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PubMed2026

Multiple local PfDHFR I164L haplotype expansions drive Plasmodium falciparum antifolate resistance in Uganda.

Mutations in the Plasmodium falciparum genes, pfdhfr and pfdhps, drive antifolate resistance and threaten malaria control in regions where sulfadoxine-pyrimethamine (SP) is the primary chemoprevention strategy. The spatial patterns and evolutionary dynamics of these mutations in high-transmission settings remain incompletely understood. Here we genotyped 11 resistance-associated mutations in pfdhfr and pfdhps in 4,725 P. falciparum isolates collected from 16 Ugandan health facilities as part of annual surveillance between 2016 and 2022. Notably, we show that the frequency of PfDHFR I164L, which confers higher pyrimethamine resistance, increased over time from 19.4% to 32.4%. Using identity-by-descent, haplotype structure, and extended haplotype homozygosity analyses, we show that PfDHFR I164L is present on multiple haplotype backgrounds and undergoes localised expansions, without detectable signatures of recent positive selection at all but one site. Our results suggest that the evolution of antifolate resistance, driven by PfDHFR I164L, is spatially heterogeneous and complex in regions that primarily use SP chemoprevention programmes.

Plasmodium falciparum↗

PubMed1997

Cerebral blood flow of the exposed brain surface measured by laser Doppler perfusion imaging.

A novel application of laser Doppler flowmetry (LDF) laser Doppler perfusion imaging (LDPI), was used to study cerebral cortical blood flow (CBFcortex). In contrast to the conventional laser Doppler perfusion monitor, LDPI creates two dimensional maps of the tissue perfusion in a well defined area of up to 120 x 120 mm comprising 4096 measurements points. Measurements of CBFcortex were made through an optically transparent polyester film applied to a cranial window preparation in ventilated anaesthetized pigs. Temporal and spatial heterogeneity in CBFcortex were visualized by LDPI during provocations which are known to alter CBF (varying arterial PCO2 or MABP, or infusion of adenosine at constant MABP (concomitant angiotensin administration) or by hyperoxemia). During hypercapnia the recorded CBFcortex increased homogeneously. The adenosine-mediated increase in recorded CBFcortex was concentrated on the lower flow interval, as was the hyperoxemia-caused decline. At decreasing MABP the autoregulatory threshold was found to vary locally within the cortex. The results suggest that LDPI, apart from detecting localized changes in CBFcortex' also visualizes flow changes within different vascular segments. Together with the practical advantages of the system, i.e. not necessitating direct contact with the tissues, this feature makes the technique suitable for studies of CBFcortex distributions.

Animals↗

PubMed1997

Three-dimensional reconstruction of colon carcinoma metastases in liver.

Resection of liver metastases in patients with colon cancer increases survival but success depends on removal of all tumour tissue. For this purpose, understanding of spatial relationships between metastases and liver architecture is essential. Because metastatic cancer growth is essentially a three-dimensional (3D) event, we decided to apply 3D reconstruction techniques to study these spatial relationships between metastases and liver structures such as blood vessels, stroma and the liver capsule (Glisson's capsule). Colon carcinoma metastases were experimentally induced in rat liver by injection of colon cancer cells (CC531) into the portal vein. Three weeks later, livers from these animals and control livers were removed and immediately frozen in liquid nitrogen. Thirty-seven to 110 consecutive sections were used for each 3D reconstruction of 26 metastases in eight livers. Contours of different structures were stained by (immuno)histochemical means, traced in each section and stored in a database. From the contour model, a volume model was generated. Among the 26 metastases, seven were found to grow distantly from the liver capsule. They were small and consisted of well-differentiated cancer cells that were totally surrounded by a basement membrane and stroma which was always connected with adjacent blood vessels of a portal tract. The remaining 19 metastases showed a more advanced pattern of development. Infiltration of poorly differentiated colon cancer cells progressed through the stroma at various sites and areas of direct contact between cancer cells and hepatocytes were frequently found. This type of outgrowth of cancer cells was only found when metastases had made contact with the liver capsule. However, some areas in sections of these advanced stages still resembled small metastases. On the basis of these findings, we conclude that stroma-affects the differentiation pattern of cancer cells and has at least a dual role in tumour growth. On the one hand it limits invasion of cancer cells in the surrounding host tissue. On the other hand, stroma formation at the capsule, which consists mainly of granulation tissue, facilitates outgrowth of the tumours. Furthermore, our 3D reconstructions demonstrate the spatial heterogeneity of larger metastases and the importance of a 3D approach to understand growth and development of metastases in general and colon cancer metastases in the liver in particular.

