and 15 field sites in Germany. These sites cover a range of geologies, soils, topographic positions and types of vegetation. Vegetation types include pasture, pine forest (young and old) and different deciduous forest stands. Available data at all sites includes information at high temporal resolution from 3-5 soil moisture and soil temperature profiles, matrix potential, piezometers and sapflow sensors as well as standard climate data. At sites with access to a stream, discharge or water level is also recorded. The analysis of soil moisture patterns over time indicates a shift in regime depending on season. Depth profiles of root water uptake show strong differences between different forest stands, with maximum depths ranging between 50 and 200 cm. Temporal dynamics of signal strength within the profile furthermore suggest a locally shifting spatial distribution of root water uptake depending on water availability. We will investigate temporal thresholds (under which conditions spatial patterns of root water uptake become most distinct) as well as landscape controls on soil moisture and root water uptake dynamics.

234U/238U evidence for local recharge and patterns of groundwater flow in the vicinity of Yucca Mountain, Nevada, USA

USGS Publications Warehouse

Paces, J.B.; Ludwig, K. R.; Peterman, Z.E.; Neymark, L.A.

2002-01-01

Uranium concentrations and 234U/238U ratios in saturated-zone and perched ground water were used to investigate hydrologic flow and downgradient dilution and dispersion in the vicinity of Yucca Mountain, a potential high-level radioactive waste disposal site. The U data were obtained by thermal ionization mass spectrometry on more than 280 samples from the Death Valley regional flow system. Large variations in both U concentrations (commonly 0.6-10 ??g 1-1) and 234U/238U activity ratios (commonly 1.5-6) are present on both local and regional scales; however, ground water with 234U/238U activity ratios from 7 up to 8.06 is restricted largely to samples from Yucca Mountain. Data from ground water in the Tertiary volcanic and Quaternary alluvial aquifers at and adjacent to Yucca Mountain plot in 3 distinct fields of reciprocal U concentration versus 234U/238U activity ratio correlated to different geographic areas. Ground water to the west of Yucca Mountain has large U concentrations and moderate 234U/238U whereas ground water to the east in the Fortymile flow system has similar 234U/238U, but distinctly smaller U concentrations. Ground water beneath the central part of Yucca Mountain has intermediate U concentrations but distinctive 234U/238U activity ratios of about 7-8. Perched water from the lower part of the unsaturated zone at Yucca Mountain has similarly large values of 234U/238U. These U data imply that the Tertiary volcanic aquifer beneath the central part of Yucca Mountain is isolated from north-south regional flow. The similarity of 234U/238U in both saturated- and unsaturated-zone ground water at Yucca Mountain further indicates that saturated-zone ground water beneath Yucca Mountain is dominated by local recharge rather than regional flow. The distinctive 234U/238U signatures also provide a natural tracer of downgradient flow. Elevated 234U/238U in ground water from two water-supply wells east of Yucca Mountain are interpreted as the result of induced flow from 40 a of ground-water withdrawal. Elevated 234U/238U in a borehole south of Yucca Mountain is interpreted as evidence that natural downgradient flow is more likely to follow southerly paths in the structurally anisotropic Tertiary volcanic aquifer where it becomes diluted by regional flow in the Fortymile system.

Generalization of the slip line field theory for temperature sensitive visco-plastic materials

NASA Astrophysics Data System (ADS)

Paesold, Martin; Peters, Max; Regenauer-Lieb, Klaus; Veveakis, Manolis; Bassom, Andrew

2015-04-01

Geological processes can be a combination of various effects such as heat production or consumption, chemical reactions or fluid flow. These individual effects are coupled to each other via feedbacks and the mathematical analysis becomes challenging due to these interdependencies. Here, we concentrate solely on thermo-mechanical coupling and a main result of this work is that the coupling can depend on material parameters and boundary conditions and the coupling is more or less pronounced depending on theses parameters. The transitions from weak to strong coupling can be studied in the context of a bifurcation analysis. classically, Material instabilities in solids are approached as material bifurcations of a rate-independent, isothermal, elasto-plastic solid. However, previous research has shown that temperature and deformation rate are important factors and are fully coupled with the mechanical deformation. Early experiments in steel revealed a distinct pattern of localized heat dissipation and plastic deformation known as heat lines. Further, earth materials, soils, rocks and ceramics are known to be greatly influenced by temperature with strain localization being strongly affected by thermal loading. In this work, we provide a theoretical framework for the evolution of plastic deformation for such coupled systems, with a two-pronged approach to the prediction of localized failure. First, slip line field theory is employed to predict the geometry of the failure patterns and second, failure criteria are derived from an energy bifurcation analysis. The bifurcation analysis is concerned with the local energy balance of a material and compares the effects of heat diffusion terms and heat production terms where the heat production is due to mechanical processes. Commonly, the heat is produced locally along the slip lines and if the heat production outweighs diffusion the material is locally weakened which eventually leads to failure. The effect of diffusion and heat production is captured by a dimensionless quantity, the Gruntfest number, and only if the Gruntfest number is larger than a critical value localized failure occurs. This critical Gruntfest number depends on boundary conditions such as temperature or pressure and hence this critical value gives rise to localization criteria. We find that the results of this approach agree with earlier contributions to the theory of plasticity but gives the advantage of a unified framework which might prove useful in numerical schemes for visco-plasticity.

Successive Respiratory Syncytial Virus Epidemics in Local Populations Arise from Multiple Variant Introductions, Providing Insights into Virus Persistence

PubMed Central

Otieno, James R.; Ngama, Mwanajuma; Mwihuri, Alexander G.; Medley, Graham F.; Cane, Patricia A.; Nokes, D. James

2015-01-01

ABSTRACT Respiratory syncytial virus (RSV) is a global respiratory pathogen of humans, with infection occurring characteristically as recurrent seasonal epidemics. Unlike influenza viruses, little attention has been paid to the mechanism underlying worldwide spread and persistence of RSV and how this may be discerned through an improved understanding of the introduction and persistence of RSV in local communities. We analyzed 651 attachment (G) glycoprotein nucleotide sequences of RSV B collected over 11 epidemics (2002 to 2012) in Kilifi, Kenya, and contemporaneous data collected elsewhere in Kenya and 18 other countries worldwide (2002 to 2012). Based on phylogeny, genetic distance and clustering patterns, we set out pragmatic criteria to classify local viruses into distinct genotypes and variants, identifying those newly introduced and those locally persisting. Three genotypes were identified in the Kilifi data set: BA (n = 500), SAB1 (n = 148), and SAB4 (n = 3). Recurrent RSV epidemics in the local population were composed of numerous genetic variants, most of which have been newly introduced rather than persisting in the location from season to season. Global comparison revealed that (i) most Kilifi variants do not cluster closely with strains from outside Kenya, (ii) some Kilifi variants were closely related to those observed outside Kenya (mostly Western Europe), and (iii) many variants were circulating elsewhere but were never detected in Kilifi. These results are consistent with the hypothesis that year-to-year presence of RSV at the local level (i.e., Kilifi) is achieved primarily, but not exclusively, through introductions from a pool of variants that are geographically restricted (i.e., to Kenya or to the region) rather than global. IMPORTANCE The mechanism by which RSV persists and reinvades local populations is poorly understood. We investigated this by studying the temporal patterns of RSV variants in a rural setting in tropical Africa and comparing these variants with contemporaneous variants circulating in other countries. We found that periodic seasonal RSV transmission at the local level appears to require regular new introductions of variants. However, importantly, the evidence suggests that the source of new variants is mostly geographically restricted, and we hypothesize that year-to-year RSV persistence is at the country level rather than the global level. This has implications for control. PMID:26355091

Folliculotropic T-cell infiltrates associated with B-cell chronic lymphocytic leukaemia or MALT lymphoma may reveal either true mycosis fungoides or pseudolymphomatous reaction: seven cases and review of the literature.

