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PubMed1996

Active and inactive genes localize preferentially in the periphery of chromosome territories.

The intranuclear position of a set of genes was analyzed with respect to the territories occupied by the whole chromosomes in which these genes are localized. Genes and their respective chromosome territories were simultaneously visualized in three-dimensionally preserved nuclei applying dual color fluorescence in situ hybridization. Three coding (DMD, MYH7, and HBB) and two noncoding sequences (D1Z2 and an anonymous sequence) were analyzed in four different cell types, including cells where DMD and MYH7 are actively transcribed. Spatial analysis by confocal laser scanning microscopy revealed that the genes are preferentially located in the periphery of chromosome territories. This positioning was independent from the activity of the genes. In contrast, the non-expressed anonymous fragment was found randomly distributed or localized preferentially in the interior of the corresponding chromosome territory. Furthermore, the distribution of the analyzed genes within the territorial peripheries was found to be highly characteristic for each gene, and, again, independent from its expression. The impact of these findings with regard to the three-dimensional arrangement of the linear DNA string within chromosome territories, as well as with respect to a putative nuclear subcompartment confining gene expression, are discussed.

Cells, Cultured↗
PubMed2002

Does herbivore diversity depend on plant diversity? The case of California butterflies.

It is widely believed that the diversity of plants influences the diversity of animals, and this should be particularly true of herbivores. We examine this supposition at a moderate spatial extent by comparing the richness patterns of the 217 butterfly species resident in California to those of plants, including all 5,902 vascular plant species and the 552 species known to be fed on by caterpillars. We also examine the relationships between plant/butterfly richness and 20 environmental variables. We found that although plant and butterfly diversities are positively correlated, multiple regression, path models, and spatial analysis indicate that once primary productivity (estimated by a water-energy variable, actual evapotranspiration) and topographical variability are incorporated into models, neither measure of plant richness has any relationship with butterfly richness. To examine whether butterflies with the most specialized diets follow the pattern found across all butterflies, we repeated the analyses for 37 species of strict monophages and their food plants and found that plant and butterfly richness were similarly weakly associated after incorporating the environmental variables. We condude that plant diversity does not directly influence butterfly diversity but that both are probably responding to similar environmental factors.

Animals↗
PubMed2004

Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor.

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a refinement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.

Asia, Central↗
PubMedDate not supplied

Visual pathways for object-oriented action and object recognition: functional anatomy with PET.

The purpose of this study was to identify the functional anatomy of the mechanisms involved in visually guided prehension and in object recognition in humans. The cerebral blood flow of seven subjects was investigated by positron emission tomography. Three conditions were performed using the same set of stimuli. In the 'grasping' condition, subjects were instructed to accurately grasp the objects. In the 'matching' condition, subjects were requested to compare the shape of the presented object with that of the previous one. In the 'pointing' condition (control), subjects pointed towards the objects. The comparison between grasping and pointing showed a regional cerebral blood flow (rCBF) increase in the anterior part of the inferior parietal cortex and part of the posterior parietal cortex. The comparison between grasping and matching showed an rCBF increase in the cerebellum, the left frontal cortex around the central sulcus, the mesial frontal cortex and the left inferior parietal cortex. Finally, the comparison between matching and pointing showed an rCBF increase in the right temporal cortex and the right posterior parietal cortex. Thus object-oriented action and object recognition activate a common posterior parietal area, suggesting that some kind of within-object spatial analysis was processed by this area whatever the goal of the task.

Adult↗
PubMed2006

Cytochrome oxidase and neurofilament reactivity in monocularly deprived human primary visual cortex.