Animals↗

PubMed2002

Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest.

We have used molecular techniques to investigate the diversity and distribution of the arbuscular mycorrhizal (AM) fungi colonizing tree seedling roots in the tropical forest on Barro Colorado Island (BCI), Republic of Panama. In the first year, we sampled newly emergent seedlings of the understory treelet Faramea occidentalis and the canopy emergent Tetragastris panamensis, from mixed seedling carpets at each of two sites. The following year we sampled surviving seedlings from these cohorts. The roots of 48 plants were analysed using AM fungal-specific primers to amplify and clone partial small subunit (SSU) ribosomal RNA gene sequences. Over 1300 clones were screened for random fragment length polymorphism (RFLP) variation and 7% of these were sequenced. Compared with AM fungal communities sampled from temperate habitats using the same method, the overall diversity was high, with a total of 30 AM fungal types identified. Seventeen of these types have not been recorded previously, with the remainder being similar to types reported from temperate habitats. The tropical mycorrhizal population showed significant spatial heterogeneity and nonrandom associations with the different hosts. Moreover there was a strong shift in the mycorrhizal communities over time. AM fungal types that were dominant in the newly germinated seedlings were almost entirely replaced by previously rare types in the surviving seedlings the following year. The high diversity and huge variation detected across time points, sites and hosts, implies that the AM fungal types are ecologically distinct and thus may have the potential to influence recruitment and host composition in tropical forests.

Base Sequence↗

PubMed2003

Use of a site-specific recombination-based biosensor for detecting bioavailable toluene and related compounds on roots.

We constructed and characterized a plasmid-based genetic system that reports the expression of a toluene-responsive promoter (PtbuA1) by effecting an irreversible, heritable change in the biosensor cell. Expression of the reporter gene gfp is strongly repressed in the absence of expression from the PtbuA1 promoter, and high level gfp expression in the original cell and its progeny is mediated by the site-specific recombination machinery of bacteriophage P22 to initiate removal of a repressor cassette. The reporter plasmid pTolLHB was functional in two soil saprophytes, Pseudomonas fluorescens A506 and Enterobacter cloacae JL1157, with the efficiency and sensitivity to low toluene concentrations being optimal in P. fluorescens A506. In culture, 80-100% of the A506 (pTolLHB) population expressed gfp following exposure to 0.2 micro m toluene for one to three hours. Compared to the response of A506 containing a plasmid-borne PtbuA1-gfp fusion, the recombination-based biosensor was more sensitive at detecting low toluene and trichloroethylene concentrations. An A506 (pTolLHB) inoculum, which had a background of 2.5% of the cells expressing gfp, was introduced onto barley roots in soil microcosms. If toluene was introduced into the microcosms, after 24 h, 72% of the A506 (pTolLHB) cells recovered from roots expressed gfp, indicating bioavailable toluene to rhizosphere bacteria. When toluene was not introduced, 16.5% of the A506 (pTolLHB) cells recovered from the roots expressed gfp, indicating that natural inducers of the PtbuA1 promoter were present in the barley rhizosphere. When introduced into rhizotrons containing barley plants and toluene vapours, the biosensor allowed localization of the availability of toluene along the seminal roots. In rhizotrons that were not exposed to toluene vapours, the biosensor exhibited high PtbuA1-promoter activity in distinct regions along the seminal roots, indicating spatial heterogeneity plant- or rhizosphere microbial community-derived inducers of the PtbuA1 promoter. This recombination-based toluene biosensor thus was useful in identifying bacterial exposure to transient or low levels of toluene, or related compounds, directly in the environment.