PubMed

Ingen-Housz-Oro, S; Franck, N; Beneton, N; Fauconneau, A; Do-Pham, G; Carlotti, A; Petit, T; Liolios, I; Bara, C; Carpentier, H; Storelli, D; Prophette, B; Garderet, L; Haioun, C; Petit, E; Delfau-Larue, M-H; Vergier, B; Chosidow, O; Beylot-Barry, M; Ortonne, N

2015-01-01

Mycosis fungoides (MF) and pseudo-MF (or MF simulant) can be associated with B-cell malignancies, but distinction between a true neoplasm and a reactive process may be difficult. To report seven patients with B-cell malignancy and folliculotropic MF or pseudo-MF and emphasize on criteria allowing distinction between the two conditions. We retrospectively and prospectively included seven patients with B-cell malignancy who presented skin lesions histologically consisting in a folliculotropic T-cell infiltrate and reviewed the literature on the topic. Four men and three women had a chronic lymphocytic leukaemia (n = 6) or a MALT-type lymphoma (n = 1). Five patients had localized papules, and two had patches and plaques. Histological examination showed in all cases a diffuse dermal T-cell infiltrate with folliculotropic involvement and follicular mucinosis associated with clusters of the B-cell lymphoma, without significant expression of follicular helper T-cell markers. T-cell rearrangement studies showed a polyclonal pattern in the patients with papules and a monoclonal pattern in the cases of patches and plaques. Papular lesions had an indolent evolution, whereas patches and plaques persisted or worsened into transformed MF. Folliculotropic T-cell infiltrates associated with B-cell malignancies can be either a true folliculotropic MF or a pseudo-MF. The distinction between both conditions cannot rely only on the histopathological aspect, but needs both a clinical pathological correlation and the search for a dominant T-cell clone. Whether the neoplastic T and B cells derive from a common ancestor or the T-cell proliferation is promoted by the underlying B-cell lymphoma remains unsolved, but interaction between B and T cell in the skin does not appear to be dependent on a TFH differentiation of the T-cell infiltrate. © 2014 European Academy of Dermatology and Venereology.

The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

PubMed Central

Luiz, Amom Mendes; Sawaya, Ricardo J.

2018-01-01

Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575

Discursive Hierarchical Patterning in Economics Cases

ERIC Educational Resources Information Center

Lung, Jane

2011-01-01

This paper attempts to apply Lung's (2008) model of the discursive hierarchical patterning of cases to a closer and more specific study of Economics cases and proposes a model of the distinct discursive hierarchical patterning of the same. It examines a corpus of 150 Economics cases with a view to uncovering the patterns of discourse construction.…

Distinctive ribonucleic acid patterns of human rotavirus subgroups 1 and 2.

PubMed Central

Kalica, A R; Greenberg, H B; Espejo, R T; Flores, J; Wyatt, R G; Kapikian, A Z; Chanock, R M

1981-01-01

The ribonucleic acid migration patterns of 7 subgroup 1 and 16 subgroup 2 human rotaviruses recovered from four geographic areas were compared. The subgroup 1 ribonucleic acid patterns had strikingly slower-moving segments 10 and 11, suggesting a correlation between the ribonucleic acid pattern and the subgroup specificity. Images PMID:6270002

Neighborhood binary speckle pattern for deformation measurements insensitive to local illumination variation by digital image correlation.

PubMed

Zhao, Jian; Yang, Ping; Zhao, Yue

2017-06-01

Speckle pattern-based characteristics of digital image correlation (DIC) restrict its application in engineering fields and nonlaboratory environments, since serious decorrelation effect occurs due to localized sudden illumination variation. A simple and efficient speckle pattern adjusting and optimizing approach presented in this paper is aimed at providing a novel speckle pattern robust enough to resist local illumination variation. The new speckle pattern, called neighborhood binary speckle pattern, derived from original speckle pattern, is obtained by means of thresholding the pixels of a neighborhood at its central pixel value and considering the result as a binary number. The efficiency of the proposed speckle pattern is evaluated in six experimental scenarios. Experiment results indicate that the DIC measurements based on neighborhood binary speckle pattern are able to provide reliable and accurate results, even though local brightness and contrast of the deformed images have been seriously changed. It is expected that the new speckle pattern will have more potential value in engineering applications.

The phenology pattern of rubber trees in plantation and its impacts on rubber tree structure, water and carbon cycles

NASA Astrophysics Data System (ADS)

Liu, W.; Giambelluca, T. W.; Mudd, R. G.

2012-12-01

Commercial rubber (Hevea Brasiliensis) is originally native to the Amazon rainforest and it has become one of the important commercial crops in Mainland Southeast Asia. Similarly to some trees species in Amazon but quite distinctly from other native forests in Southeast Asia, rubber tree sheds its leaves in the middle of dry season and flushes new leaves before the onset of the wet season. Moreover, the mountane mainland Southeast Asia is heavily influenced by the monsoon climate which has most the precipitation in the wet season while almost no rainfall in the dry season. It is believed that the phenology pattern of rubber interacted with local climate would not only regulate the seasonal rubber plantation structures but also further alter the local energy and water budget. However, it is still lack of solid understandings of how the phenology patterns in terms of the leaf area index (LAI) changes of the rubber tree response to environmental drivers. The study tries to shed lights on the issue from analyses of a various types of in-situ field data combined with 3 years' tower flux measurements collected within the rubber plantations. It concludes that: 1) Both the monthly tree height increment and the monthly biomass accumulation are highly correlated with the LAI changes, which have the low rate of changes in the dry season versus the relative high rate of changes in the wet season; 2) the daily evapotranspiration (ET) of the rubber tree is very sensitive to the daily LAI changes in the dry season (R2 > 0.9); 3) the LAI changes, especially the leaf drops, are majorly determined by the accumulated precipitation in the past three months.

Brain Oscillatory Correlates of Altered Executive Functioning in Positive and Negative Symptomatic Schizophrenia Patients and Healthy Controls.