Previous studies of human primary visual cortex (V1) have demonstrated a significant eye-specific decrease in cytochrome oxidase (CO) staining following monocular enucleation. We have extended these results by examining CO staining and neurofilament labeling in V1 from a patient with long-standing monocular blindness. A pattern of reduced neurofilament reactivity was found to align with pale CO-stained ocular dominance columns. Neurons located within deprived ocular dominance columns were significantly smaller compared with those in nondeprived columns. A spatial analysis of the relationship between CO blobs and ocular dominance columns revealed that both deprived and nondeprived blobs tended to align with the centers of ocular dominance columns.

Aged, 80 and over↗
PubMed1995

Site-specific integrated pest management for high value crops: sample units for map generation using the Colorado potato beetle (Coleoptera: Chrysomelidae) as a model system.

Site-specific agriculture uses maps to optimize within-field placement of agricultural practices. This technology introduces the potential to optimize pest management by varying pesticide or other inputs to better match within-field variation in pest density. Current sampling plans are designed to estimate mean density and may not be suitable for mapping, although useful sampling plans could be developed for map generation for integrated pest management. Using Colorado potato beetle, Leptinotarsa decemlineata (Say), adults, larvae, and egg masses as model systems, the influence of the sample unit on map validity was explored. Adapting currently used sampling plans for potato integrated pest management by spatially referencing each sampled stem failed to resolve spatial dependence and resulted in maps with poor reliability. Increasing the sample unit improved resolution of spatial dependence and map reliability for each life stage. A distance-walk sample unit for adult and late instar Colorado potato beetles which has high potential for map generation is introduced. Using this sample unit, generalizations about Colorado potato beetle spatial dependence are made to discuss issues of developing sampling programs for map generation. An iterative process of sampling, spatial analysis, and error analysis is suggested for evaluating sample units for mapping pest density in high value crops.

Animals↗
PubMed2003

Three-dimensional reconstruction of tubular structure of vacuolar membrane throughout mitosis in living tobacco cells.

Plant vacuoles are the largest of organelles, performing various functions in cellular metabolism, morphogenesis and cell division. Dynamic changes in vacuoles during mitosis were studied by monitoring tubular structure of vacuolar membrane (TVM) in living transgenic tobacco BY-2 cells stably expressing a GFP-AtVam3p fusion protein (BY-GV). Comprehensive images of the complicated TVM configurations were obtained by reconstructing three-dimensional (3-D) surface structures from sequential confocal sections, using newly developed software, SSR (stereo-structure reconstructor). Using the surface modeling technique, we succeeded for the first time in clarifying the development process of TVMs and the topological relationship between TVMs and large vacuoles. TVMs, initially organized from large vacuoles, elongated to encircle the spindle at metaphase. Subsequently, the TVMs invaded the equatorial region from anaphase to telophase, and then they were divided to the two daughter cells by the cell plate at cytokinesis. When the daughter nuclei were separating from the cell plate, some TVMs enlarged to form large vacuoles near the division site. Spatial analysis revealed that from anaphase until cytokinesis, TVMs connected the two large vacuoles and functioned as a route for inter-vacuolar transport. Furthermore, the experiments using the inhibitor for actin microfilaments indicated that the microfilaments were indispensable for the development and the maintenance of TVMs.

Agrobacterium tumefaciens↗
PubMed2000

Spatial distribution of cannibalism mortalities in commercial laying hens.

The distribution of cannibalism cases in a flock of 19,776 Babcock White Leghorns was monitored from 21 to 54 wk of age. The hens were kept in a single-floor house consisting of four banks of two-deck stair-step cages. Each of the 4,944 cages held four hens at a density of 152 cm(2) (60 inches(2)) per hen. Each cage was assigned a number from 1 to 4,944, and each dead bird was tagged according to its cage of origin. Dead birds were collected daily, kept in a freezer, and necropsied weekly. Farm personnel routinely transferred a live hen from an end cage to a cage where a mortality had occurred. The cause of death, age, cage number, and cage location were recorded for each dead hen. Of the 1,173 hens that died during the study period, 253 (21.6%) died from egg peritonitis, 184 (15.7%) from hypocalcemia, 167 (14.1%) from cannibalism, 164 (14%) from neoplastic disease, and the rest from various other causes. Cannibalism cases were analyzed statistically for clustering. Cannibalism was defined as death from tissue trauma and hemorrhage inflicted by cage mates. A spatial analysis showed that cannibalism is not a random event but one that occurs in clusters. The incidence of cannibalism was also found to be significantly higher on the top rows of cages as compared with the bottom rows.