Bacteria↗

PubMedDate not supplied

[Myc and cell competition in Drosophila].

Cell differentiation and organ shaping proceed not only upon instructive but also upon competitive cell-cell interactions. In the proliferating epithelium forming the larval Drosophila wing disc, cell competition contributes to the fidelity of the organogenesis. Several recent studies show how d-myc, encoding a bHLH/LZ transcription factor homologous to vertebrate Myc proteins, controls cell competition during wing development. In this model, any experiment leading to the confrontation of two populations differing by their levels of d-Myc expression, even in a two-fold ratio, gives rise to a competition characterized both by an overgrowth of the population having the highest level and an apoptotic elimination of the neighbouring << weakly >> expressing cells. As a consequence of the mutually compensating nature of these two processes, the final size of the wing remains unchanged. Importantly, lowering or elevating d-Myc expression to the same extent in all cells of the disc does not trigger competition. This indicates that competition is linked to a spatial heterogeneity in, and not to the absolute level of, d-Myc expression. Both vertebrate and Drosophila Myc proteins stimulate ribosome biogenesis, and genetic evidence in Drosophila suggests that this property underlies the strong competitive advantage imparted by its relatively high expression. Accordingly, it is proposed, although not proved, that the more the wing cells express d-Myc and amplify their protein synthesis apparatus, the more they bind, internalize, and transduce the vital and limiting growth factor Dpp, which in turn is presumed to increase d-Myc protein level. These findings suggest that wing organogenesis is a self-corrected process whereby d-Myc induction in overgrowing cells ensures the compensatory elimination of their neighbours. Moreover, they have important implications for the oncogenic role of vertebrate Myc proteins and possibly of related transcription factors.

Animals↗

PubMedDate not supplied

Effects of antiarrhythmic drugs on QT interval dispersion--relationship to antiarrhythmic action and proarrhythmia.

Class IA, IC, and III antiarrhythmic drugs prolong ventricular repolarization (VR) which is manifest as QT interval prolongation on the surface electrocardiogram. These drugs may prolong VR in a spatially heterogeneous manner which results in increased dispersion of VR. This may be manifest as increased QT interval dispersion. Antiarrhythmic drug-induced decreases in QT interval dispersion are associated with antiarrhythmic efficacy in patients with the long QT syndrome and in patients with sustained ventricular tachycardia. Antiarrhythmic drug-induced increases in QT interval dispersion are associated with ventricular proarrhythmia secondary to torsades de points ventricular tachycardia. A number of factors may modulate the effects of antiarrhythmic drugs on dispersion of VR, including the disease state, transient ischemia, electrolyte abnormalities, changes in autonomic tone, and hemodynamic stress.

Anti-Arrhythmia Agents↗

PubMedDate not supplied

Spatiotemporal analysis of [Ca2+]i rises in mouse eggs after intracytoplasmic sperm injection (ICSI).

Intracytoplasmic sperm injection (ICSI) into mammalian eggs induces repetitive rises in intracellular Ca2+ concentration ([Ca2+]i) which are the pivotal signal in fertilization. Spatiotemporal aspects of [Ca2+]i rises following ICSI into the periphery of mouse eggs were investigated with high-speed confocal microscopy. The first Ca2+ response was generated 25-30 min after ICSI, when [Ca2+]i increased slowly and reached a certain level. The [Ca2+]i rise occurred synchronously over the ooplasm, attained the peak in 40-70 s, and lasted for 5-7 min. Succeeding Ca2+ responses occurred at intervals of 20-30 min, associated with the faster rate of [Ca2+]i rise and the shorter duration as Ca2+ oscillations progressed. The [Ca2+]i rises took the form of a wave that started from an arbitrary cortical region, but not from the vicinity of the injected sperm head. The Ca2+ wave became more pronounced and propagated across the egg faster in the later Ca2+ responses. An artifactual [Ca2+]i rise was inevitably produced during the ICSI procedure. The larger artifact affected the subsequent first Ca2+ response, resulting in the faster [Ca2+]i rise (time to peak, 10-20 s), slight spatial heterogeneity of [Ca2+]i rise in the ooplasm (but not a wave) and the shorter duration (3-4 min). The artifact slightly affected the amplitude of the second Ca2+ response, but little affected the later Ca2+ responses. It is suggested that the factor(s) that leaked out of the injected spermatozoon diffuses to a wide area and sensitizes Ca2+ channels of the endoplasmic reticulum to induce Ca2+ release synchronously over the ooplasm. The enhanced sensitization leads to propagating Ca2+ release initiated from the cortex that is more sensitive to the sperm factor.