PubMed

Berger, Barbara; Minarik, Tamas; Griesmayr, Birgit; Stelzig-Schoeler, Renate; Aichhorn, Wolfgang; Sauseng, Paul

2016-01-01

Working Memory and executive functioning deficits are core characteristics of patients suffering from schizophrenia. Electrophysiological research indicates that altered patterns of neural oscillatory mechanisms underpinning executive functioning are associated with the psychiatric disorder. Such brain oscillatory changes have been found in local amplitude differences at gamma and theta frequencies in task-specific cortical areas. Moreover, interregional interactions are also disrupted as signified by decreased phase coherence of fronto-posterior theta activity in schizophrenia patients. However, schizophrenia is not a one-dimensional psychiatric disorder but has various forms and expressions. A common distinction is between positive and negative symptomatology but most patients have both negative and positive symptoms to some extent. Here, we examined three groups-healthy controls, predominantly negative, and predominantly positive symptomatic schizophrenia patients-when performing a working memory task with increasing cognitive demand and increasing need for executive control. We analyzed brain oscillatory activity in the three groups separately and investigated how predominant symptomatology might explain differences in brain oscillatory patterns. Our results indicate that differences in task specific fronto-posterior network activity (i.e., executive control network) expressed by interregional phase synchronization are able to account for working memory dysfunctions between groups. Local changes in the theta and gamma frequency range also show differences between patients and healthy controls, and more importantly, between the two patient groups. We conclude that differences in oscillatory brain activation patterns related to executive processing can be an indicator for positive and negative symptomatology in schizophrenia. Furthermore, changes in cognitive and especially executive functioning in patients are expressed by alterations in a task-specific fronto-posterior connectivity even in the absence of behavioral impairment.

Relation of Total and Cardiovascular Death Rates to Climate System, Temperature, Barometric Pressure, and Respiratory Infection.

PubMed

Schwartz, Bryan G; Qualls, Clifford; Kloner, Robert A; Laskey, Warren K

2015-10-15

A distinct seasonal pattern in total and cardiovascular death rates has been reported. The factors contributing to this pattern have not been fully explored. Seven locations (average total population 71,354,000) were selected where data were available including relatively warm, cold, and moderate temperatures. Over the period 2004 to 2009, there were 2,526,123 all-cause deaths, 838,264 circulatory deaths, 255,273 coronary heart disease deaths, and 135,801 ST-elevation myocardial infarction (STEMI) deaths. We used time series and multivariate regression modeling to explore the association between death rates and climatic factors (temperature, dew point, precipitation, barometric pressure), influenza levels, air pollution levels, hours of daylight, and day of week. Average seasonal patterns for all-cause and cardiovascular deaths were very similar across the 7 locations despite differences in climate. After adjusting for multiple covariates and potential confounders, there was a 0.49% increase in all-cause death rate for every 1°C decrease. In general, all-cause, circulatory, coronary heart disease and STEMI death rates increased linearly with decreasing temperatures. The temperature effect varied by location, including temperature's linear slope, cubic fit, positional shift on the temperature axis, and the presence of circulatory death increases in locally hot temperatures. The variable effect of temperature by location suggests that people acclimatize to local temperature cycles. All-cause and circulatory death rates also demonstrated sizable associations with influenza levels, dew point temperature, and barometric pressure. A greater understanding of how climate, temperature, and barometric pressure influence cardiovascular responses would enhance our understanding of circulatory and STEMI deaths. Copyright © 2015 Elsevier Inc. All rights reserved.

Temporal variability (1997-2015) of trophic fish guilds and its relationships with El Niño events in a subtropical estuary

NASA Astrophysics Data System (ADS)

Possamai, Bianca; Vieira, João P.; Grimm, Alice M.; Garcia, Alexandre M.

2018-03-01

Global climatic phenomena like El Niño events are known to alter hydrological cycles and local abiotic conditions leading to changes in structure and dynamics of terrestrial and aquatic biological communities worldwide. Based on a long-term (19 years) standardized sampling of shallow water estuarine fishes, this study investigated the temporal variability in composition and dominance patterns of trophic guilds in a subtropical estuary (Patos Lagoon estuary, Southern Brazil) and their relationship with local and regional driving forces associated with moderate (2002-2003 and 2009-2010) and very strong (1997-1998 and 2015-2016) El Niño events. Fish species were classified into eight trophic guilds (DTV detritivore, HVP herbivore-phytoplankton, HVM macroalgae herbivore, ISV insectivore, OMN omnivore, PSV piscivore, ZBV zoobenthivore and ZPL zooplanktivore) and their abundances were correlated with environmental factors. Canonical correspondence analysis revealed that less dominant (those comprising < 10% of total abundance) trophic guilds, such as HVP, HVM, ISV, PSV, increased their relative abundance in the estuary during higher rainfall and lower salinity conditions associated with moderate and very strong El Niño events. An opposite pattern was observed for the dominant trophic fish guilds like OMN and, at lesser extent, DTV and ZPL, which had greater association with higher values of salinity and water transparency occurring mostly during non-El Niño conditions. In contrast, ZBV's abundance was not correlated with contrasting environmental conditions, but rather, had higher association with samples characterized by intermediate environmental values. Overall, these findings show that moderate and very strong El Niño events did not substantially disrupt the dominance patterns among trophic fish guilds in the estuary. Rather, they increased trophic estuarine diversity by flushing freshwater fishes with distinct feeding habits into the estuary.

Immunohistochemistry Analysis of CD44, EGFR, and p16 in Oral Cavity and Oropharyngeal Squamous Cell Carcinoma.

PubMed

Cohen, Erin R; Reis, Isildinha M; Gomez, Carmen; Pereira, Lutecia; Freiser, Monika E; Hoosien, Gia; Franzmann, Elizabeth J

2017-08-01

Objectives We analyze the relationship between CD44, epidermal growth factor receptor (EGFR), and p16 expression in oral cavity and oropharyngeal cancers in a diverse population. We also describe whether particular patterns of staining are associated with progression-free survival and overall survival. Study Design Prospective study, single-blind to pathologist and laboratory technologist. Setting Hospital based. Subjects and Methods Immunohistochemistry, comprising gross staining and cellular expression, was performed and interpreted in a blinded fashion on 24 lip/oral cavity and 40 oropharyngeal cancer specimens collected between 2007 and 2012 from participants of a larger study. Information on overall survival and progression-free survival was obtained from medical records. Results Nineteen cases were clinically p16 positive, 16 of which were oropharyngeal. Oral cavity lesions were more likely to exhibit strong CD44 membrane staining ( P = .0002). Strong CD44 membrane and strong EGFR membrane and/or cytoplasmic staining were more common in p16-negative cancers ( P = .006). Peripheral/mixed gross p16 staining pattern was associated with worse survival than the universal staining on univariate and multivariate analyses ( P = .006, P = .030). This held true when combining gross and cellular localization for p16. For CD44, universal gross staining demonstrated poorer overall survival compared with the peripheral/mixed group ( P = .039). CD44 peripheral/mixed group alone and when combined with universal p16 demonstrated the best survival on multivariate analysis ( P = .010). Conclusion In a diverse population, systematic analysis applying p16, CD44, and EGFR gross staining and cellular localization on immunohistochemistry demonstrates distinct patterns that may have prognostic potential exceeding current methods. Larger studies are warranted to investigate these findings further.

Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

PubMed

Sedova, Ada; Banavali, Nilesh K

2017-03-14

Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.