Age Factors↗
PubMed2002

Glasslike relaxation of labyrinthine domain patterns.

A spatial analysis of globally disordered (labyrinthine) stripe domain patterns in thin ferrimagnetic garnet films is applied to investigate the pattern evolution. After demagnetization of the sample we obtain a branched (fernlike) structure. By periodic modulation of the magnetic field the number of the branches diminishes and a labyrinthine pattern develops. We describe the evolution of the pattern by a measure extracted from the curvature of the border line of the magnetic domains. The relaxation of this measure is found to be nonexponential and can be described by the Kohlrausch-Williams-Watts law.

Journal Article↗
PubMed2006

Centrality measures in spatial networks of urban streets.

We study centrality in urban street patterns of different world cities represented as networks in geographical space. The results indicate that a spatial analysis based on a set of four centrality indices allows an extended visualization and characterization of the city structure. A hierarchical clustering analysis based on the distributions of centrality has a certain capacity to distinguish different classes of cities. In particular, self-organized cities exhibit scale-free properties similar to those found in nonspatial networks, while planned cities do not.

Journal Article↗
PubMed2002

The physiology and biophysics of an aluminum tolerance mechanism based on root citrate exudation in maize.

Al-induced release of Al-chelating ligands (primarily organic acids) into the rhizosphere from the root apex has been identified as a major Al tolerance mechanism in a number of plant species. In the present study, we conducted physiological investigations to study the spatial and temporal characteristics of Al-activated root organic acid exudation, as well as changes in root organic acid content and Al accumulation, in an Al-tolerant maize (Zea mays) single cross (SLP 181/71 x Cateto Colombia 96/71). These investigations were integrated with biophysical studies using the patch-clamp technique to examine Al-activated anion channel activity in protoplasts isolated from different regions of the maize root. Exposure to Al nearly instantaneously activated a concentration-dependent citrate release, which saturated at rates close to 0.5 nmol citrate h(-1) root(-1), with the half-maximal rates of citrate release occurring at about 20 microM Al(3+) activity. Comparison of citrate exudation rates between decapped and capped roots indicated the root cap does not play a major role in perceiving the Al signal or in the exudation process. Spatial analysis indicated that the predominant citrate exudation is not confined to the root apex, but could be found as far as 5 cm beyond the root cap, involving cortex and stelar cells. Patch clamp recordings obtained in whole-cell and outside-out patches confirmed the presence of an Al-inducible plasma membrane anion channel in protoplasts isolated from stelar or cortical tissues. The unitary conductance of this channel was 23 to 55 pS. Our results suggest that this transporter mediates the Al-induced citrate release observed in the intact tissue. In addition to the rapid Al activation of citrate release, a slower, Al-inducible increase in root citrate content was also observed. These findings led us to speculate that in addition to the Al exclusion mechanism based on root citrate exudation, a second internal Al tolerance mechanism may be operating based on Al-inducible changes in organic acid synthesis and compartmentation. We discuss our findings in terms of recent genetic studies of Al tolerance in maize, which suggest that Al tolerance in maize is a complex trait.

Adaptation, Physiological↗
PubMed2000

Complex spatial responses to cucumber mosaic virus infection in susceptible Cucurbita pepo cotyledons.