Animals↗

PubMed2004

Particle rearrangements during transitions between local minima of the potential energy landscape of a binary Lennard-Jones liquid.

The potential energy landscape (PEL) of binary Lennard-Jones (BLJ) mixtures exhibits local minima, or inherent structures (IS), which are organized into metabasins (MBs). We study the particle rearrangements related to transitions between both successive IS and successive MB for a small 80:20 BLJ system near the mode-coupling temperature TMCT. The analysis includes the displacements of individual particles, the localization of the rearrangements, and the relevance of string-like motion. We find that the particle rearrangements during IS and MB transitions do not change significantly at TMCT. In particular, an onset of single particle hopping on the length scale of the interparticle distance is not observed. Further, it is demonstrated that IS and MB dynamics are spatially heterogeneous and facilitated by string-like motion. To investigate the mechanism of string-like motion, we follow the particle rearrangements during suitable sequences of IS transitions. We find that most strings observed after a series of transitions do not move coherently during a single transition, but subunits of different sizes are active at different times. Several findings suggest that, though string-like motion is of comparable relevance when the system explores a MB and when it moves from one MB to another, the occurrence of a successful string enables the system to exit a MB. Moreover, we show that the particle rearrangements during two consecutive MB transitions are basically uncorrelated. In particular, different groups of particles are highly mobile. We further find the positions of strings during successive MB transitions weakly but positively correlated, supporting the idea of dynamic facilitation. Finally, the relation between the features of the potential energy landscape and the relaxation processes in supercooled liquids is discussed.

Journal Article↗

PubMed2006

Stacking fault structure in shear-induced colloidal crystallization.

We report measurements of the spatial distribution of stacking faults in colloidal crystals formed by means of an oscillatory shear field at a particle volume fraction of 52% in a system where the pair potential interactions are mildly repulsive. Stacking faults are directly visualized via confocal laser scanning microscopy. Consistent with previous scattering studies, shear orders the initially amorphous colloids into close-packed planes parallel to the shearing surface. Upon increasing the strain amplitude, the close-packed direction of the (111) crystal plane shifts from an orientation parallel to the vorticity direction to parallel the flow direction. The quality of the layer ordering, as characterized by the mean stacking parameter, decreases with strain amplitude. In addition, we directly observe the three-dimensional structure of stacking faults in sheared crystals. We observe and quantify spatial heterogeneity in the stacking fault arrangement in both the flow-vorticity plane and the gradient direction, particularly at high strain amplitudes (gamma> or =3). At these conditions, layer ordering persists in the flow-vorticity plane only over scales of approximately 5-10 particle diameters. This heterogeneity is one component of the random layer ordering deduced from previous scattering studies. In addition, in the gradient direction, the stacking registry shows that crystals with intermediate global mean stacking probability are comprised of short sequences of face-centered cubic and hexagonal close-packed layers with a stacking that includes a component that is nonrandom and alternating in character.

Journal Article↗

PubMed2004

Functional organization of sensory input to the olfactory bulb glomerulus analyzed by two-photon calcium imaging.