Changing exhumation patterns during Cenozoic growth and glaciation of the Alaska Range: Insights from detrital thermochronology and geochronology

USGS Publications Warehouse

Lease, Richard O.; Haeussler, Peter J.; O'Sullivan, Paul

2016-01-01

Cenozoic growth of the Alaska Range created the highest topography in North America, but the space-time pattern and drivers of exhumation are poorly constrained. We analyzed U/Pb and fission-track double dates of detrital zircon and apatite grains from 12 catchments that span a 450 km length of the Alaska Range to illuminate the timing and extent of exhumation during different periods. U/Pb ages indicate a dominant Late Cretaceous to Oligocene plutonic provenance for the detrital grains, with only a small percentage of grains recycled from the Mesozoic and Paleozoic sedimentary cover. Fission-track ages record exhumation during Alaska Range growth and incision and reveal three distinctive patterns. First, initial Oligocene exhumation was focused in the central Alaska Range at ~30 Ma and expanded outward along the entire length of the range until 18 Ma. Oligocene exhumation, coeval with initial Yakutat microplate collision >600 km to the southeast, suggests a far-field response to collision that was localized by the Denali Fault within a weak Mesozoic suture zone. Second, the variable timing of middle to late Miocene exhumation suggests independently evolving histories influenced by local structures. Time-transgressive cooling ages suggest successive rock uplift and erosion of Mounts Foraker (12 Ma) through Denali (6 Ma) as crust was advected through a restraining bend in the Denali Fault and indicate a long-term slip rate ~4 mm/yr. Third, Pliocene exhumation is synchronous (3.7–2.7 Ma) along the length of the Alaska Range but only occurs in high-relief, glacier-covered catchments. Pliocene exhumation may record an acceleration in glacial incision that was coincident with the onset of Northern Hemisphere glaciation.

Distinct subtypes of behavioral-variant frontotemporal dementia based on patterns of network degeneration

PubMed Central

Ranasinghe, Kamalini G; Rankin, Katherine P; Pressman, Peter S; Perry, David C; Lobach, Iryna V; Seeley, William W; Coppola, Giovanni; Karydas, Anna M; Grinberg, Lea T; Shany-Ur, Tal; Lee, Suzee E; Rabinovici, Gil D; Rosen, Howard J; Gorno-Tempini, Maria Luisa; Boxer, Adam L; Miller, Zachary A; Chiong, Winston; DeMay, Mary; Kramer, Joel H; Possin, Katherine L; Sturm, Virginia E; Bettcher, Brianne M; Neylan, Michael; Zackey, Diana D; Nguyen, Lauren A; Ketelle, Robin; Block, Nikolas; Wu, Teresa Q; Dallich, Alison; Russek, Natanya; Caplan, Alyssa; Geschwind, Daniel H; Vossel, Keith A; Miller, Bruce L

2016-01-01

Importance Clearer delineation of the phenotypic heterogeneity within behavioral variant frontotemporal dementia (bvFTD) will help uncover underlying biological mechanisms, and will improve clinicians’ ability to predict disease course and design targeted management strategies. Objective To identify subtypes of bvFTD syndrome based on distinctive patterns of atrophy defined by selective vulnerability of specific functional networks targeted in bvFTD, using statistical classification approaches. Design, Setting and Participants In this retrospective observational study, 104 patients meeting the Frontotemporal Dementia Consortium consensus criteria for bvFTD were evaluated at the Memory and Aging Center of Department of Neurology at University of California, San Francisco. Patients underwent a multidisciplinary clinical evaluation, including clinical demographics, genetic testing, symptom evaluation, neurological exam, neuropsychological bedside testing, and socioemotional assessments. Ninety patients underwent structural Magnetic Resonance Imaging at their earliest evaluation at the memory clinic. From each patients’ structural imaging, the mean volumes of 18 regions of interest (ROI) comprising the functional networks specifically vulnerable in bvFTD, including the ‘salience network’ (SN), with key nodes in the frontoinsula and pregenual anterior cingulate, and the ‘semantic appraisal network’ (SAN) anchored in the anterior temporal lobe and subgenual cingulate, were estimated. Principal component and cluster analyses of ROI volumes were used to identify patient clusters with anatomically distinct atrophy patterns. Main Outcome Measures We evaluated brain morphology and other clinical features including presenting symptoms, neurologic exam signs, neuropsychological performance, rate of dementia progression, and socioemotional function in each patient cluster. Results We identified four subgroups of bvFTD patients with distinct anatomic patterns of network degeneration, including two separate salience network–predominant subgroups: frontal/temporal (SN-FT), and frontal (SN-F), and a semantic appraisal network–predominant group (SAN), and a subcortical–predominant group. Subgroups demonstrated distinct patterns of cognitive, socioemotional, and motor symptoms, as well as genetic compositions and estimated rates of disease progression. Conclusions Divergent patterns of vulnerability in specific functional network components make an important contribution to clinical heterogeneity of bvFTD. The data-driven anatomical classification identifies biologically meaningful phenotypes and provides a replicable approach to disambiguate the bvFTD syndrome. PMID:27429218

Walking-age analyzer for healthcare applications.

PubMed

Jin, Bo; Thu, Tran Hoai; Baek, Eunhye; Sakong, SungHwan; Xiao, Jin; Mondal, Tapas; Deen, M Jamal

2014-05-01

This paper describes a walking-age pattern analysis and identification system using a 3-D accelerometer and a gyroscope. First, a walking pattern database from 79 volunteers of ages ranging from 10 to 83 years is constructed. Second, using feature extraction and clustering, three distinct walking-age groups, children of ages 10 and below, adults in 20-60s, and elders in 70s and 80s, were identified. For this study, low-pass filtering, empirical mode decomposition, and K-means were used to process and analyze the experimental results. Analysis shows that volunteers' walking-ages can be categorized into distinct groups based on simple walking pattern signals. This grouping can then be used to detect persons with walking patterns outside their age groups. If the walking pattern puts an individual in a higher "walking age" grouping, then this could be an indicator of potential health/walking problems, such as weak joints, poor musculoskeletal support system or a tendency to fall.

Role of endothelial permeability hotspots and endothelial mitosis in determining age-related patterns of macromolecule uptake by the rabbit aortic wall near branch points.

PubMed

Chooi, K Yean; Comerford, Andrew; Cremers, Stephanie J; Weinberg, Peter D

2016-07-01

Transport of macromolecules between plasma and the arterial wall plays a key role in atherogenesis. Scattered hotspots of elevated endothelial permeability to macromolecules occur in the aorta; a fraction of them are associated with dividing cells. Hotspots occur particularly frequently downstream of branch points, where lesions develop in young rabbits and children. However, the pattern of lesions varies with age, and can be explained by similar variation in the pattern of macromolecule uptake. We investigated whether patterns of hotspots and mitosis also change with age. Evans' Blue dye-labeled albumin was injected intravenously into immature or mature rabbits and its subsequent distribution in the aortic wall around intercostal branch ostia examined by confocal microscopy and automated image analysis. Mitosis was detected by immunofluorescence after adding 5-bromo-2-deoxiuridine to drinking water. Hotspots were most frequent downstream of branches in immature rabbits, but a novel distribution was observed in mature rabbits. Neither pattern was explained by mitosis. Hotspot uptake correlated spatially with the much greater non-hotspot uptake (p < 0.05), and the same pattern was seen when only the largest hotspots were considered. The pattern of hotspots changes with age. The data are consistent with there being a continuum of local permeabilities rather than two distinct mechanisms. The distribution of the dye, which binds to elastin and collagen, was similar to that of non-binding tracers and to lesions apart from a paucity at the lateral margins of branches that can be explained by lower levels of fibrous proteins in those regions. Copyright © 2016. Published by Elsevier Ireland Ltd.