Cucumber mosaic virus infection of its susceptible host Cucurbita pepo results in a program of biochemical changes after virus infection. Applying a spatial analysis to expanding infected lesions, we investigated the relationship between the changes in enzyme activity and gene expression. Patterns of altered expression were seen that could not be detected by RNA gel blot analysis. For all the host genes studied, there was a downregulation (shutoff) of expression within the lesion. In addition, two distinct types of upregulation were observed. The expression of heat shock protein 70 (HSP70) and NADP(+)-dependent malic enzyme (NADP-ME) showed induction in apparently uninfected cells ahead of the infection. This response was more localized than the upregulation exhibited by catalase expression, which occurred throughout the uninfected regions of the tissue. The experiments showed that virus infection induced immediate and subsequent changes in gene expression by the host and that the infection has the potential to give advance signaling of the imminent infection.

Catalase↗
PubMed2006

BCI Meeting 2005--workshop on BCI signal processing: feature extraction and translation.

This paper describes the outcome of discussions held during the Third International BCI Meeting at a workshop charged with reviewing and evaluating the current state of and issues relevant to brain-computer interface (BCI) feature extraction and translation. The issues discussed include a taxonomy of methods and applications, time-frequency spatial analysis, optimization schemes, the role of insight in analysis, adaptation, and methods for quantifying BCI feedback.

Algorithms↗
PubMed2004

Where to go? Strategic modelling of access to emergency shelters in Mozambique.

This paper, through spatial-analysis techniques, examines the accessibility of emergency shelters for vulnerable populations, and outlines the benefits of an extended and permanently established shelter network in central Mozambique. The raster-based modelling approach considers data on land cover, locations of accommodation centres in 2000, settlements and infrastructure. The shelter analysis is a two-step process determining access for vulnerable communities first, followed by a suitability analysis for additional emergency shelter sites. The results indicate the need for both retrofitting existing infrastructure (schools, health posts) to function as shelters during an emergency, and constructing new facilities - at best multi-purpose facilities that can serve as social infrastructure and shelter. Besides assessing the current situation in terms of availability and accessibility of emergency shelters, this paper provides an example of evaluating the effectiveness of humanitarian assistance without conventional mechanisms like food tonnage and number of beneficiaries.

Community Networks↗
PubMed2006

Microgeographical breeding structure of the tsetse fly, Glossina pallidipes in south-western Kenya.

The origins of extant Glossina pallidipes Austen (Diptera: Glossinidae) populations in the ecologically well-studied Lambwe and Nguruman valleys in Kenya are controversial because populations have recovered after seemingly effective attempts to achieve high levels of control. The microgeographical breeding structure of the tsetse fly, G. pallidipes, was investigated by analysing spatial and temporal variation at eight microsatellite loci to test hypotheses about endemism and immigration. Samples were obtained at seasonal intervals from trap sites separated by 200 m to 14 km and arranged into blocks. G. pallidipes populations nearest to Lambwe and Nguruman also were sampled. Spatial analysis indicated that genetic differentiation by genetic drift was much less among trapping sites within Lambwe and Nguruman (F(ST) < or = 0.049) than between them (F(ST) = 0.232). F(ST) between Serengeti and Nguruman was 0.16 and F(ST) between Kodera Forest and Lambwe was 0.15. The genetic variance in G. pallidipes explained by dry and wet seasons (0.33%) was about one-fifth the variance among collection dates (1.6%), thereby indicating reasonable temporal stability of genetic variation. Gene frequencies in Kodera and Serengeti differed greatly from Lambwe and Nguruman, thereby falsifying the hypothesis that Lambwe and Nguruman were repopulated by immigrants. Harmonic mean effective (= breeding) population sizes were 180 in Lambwe and 551 in Nguruman. The genetic data suggest that G. pallidipes in Lambwe and Nguruman have been endemic for long intervals.

Animals↗
PubMed2006

Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia.