Glomeruli in the olfactory bulb are anatomically discrete modules receiving input from idiotypic olfactory sensory neurons. To examine the functional organization of sensory inputs to individual glomeruli, we loaded olfactory sensory neurons with a Ca(2+) indicator and measured odorant-evoked presynaptic Ca(2+) signals within single glomeruli by using two-photon microscopy in anaesthetized mice. Odorants evoked patterns of discrete Ca(2+) signals throughout the neuropil of a glomerulus. Across glomeruli, Ca(2+) signals occurred with equal probability in all glomerular regions. Within single glomeruli, the pattern of intraglomerular Ca(2+) signals was indistinguishable for stimuli of different duration, identity, and concentration. Moreover, the response time course of the signals was similar throughout the glomerulus. Hence, sensory inputs to individual glomeruli are spatially heterogeneous but seem to be functionally indiscriminate. These results support the view of olfactory glomeruli as functional units in representing sensory information.

Animals↗

PubMed2004

The effects of host contact network structure on pathogen diversity and strain structure.

For many important pathogens, mechanisms promoting antigenic variation, such as mutation and recombination, facilitate immune evasion and promote strain diversity. However, mathematical models have shown that host immune responses to polymorphic antigens can structure pathogen populations into discrete strains with nonoverlapping antigenic repertoires, despite recombination. Until now, models of strain evolution incorporating host immunity have assumed a randomly mixed host population. Here, we illustrate the effects of different host contact networks on strain diversity and dynamics by using a stochastic, spatially heterogeneous analogue of this model. For randomly mixed populations, our model confirms that cross-immunity to strains sharing alleles at antigenic loci may structure the pathogen population into discrete, nonoverlapping strains. However, this structure breaks down once the assumption of random mixing is relaxed, and an increasingly diverse pathogen population emerges as contacts between hosts become more localized. These results imply that host contact network structure plays a significant role in mediating the emergence of pathogen strain structure and dynamics.

Animals↗

PubMed2004

Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly.

Stochastic niche theory resolves many of the differences between neutral theory and classical tradeoff-based niche theories of resource competition and community structure. In stochastic niche theory, invading species become established only if propagules can survive stochastic mortality while growing to maturity on the resources left unconsumed by established species. The theory makes three predictions about community structure. First, stochastic niche assembly creates communities in which species dominate approximately equally wide "slices" of the habitat's spatial heterogeneity. These niche widths generate realistic distributions of species relative abundances for which, contrary to neutral theory but consistent with numerous observations, there are strong correlations among species traits, species abundances, and environmental conditions. Second, slight decreases in resource levels are predicted to cause large decreases in the probability that a propagule would survive to be an adult. These decreases cause local diversity to be limited by the inhibitory effects of resource use by established species on the establishment (recruitment) of potential invaders. If resource pulses or disturbance allowed invaders to overcome this recruitment limitation, many more species could indefinitely coexist. Third, the low invasibility of high diversity communities is predicted to result not from diversity per se, but from the uniformly low levels of resources that occur in high-diversity communities created by stochastic competitive assembly. This prediction provides a potential solution to the invasion paradox, which is the tendency for highly diverse regions to be more heavily invaded.

Computer Simulation↗

PubMed2005

Barnacle reproductive hotspots linked to nearshore ocean conditions.

Coastal marine ecosystems provide important ecosystem services to human populations worldwide. Understanding the contexts in which a species has markedly higher reproductive output is vital for effective management and conservation of these valuable and highly impacted systems. We documented reproductive hotspots along the Oregon coast for an ecologically significant marine invertebrate, the intertidal barnacle Balanus glandula. Greater larval production in both natural and experimental populations was associated with higher primary productivity in the adjacent nearshore ocean, providing strong evidence for bottom-up forcing. Mean cumulative larval production per 100 cm2 in natural barnacle populations in the region of higher primary productivity was almost 5x that of populations in the less productive region. Mean estimated larval production per individual in experimental populations in the region of higher primary productivity was >2x that of populations in the region of lower productivity, and mean larval production per 100 cm2 was >120x greater in the region of higher productivity. Our results highlight the importance of spatial heterogeneity in reproduction and other ecological processes in the marine environment and provide a mechanistic basis for evaluating the relative contributions of different sites when designing marine reserves and other protected areas. Our findings also advance the understanding of the role of bottom-up influences on population and community dynamics and contribute data for the next generation of models of marine community dynamics.

Analysis of Variance↗

PubMed2005

Fine-scale processes regulate the response of extreme events to global climate change.