Compassion: an evolutionary analysis and empirical review.

PubMed

Goetz, Jennifer L; Keltner, Dacher; Simon-Thomas, Emiliana

2010-05-01

What is compassion? And how did it evolve? In this review, we integrate 3 evolutionary arguments that converge on the hypothesis that compassion evolved as a distinct affective experience whose primary function is to facilitate cooperation and protection of the weak and those who suffer. Our empirical review reveals compassion to have distinct appraisal processes attuned to undeserved suffering; distinct signaling behavior related to caregiving patterns of touch, posture, and vocalization; and a phenomenological experience and physiological response that orients the individual to social approach. This response profile of compassion differs from those of distress, sadness, and love, suggesting that compassion is indeed a distinct emotion. We conclude by considering how compassion shapes moral judgment and action, how it varies across different cultures, and how it may engage specific patterns of neural activation, as well as emerging directions of research. (c) 2010 APA, all rights reserved.

Geochemistry and structure of the Hawley Formation: Northwestern Massachusetts

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

Kim, J.; Jacobi, R.

1993-03-01

The Hawley Formation in northwestern Massachusetts is composed of mafic and felsic, (trondhjemitic) igneous units and black sulfidic schists and quartzites. The dominant lithology is a thinly foliated hbd-plag.-chi-qtz.-Fe carbonate schist with or without hornblende fasicules. Locally, this schist has alternating folia of chl/hbd and plag. and probably has a volcaniclastic protolith. Distinct pillows and tuffs are observed locally. In general, these schists have flat REE patterns at 10X chondrite and plot as IABs on discrimination diagrams. In the eastern part of the Hawley, some amphibolites show concave upward REE patterns, plot in the IAT or boninite field on discriminationmore » diagrams, and appear to have boninitic affinities. The felsic lithologies are trondhjemitic and are intrusive into the IAT/boninite amphibolites. The intrusive nature is based on the presence of mafic xenoliths and intruded rafts of country rock in the trondhjemite as well as the occurrence of thin tabular trondhjemite bodies in sharp contact with the surrounding amphibolite. The trondhjemite varies from coarse-grained weakly foliated qtz-plag.-biotite gneiss with probable relict igneous zoned plagioclases to finer-grained well foliated qtz-plag.-garnet-hbd gneiss. REE patterns for the trondhjemites are weakly U-shaped with moderate to pronounced negative Eu anomalies. The trondhjemites, surrounding amphibolites, and black sulfidic schists and quartzites of the eastern part of the Hawley are intruded by massive, granular, medium grained, plagioclase phenocryst amphibolites with chilled margins. These intrusive sills predate or are coeval with the dominant foliation in the Hawley. Both sills and country rock contain a contact-parallel foliation as well as a later foliation at a low angle to the earlier foliation. The sill amphibolites are high TiO2 high Zr varieties that plot as MORBs to WPBs on discrimination diagrams and exhibit slightly LREE enriched MORB-like to T-MORB REE patterns.« less

Influence of Ethnolinguistic Diversity on the Sorghum Genetic Patterns in Subsistence Farming Systems in Eastern Kenya

PubMed Central

Labeyrie, Vanesse; Deu, Monique; Barnaud, Adeline; Calatayud, Caroline; Buiron, Marylène; Wambugu, Peterson; Manel, Stéphanie; Glaszmann, Jean-Christophe; Leclerc, Christian

2014-01-01

Understanding the effects of actions undertaken by human societies on crop evolution processes is a major challenge for the conservation of genetic resources. This study investigated the mechanisms whereby social boundaries associated with patterns of ethnolinguistic diversity have influenced the on-farm distribution of sorghum diversity. Social boundaries limit the diffusion of planting material, practices and knowledge, thus shaping crop diversity in situ. To assess the effect of social boundaries, this study was conducted in the contact zone between the Chuka, Mbeere and Tharaka ethnolinguistic groups in eastern Kenya. Sorghum varieties were inventoried and samples collected in 130 households. In all, 297 individual plants derived from seeds collected under sixteen variety names were characterized using a set of 18 SSR molecular markers and 15 morphological descriptors. The genetic structure was investigated using both a Bayesian assignment method and distance-based clustering. Principal Coordinates Analysis was used to describe the structure of the morphological diversity of the panicles. The distribution of the varieties and the main genetic clusters across ethnolinguistic groups was described using a non-parametric MANOVA and pairwise Fisher tests. The spatial distribution of landrace names and the overall genetic spatial patterns were significantly correlated with ethnolinguistic partition. However, the genetic structure inferred from molecular makers did not discriminate the short-cycle landraces despite their morphological distinctness. The cases of two improved varieties highlighted possible fates of improved materials. The most recent one was often given the name of local landraces. The second one, that was introduced a dozen years ago, displays traces of admixture with local landraces with differential intensity among ethnic groups. The patterns of congruence or discordance between the nomenclature of farmers’ varieties and the structure of both genetic and morphological diversity highlight the effects of the social organization of communities on the diffusion of seed, practices, and variety nomenclature. PMID:24637745

Distinct Dendritic Arborization and In Vivo Firing Patterns of Parvalbumin-Expressing Basket Cells in the Hippocampal Area CA3

PubMed Central

Tukker, John J.; Lasztóczi, Bálint; Katona, Linda; Roberts, J. David B.; Pissadaki, Eleftheria K.; Dalezios, Yannis; Márton, László; Zhang, Limei; Klausberger, Thomas; Somogyi, Peter

2015-01-01

Hippocampal CA3 area generates temporally structured network activity such as sharp waves and gamma and theta oscillations. Parvalbumin-expressing basket cells, making GABAergic synapses onto cell bodies and proximal dendrites of pyramidal cells, control pyramidal cell activity and participate in network oscillations in slice preparations, but their roles in vivo remain to be tested. We have recorded the spike timing of parvalbumin-expressing basket cells in areas CA2/3 of anesthetized rats in relation to CA3 putative pyramidal cell firing and activity locally and in area CA1. During theta oscillations, CA2/3 basket cells fired on the same phase as putative pyramidal cells, but, surprisingly, significantly later than downstream CA1 basket cells. This indicates a distinct modulation of CA3 and CA1 pyramidal cells by basket cells, which receive different inputs. We observed unexpectedly large dendritic arborization of CA2/3 basket cells in stratum lacunosum moleculare (33% of length, 29% surface, and 24% synaptic input from a total of ~35,000), different from the dendritic arborizations of CA1 basket cells. Area CA2/3 basket cells fired phase locked to both CA2/3 and CA1 gamma oscillations, and increased firing during CA1 sharp waves, thus supporting the role of CA3 networks in the generation of gamma oscillations and sharp waves. However, during ripples associated with sharp waves, firing of CA2/3 basket cells was phase locked only to local but not CA1 ripples, suggesting the independent generation of fast oscillations by basket cells in CA1 and CA2/3. The distinct spike timing of basket cells during oscillations in CA1 and CA2/3 suggests differences in synaptic inputs paralleled by differences in dendritic arborizations. PMID:23595740

A map of local adaptation in Arabidopsis thaliana.