The badger, Meles meles, is a widely distributed mustelid in Eurasia and shows large geographic variability in morphological characters whose evolutionary significance is unclear and needs to be contrasted with molecular data. We sequenced 512 bp of the mitochondrial DNA control region in 115 Eurasian badgers from 21 countries in order to test for the existence of structuring in their phylogeography, to describe the genetic relationships among their populations across its widespread geographic range, and to infer demographic and biogeographic processes. We found that the Eurasian badger is divided into four groups regarding their mitochondrial DNA: Europe, Southwest Asia, North and East Asia, and Japan. This result suggests that the separation of badgers into phylogeographic groups was influenced by cold Pleistocene glacial stages and permafrost boundaries in Eurasia, and by geographic barriers, such as mountains and deserts. Genetic variation within phylogeographic groups based on distances assuming the Tamura-Nei model with rate heterogeneity and invariable sites (d(T-N) range: 3.3-4.2) was much lower than among them (d(T-N) range: 10.7-38.0), and 80% of the variation could be attributed to differences among regions. Spatial analysis of molecular variance (samova), median-joining network, and Mantel test did not detect genetic structuring within any of the phylogeographic groups with the exception of Europe, where 50% of variation was explained by differences among groups of populations. Our data suggest that the European, Southwest Asian, and North and East Asian badgers evolved separately since the end of Pliocene, at the beginnings of glacial ages, whereas Japanese badgers separated from continental Asian badgers during the middle Pleistocene. Endangered badgers from Crete Island, classified as Meles meles arcalus subspecies, were closely related to badgers from Southwest Asia. We also detected sudden demographic growth in European and Southwest Asian badgers that occurred during the Middle Pleistocene.

Animal Migration↗
PubMed2006

Quantifying uncertainty in the potential distribution of an invasive species: climate and the Argentine ant.

Maps of a species' potential range make an important contribution to conservation and invasive species risk analysis. Spatial predictions, however, should be accompanied by an assessment of their uncertainty. Here, we use multimodel inference to generate confidence intervals that incorporate both the uncertainty involved in model selection as well as the error associated with model fitting. In the case of the invasive Argentine ant, we found that it was most likely to occur where the mean daily temperature in mid-winter was 7-14 degrees C and maximum daily temperatures during the hottest month averaged 19-30 degrees C. Uninvaded regions vulnerable to future establishment include: southern China, Taiwan, Zimbabwe, central Madagascar, Morocco, high-elevation Ethiopia, Yemen and a number of oceanic islands. Greatest uncertainty exists over predictions for China, north-east India, Angola, Bolivia, Lord Howe Island and New Caledonia. Quantifying the costs of different errors (false negatives vs. false positives) was considered central for connecting modelling to decision-making and management processes.

Animals↗
PubMed1999

Population-based linkage of health records in Western Australia: development of a health services research linked database.

OBJECTIVES: To introduce the Western Australian Health Services Research Linked Database as infrastructure to support aetiologic, utilisation and outcomes research. To compare the study population, data resources, technical systems and organisational supports with international best practice in record linkage and health research. METHOD AND RESULTS: The WA Linked Database systematically links the available administrative health data within an Australian State of 1.7 million people. It brings together, initially, six core data elements (birth records, midwives' notifications, cancer registrations, in-patient hospital morbidity, in-patient and public out-patient mental health services data and death records). It will be updated regularly and is designed, in future extensions, to include data on primary, residential and domiciliary care and health surveys. Linkage uses probabilistic matching of patient names and other identifiers. Geocodes for spatial analysis are assigned using address linkage and mapping software. By June 1997, the project had taken 2 1/2 years to develop the system and link seven million core data records from 1980 to 1995. CONCLUSIONS: The system is consistent with international benchmarks, from four centres of excellence, for the study population, core datasets, matching and geocoding, and collaborative networks. There are prospects to redress deficiencies in primary medical contact and other data resources, validation studies, tracing systems and a more supportive legal framework. IMPLICATIONS: The WA Linked Database will be used in combination with medical record audits to provide a comprehensive evaluation of health system performance.

Data Collection↗