We find that extreme temperature and precipitation events are likely to respond substantially to anthropogenically enhanced greenhouse forcing and that fine-scale climate system modifiers are likely to play a critical role in the net response. At present, such events impact a wide variety of natural and human systems, and future changes in their frequency and/or magnitude could have dramatic ecological, economic, and sociological consequences. Our results indicate that fine-scale snow albedo effects influence the response of both hot and cold events and that peak increases in extreme hot events are amplified by surface moisture feedbacks. Likewise, we find that extreme precipitation is enhanced on the lee side of rain shadows and over coastal areas dominated by convective precipitation. We project substantial, spatially heterogeneous increases in both hot and wet events over the contiguous United States by the end of the next century, suggesting that consideration of fine-scale processes is critical for accurate assessment of local- and regional-scale vulnerability to climate change.

Climate↗

PubMed2006

Extreme heat reduces and shifts United States premium wine production in the 21st century.

Premium wine production is limited to regions climatically conducive to growing grapes with balanced composition and varietal typicity. Three central climatic conditions are required: (i) adequate heat accumulation; (ii) low risk of severe frost damage; and (iii) the absence of extreme heat. Although wine production is possible in an extensive climatic range, the highest-quality wines require a delicate balance among these three conditions. Although historical and projected average temperature changes are known to influence global wine quality, the potential future response of wine-producing regions to spatially heterogeneous changes in extreme events is largely unknown. Here, by using a high-resolution regional climate model forced by the Intergovernmental Panel on Climate Change Special Report on Emission Scenarios A2 greenhouse gas emission scenario, we estimate that potential premium winegrape production area in the conterminous United States could decline by up to 81% by the late 21st century. While increases in heat accumulation will shift wine production to warmer climate varieties and/or lower-quality wines, and frost constraints will be reduced, increases in the frequency of extreme hot days (>35 degrees C) in the growing season are projected to eliminate winegrape production in many areas of the United States. Furthermore, grape and wine production will likely be restricted to a narrow West Coast region and the Northwest and Northeast, areas currently facing challenges related to excess moisture. Our results not only imply large changes for the premium wine industry, but also highlight the importance of incorporating fine-scale processes and extreme events in climate-change impact studies.

Agriculture↗

PubMed2003

An approach to electrical modeling of single and multiple cells.

Previous theoretical approaches to understanding effects of electric fields on cells have used partial differential equations such as Laplace's equation and cell models with simple shapes. Here we describe a transport lattice method illustrated by a didactic multicellular system model with irregular shapes. Each elementary membrane region includes local models for passive membrane resistance and capacitance, nonlinear active sources of the resting potential, and a hysteretic model of electroporation. Field amplification through current or voltage concentration changes with frequency, exhibiting significant spatial heterogeneity until the microwave range is reached, where cellular structure becomes almost "electrically invisible." In the time domain, membrane electroporation exhibits significant heterogeneity but occurs mostly at invaginations and cell layers with tight junctions. Such results involve emergent behavior and emphasize the importance of using multicellular models for understanding tissue-level electric field effects in higher organisms.

Cells↗

PubMed2000

Chaotic flow: the physics of species coexistence.

Hydrodynamical phenomena play a keystone role in the population dynamics of passively advected species such as phytoplankton and replicating macromolecules. Recent developments in the field of chaotic advection in hydrodynamical flows encourage us to revisit the population dynamics of species competing for the same resource in an open aquatic system. If this aquatic environment is homogeneous and well-mixed then classical studies predict competitive exclusion of all but the most perfectly adapted species. In fact, this homogeneity is very rare, and the species of the community (at least on an ecological observation time scale) are in nonequilibrium coexistence. We argue that a peculiar small-scale, spatial heterogeneity generated by chaotic advection can lead to coexistence. In open flows this imperfect mixing lets the populations accumulate along fractal filaments, where competition is governed by an "advantage of rarity" principle. The possibility of this generic coexistence sheds light on the enrichment of phytoplankton and the information integration in early macromolecule evolution.

Ecology↗