PubMed

Fournier-Level, A; Korte, A; Cooper, M D; Nordborg, M; Schmitt, J; Wilczek, A M

2011-10-07

Local adaptation is critical for species persistence in the face of rapid environmental change, but its genetic basis is not well understood. Growing the model plant Arabidopsis thaliana in field experiments in four sites across the species' native range, we identified candidate loci for local adaptation from a genome-wide association study of lifetime fitness in geographically diverse accessions. Fitness-associated loci exhibited both geographic and climatic signatures of local adaptation. Relative to genomic controls, high-fitness alleles were generally distributed closer to the site where they increased fitness, occupying specific and distinct climate spaces. Independent loci with different molecular functions contributed most strongly to fitness variation in each site. Independent local adaptation by distinct genetic mechanisms may facilitate a flexible evolutionary response to changing environment across a species range.

Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow.

PubMed

Gryseels, S; Goüy de Bellocq, J; Makundi, R; Vanmechelen, K; Broeckhove, J; Mazoch, V; Šumbera, R; Zima, J; Leirs, H; Baird, S J E

2016-10-01

Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to humans and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180-km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city (Morogoro). We sampled M. natalensis across 10 localities and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the isolation-with-migration model implemented in IMa2, we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2N e M = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Different spatio-temporal electroencephalography features drive the successful decoding of binaural and monaural cues for sound localization.

PubMed

Bednar, Adam; Boland, Francis M; Lalor, Edmund C

2017-03-01

The human ability to localize sound is essential for monitoring our environment and helps us to analyse complex auditory scenes. Although the acoustic cues mediating sound localization have been established, it remains unknown how these cues are represented in human cortex. In particular, it is still a point of contention whether binaural and monaural cues are processed by the same or distinct cortical networks. In this study, participants listened to a sequence of auditory stimuli from different spatial locations while we recorded their neural activity using electroencephalography (EEG). The stimuli were presented over a loudspeaker array, which allowed us to deliver realistic, free-field stimuli in both the horizontal and vertical planes. Using a multivariate classification approach, we showed that it is possible to decode sound source location from scalp-recorded EEG. Robust and consistent decoding was shown for stimuli that provide binaural cues (i.e. Left vs. Right stimuli). Decoding location when only monaural cues were available (i.e. Front vs. Rear and elevational stimuli) was successful for a subset of subjects and showed less consistency. Notably, the spatio-temporal pattern of EEG features that facilitated decoding differed based on the availability of binaural and monaural cues. In particular, we identified neural processing of binaural cues at around 120 ms post-stimulus and found that monaural cues are processed later between 150 and 200 ms. Furthermore, different spatial activation patterns emerged for binaural and monaural cue processing. These spatio-temporal dissimilarities suggest the involvement of separate cortical mechanisms in monaural and binaural acoustic cue processing. © 2017 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Immunolocalization of chloride transporters to gill epithelia of euryhaline teleosts with opposite salinity-induced Na+/K+-ATPase responses.

PubMed

Tang, Cheng-Hao; Hwang, Lie-Yueh; Shen, I-Da; Chiu, Yu-Hui; Lee, Tsung-Han

2011-12-01

Opposite patterns of branchial Na(+)/K(+)-ATPase (NKA) responses were found in euryhaline milkfish (Chanos chanos) and pufferfish (Tetraodon nigroviridis) upon salinity challenge. Because the electrochemical gradient established by NKA is thought to be the driving force for transcellular Cl(-) transport in fish gills, the aim of this study was to explore whether the differential patterns of NKA responses found in milkfish and pufferfish would lead to distinct distribution of Cl(-) transporters in their gill epithelial cells indicating different Cl(-) transport mechanisms. In this study, immunolocalization of various Cl(-) transport proteins, including Na(+)/K(+)/2Cl(-) cotransporter (NKCC), cystic fibrosis transmembrane conductance regulator (CFTR), anion exchanger 1 (AE1), and chloride channel 3 (ClC-3), were double stained with NKA, the basolateral marker of branchial mitochondrion-rich cells (MRCs), to reveal the localization of these transporter proteins in gill MRC of FW- or SW-acclimated milkfish and pufferfish. Confocal microscopic observations showed that the localization of these transport proteins in the gill MRCs of the two studied species were similar. However, the number of gill NKA-immunoreactive (IR) cells in milkfish and pufferfish exhibited to vary with environmental salinities. An increase in the number of NKA-IR cells should lead to the elevation of NKA activity in FW milkfish and SW pufferfish. Taken together, the opposite branchial NKA responses observed in milkfish and pufferfish upon salinity challenge could be attributed to alterations in the number of NKA-IR cells. Furthermore, the localization of these Cl(-) transporters in gill MRCs of the two studied species was identical. It depicted the two studied euryhaline species possess the similar Cl(-) transport mechanisms in gills.

Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.

PubMed

Stegemann, Björn; Klebe, Gerhard

2012-02-01

Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Copyright © 2011 Wiley Periodicals, Inc.

Generalized avian dispersal syndrome contributes to Chinese tallow tree (Sapium sebiferum, Euphorbiaceae) invasiveness

USGS Publications Warehouse

Renne, I.J.; Barrow, W.C.; Johnson, Randall L.A.; Bridges, W.C.

2002-01-01

Plants possessing generalized dispersal syndromes are likely to be more invasive than those relying on specialist dispersal agents. To address this issue on a local and regional scale, avian seed dispersal of the invasive alien Chinese tallow tree (Sapium sebiferum (L.) Roxb.) was assessed in forests and spoil areas of South Carolina and along forest edges in Louisiana during the 1997-99 fruiting seasons. Tallow trees in these floristically distinct habitats had a few common and many casual visitors, and considerable species overlap among habitats was found. However, bird species differed in the importance of dispersing and dropping seeds among habitats. Important dispersal agents common to forests and spoil areas of South Carolina included Northern Flicker, American Robin and Redwinged Blackbird, whereas Red-bellied Woodpecker and European Starling were important in the former and latter habitat, respectively. In Louisiana, Red-bellied Woodpecker, American Robin, Northern Cardinal and Eastern Bluebird dispersed many seeds. Nearly all species foraging on seeds were winter residents. Estimated numbers of seeds dispersed and dropped were higher in spoil areas of South Carolina than in Louisiana because of higher numbers of individuals per visit, higher seed consumption and seed dropping rates, and longer foraging durations. Within South Carolina, more seeds were dispersed and dropped in spoil areas than in forests because of higher numbers of birds per visit. These findings show that among habitats, tallow tree attracts diverse but variable coteries of dispersal agents that are qualitatively similar in seed usage patterns. We suggest that its generalized dispersal syndrome contributes to effective seed dispersal by many bird species throughout its range. Effects of differential avian use among locales may include changes in local bird communities, and differing tallow tree demographics and invasion patterns.

Sequence data for two large-subunit rRNA genes from an Asian strain of Alexandrium catenella.

PubMed Central

Yeung, P K; Kong, K F; Wong, F T; Wong, J T

1996-01-01

PCR generated two distinct products from a toxic isolate of Alexandrium catenella, which had been taken from Dai Ya Bay (southern China), by using primers for large-subunit rRNA. This pattern is distinct from published data for North American Alexandrium species. Sequences of the two products suggest that the smaller was generated by a deletion event. Single-cell PCR generated the same pattern, confirming that the two products were not the results from different individuals. PMID:8900010

Proximate cues for a short-distance migratory species: An application of survival analysis

USGS Publications Warehouse

Meunier, J.; Song, R.; Lutz, R.S.; Andersen, D.E.; Doherty, K.E.; Bruggink, J.G.; Oppelt, E.

2008-01-01

Investigation of bird migration has often highlighted the importance of external factors in determining timing of migration However, little distinction has been made between short- and long-distance migrants and between local and flight birds (passage migrants) in describing migration chronology. In addition, measures of food abundance as a proximate factor influencing timing of migration are lacking in studies of migration chronology. To address the relationship between environmental variables and timing of migration we quantified the relative importance of proximate external factors on migration chronology of local American woodcock (Scolopax minor), a short distance migrant, using event-time analysis methods (survival analysis). We captured 1,094 woodcock local to our study sites in Michigan, Minnesota and Wisconsin (USA) during autumn 2002-2004 and documented 786 departure dates for these birds. Photoperiod appeared to provide an initial proximate cue for timing of departure. Moon phase was important in modifying timing of departure, which may serve as a navigational aid in piloting and possibly orientation. Local synoptic weather variables also contributed to timing of departure by changing the rate of departure from our study sites. We found no evidence that food availability influenced timing of woodcock departure. Our results suggest that woodcock use a conservative photoperiod-controlled strategy with proximate modifiers for timing of migration rather than relying on abundance of their primary food, earthworms. Managing harvest pressure on local birds by adjusting season lengths may be an effective management tool with consistent migration patterns from year to year based on photoperiod.

Fluid mechanics as a driver of tissue-scale mechanical signaling in organogenesis.

PubMed

Gilbert, Rachel M; Morgan, Joshua T; Marcin, Elizabeth S; Gleghorn, Jason P

2016-12-01

Organogenesis is the process during development by which cells self-assemble into complex, multi-scale tissues. Whereas significant focus and research effort has demonstrated the importance of solid mechanics in organogenesis, less attention has been given to the fluid forces that provide mechanical cues over tissue length scales. Fluid motion and pressure is capable of creating spatial gradients of forces acting on cells, thus eliciting distinct and localized signaling patterns essential for proper organ formation. Understanding the multi-scale nature of the mechanics is critically important to decipher how mechanical signals sculpt developing organs. This review outlines various mechanisms by which tissues generate, regulate, and sense fluid forces and highlights the impact of these forces and mechanisms in case studies of normal and pathological development.

A feature-based developmental model of the infant brain in structural MRI.

PubMed

Toews, Matthew; Wells, William M; Zöllei, Lilla

2012-01-01

In this paper, anatomical development is modeled as a collection of distinctive image patterns localized in space and time. A Bayesian posterior probability is defined over a random variable of subject age, conditioned on data in the form of scale-invariant image features. The model is automatically learned from a large set of images exhibiting significant variation, used to discover anatomical structure related to age and development, and fit to new images to predict age. The model is applied to a set of 230 infant structural MRIs of 92 subjects acquired at multiple sites over an age range of 8-590 days. Experiments demonstrate that the model can be used to identify age-related anatomical structure, and to predict the age of new subjects with an average error of 72 days.

Low upper limit to methane abundance on Mars.

PubMed

Webster, Christopher R; Mahaffy, Paul R; Atreya, Sushil K; Flesch, Gregory J; Farley, Kenneth A

2013-10-18

By analogy with Earth, methane in the Martian atmosphere is a potential signature of ongoing or past biological activity. During the past decade, Earth-based telescopic observations reported "plumes" of methane of tens of parts per billion by volume (ppbv), and those from Mars orbit showed localized patches, prompting speculation of sources from subsurface bacteria or nonbiological sources. From in situ measurements made with the Tunable Laser Spectrometer (TLS) on Curiosity using a distinctive spectral pattern specific to methane, we report no detection of atmospheric methane with a measured value of 0.18 ± 0.67 ppbv corresponding to an upper limit of only 1.3 ppbv (95% confidence level), which reduces the probability of current methanogenic microbial activity on Mars and limits the recent contribution from extraplanetary and geologic sources.

Migration and Tissue Tropism of Innate Lymphoid Cells

PubMed Central

Kim, Chang H.; Hashimoto-Hill, Seika; Kim, Myunghoo

2016-01-01

Innate lymphoid cell (ILCs) subsets differentially populate various barrier and non-barrier tissues, where they play important roles in tissue homeostasis and tissue-specific responses to pathogen attack. Recent findings have provided insight into the molecular mechanisms that guide ILC migration into peripheral tissues, revealing common features among different ILC subsets as well as important distinctions. Recent studies have also highlighted the impact of tissue-specific cues on ILC migration, and the importance of the local immunological milieu. We review these findings here and discuss how the migratory patterns and tissue tropism of different ILC subsets relate to the development and differentiation of these cells, and to ILC-mediated tissue-specific regulation of innate and adaptive immune responses. In this context we outline open questions and important areas of future research. PMID:26708278

Simulation of erosion by a particulate airflow through a ventilator

NASA Astrophysics Data System (ADS)

Ghenaiet, A.

2015-08-01

Particulate flows are a serious problem in air ventilation systems, leading to erosion of rotor blades and aerodynamic performance degradation. This paper presents the numerical results of sand particle trajectories and erosion patterns in an axial ventilator and the subsequent blade deterioration. The flow field was solved separately by using the code CFX- TASCflow. The Lagrangian approach for the solid particles tracking implemented in our inhouse code considers particle and eddy interaction, particle size distribution, particle rebounds and near walls effects. The assessment of erosion wear is based on the impact frequency and local values of erosion rate. Particle trajectories and erosion simulation revealed distinctive zones of impacts with high rates of erosion mainly on the blade pressure side, whereas the suction side is eroded around the leading edge.

Laboratory layered latte.

PubMed

Xue, Nan; Khodaparast, Sepideh; Zhu, Lailai; Nunes, Janine K; Kim, Hyoungsoo; Stone, Howard A

2017-12-12

Inducing thermal gradients in fluid systems with initial, well-defined density gradients results in the formation of distinct layered patterns, such as those observed in the ocean due to double-diffusive convection. In contrast, layered composite fluids are sometimes observed in confined systems of rather chaotic initial states, for example, lattes formed by pouring espresso into a glass of warm milk. Here, we report controlled experiments injecting a fluid into a miscible phase and show that, above a critical injection velocity, layering emerges over a time scale of minutes. We identify critical conditions to produce the layering, and relate the results quantitatively to double-diffusive convection. Based on this understanding, we show how to employ this single-step process to produce layered structures in soft materials, where the local elastic properties vary step-wise along the length of the material.

Correlated network of networks enhances robustness against catastrophic failures.

PubMed

Min, Byungjoon; Zheng, Muhua

2018-01-01

Networks in nature rarely function in isolation but instead interact with one another with a form of a network of networks (NoN). A network of networks with interdependency between distinct networks contains instability of abrupt collapse related to the global rule of activation. As a remedy of the collapse instability, here we investigate a model of correlated NoN. We find that the collapse instability can be removed when hubs provide the majority of interconnections and interconnections are convergent between hubs. Thus, our study identifies a stable structure of correlated NoN against catastrophic failures. Our result further suggests a plausible way to enhance network robustness by manipulating connection patterns, along with other methods such as controlling the state of node based on a local rule.

Correlated network of networks enhances robustness against catastrophic failures

PubMed Central

Zheng, Muhua

2018-01-01

Networks in nature rarely function in isolation but instead interact with one another with a form of a network of networks (NoN). A network of networks with interdependency between distinct networks contains instability of abrupt collapse related to the global rule of activation. As a remedy of the collapse instability, here we investigate a model of correlated NoN. We find that the collapse instability can be removed when hubs provide the majority of interconnections and interconnections are convergent between hubs. Thus, our study identifies a stable structure of correlated NoN against catastrophic failures. Our result further suggests a plausible way to enhance network robustness by manipulating connection patterns, along with other methods such as controlling the state of node based on a local rule. PMID:29668730

No vacancy: the political geography of immigration control in advanced industrial countries.

PubMed

Money, J

1997-01-01

This article presents a unique framework for analyzing the politics of immigration control in developed countries and reviews related political theories. The author describes distinctive patterns of immigration in selected OECD countries and standard explanations. The author argues that the costs and benefits of immigration are spatially unevenly distributed and explains how spatial concentrations affect costs and benefits, as well as how local conditions, population, and the business community create support for and opposition to immigration. Evidence from Great Britain is used to support the framework. Control of immigration is due to the power of local constituencies in creating and maintaining a national political coalition. Local constituency preferences are a systematic, but not exclusive, feature that underpin the politics of immigration control. Other factors may have periodic impacts. The case of Great Britain, during 1955-81, illustrates the importance of disaggregated analysis. Cross national analyses will reveal the variation in level of impact. Japan and Germany, with similar economic and political histories, indicate substantial differences in net demand for immigration. Conditions, such as high, rapidly increasing immigration proportions, access to social services, and higher unemployment, may lead to hostility and less community support for immigration. The theory is based on native-immigrant competition over scarce resources, variable business support depending upon the flexibility of local markets and potential for capital mobility, and the dynamics of party competition as influenced by underlying structural conditions.

Patterns of seasonal variation in lagoonal macrozoobenthic assemblages (Mellah lagoon, Algeria).

PubMed

Magni, Paolo; Draredja, Brahim; Melouah, Khalil; Como, Serena

2015-08-01

In coastal lagoons, many studies indicated that macrozoobenthic assemblages undergo marked temporal fluctuations as related to the strong environmental variability of these systems. However, most of these studies have not assessed the seasonal patterns of these fluctuations and none of them has investigated the consistency of this variation in different areas within the same lagoon system. In this study, we assessed patterns of variation at multiple temporal (date, season and year) scales in two different areas in the coastal lagoon of Mellah (northeast Algeria). These areas (hereafter Shore and Center) are representative of two different environments typically found in coastal lagoons. The Shore (water depth of about 1.5-2 m) is characterized by relatively higher hydrodynamics, sand to silty-sand sediments and the presence of vegetation (Ruppia maritima), the Center (water depth of about 3-3.5 m) is characterized by mud to sandy-mud, organic-enriched sediments due to fine particle accumulation. Results showed two distinct patterns of seasonal variation in Shore and Center assemblages for two consecutive years. In Shore, species richness (S), total abundance (N) and the abundance of several dominant taxa were highest in summer and/or autumn. This pattern can be related to the local environmental conditions maintaining relatively well oxidized conditions, while increasing food availability, and favoring the recruitment of species and individuals in summer/autumn. On the contrary in Center, S was lowest in summer and autumn, and N and the abundance of fewer dominant taxa were lowest in summer. In Center, the bivalve Loripes lucinalis showed a 10-fold increase from summer to autumn in both years, likely related to the lagoon's hydrodynamics favoring larval transport and settlement in the central sector of the lagoon. Overall, the seasonal variation found in Center followed a regression/recovery pattern typical of opportunistic assemblages occurring in confined organic-enriched environments. In conclusion, our results provide new insight into the patterns of seasonal variation in lagoon soft-sediment benthos and highlight the importance of local environmental conditions on this variation. This study provides a valuable tool for adopting appropriate monitoring strategies in these systems, with special reference to Southern-Eastern Mediterranean lagoons which are expected to suffer from increasing coastal development and human pressure in the near future. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular signaling along the anterior–posterior axis of early palate development

PubMed Central

Smith, Tara M.; Lozanoff, Scott; Iyyanar, Paul P.; Nazarali, Adil J.

2013-01-01

Cleft palate is a common congenital birth defect in humans. In mammals, the palatal tissue can be distinguished into anterior bony hard palate and posterior muscular soft palate that have specialized functions in occlusion, speech or swallowing. Regulation of palate development appears to be the result of distinct signaling and genetic networks in the anterior and posterior regions of the palate. Development and maintenance of expression of these region-specific genes is crucial for normal palate development. Numerous transcription factors and signaling pathways are now recognized as either anterior- (e.g., Msx1, Bmp4, Bmp2, Shh, Spry2, Fgf10, Fgf7, and Shox2) or posterior-specific (e.g., Meox2, Tbx22, and Barx1). Localized expression and function clearly highlight the importance of regional patterning and differentiation within the palate at the molecular level. Here, we review how these molecular pathways and networks regulate the anterior–posterior patterning and development of secondary palate. We hypothesize that the anterior palate acts as a signaling center in setting up development of the secondary palate. PMID:23316168

Flexible foraging movements of leatherback turtles across the North Atlantic Ocean.

PubMed

Hays, Graeme C; Hobson, Victoria J; Metcalfe, Julian D; Righton, David; Sims, David W

2006-10-01

Some marine species have been shown to target foraging at particular hotspots of high prey abundance. However, we show here that in the year after a nesting season, female leatherback turtles (Dermochelys coriacea) in the Atlantic generally spend relatively little time in fixed hotspots, especially those with a surface signature revealed in satellite imagery, but rather tend to have a pattern of near continuous traveling. Associated with this traveling, distinct changes in dive behavior indicate that turtles constantly fine tune their foraging behavior and diel activity patterns in association with local conditions. Switches between nocturnal vs. diurnal activity are rare in the animal kingdom but may be essential for survival on a diet of gelatinous zooplankton where patches of high prey availability are rare. These results indicate that in their first year after nesting, leatherback turtles do not fit the general model of migration where responses to resources are suppressed during transit. However, their behavior may be different in their sabbatical years away from nesting beaches. Our results highlight the importance of whole-ocean fishing gear regulations to minimize turtle bycatch.

Self-organization: the fundament of cell biology

PubMed Central

Betz, Timo

2018-01-01

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order—and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution. This article is part of the theme issue ‘Self-organization in cell biology’. PMID:29632257