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PubMed2003

Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification.

The Otx2 gene, containing a highly conserved paired-type homeobox, plays a pivotal role in the development of the rostral head throughout vertebrates. Precise regulation of the temporal and spatial expression of Otx2 is likely to be crucial for proper head specification. However, regulatory mechanisms of Otx2 expression remain largely unknown. In this study, the Otx2 genome of the puffer fish Fugu rubripes, which has been proposed as a model vertebrate owing to its highly compact genome, was cloned. Consistently, Fugu Otx2 possesses introns threefold smaller in size than those of the mouse Otx2 gene. Otx2 mRNA was transcribed after MBT, and expressed in the rostral head region throughout the segmentation and pharyngula periods of wild-type Fugu embryos. To elucidate regulatory mechanisms of Otx2 expression, the expression of Otx2-lacZ reporter genes nearly covering the Fugu Otx2 locus, from -30.5 to +38.5 kb, was analyzed, by generating transgenic mice. Subsequently, seven independent cis-regulators were identified over an expanse of 60 kb; these regulators are involved in the mediation of spatiotemporally distinct subdomains of Otx2 expression. Additionally, these expression domains appear to coincide with local signaling centers and developing sense organs. Interestingly, most domains do not overlap with one another, which implies that cis-regulators for redundant expression may be abolished exclusively in the pufferfish so as to reduce its genome size. Moreover, these cis-regions were also able to direct expression in zebrafish embryos equivalent to that observed in transgenic mice. Further comparative sequence analysis of mouse and pufferfish intergenic regions revealed eight highly conserved elements within these cis-regulators. Therefore, we propose that, in vertebrate evolution, the Otx2 promoter acquires multiple, spatiotemporally specific cis-regulators in order to precisely control highly coordinated processes in head development.

Amino Acid Sequence↗
PubMedDate not supplied

Temporal clustering analysis of cerebral blood flow activation maps measured by laser speckle contrast imaging.

Temporal and spatial orchestration of neurovascular coupling in brain neuronal activity is crucial for comprehending the mechanism of functional cerebral metabolism and pathophysiology. Laser speckle contrast imaging (LSCI) through a thinned skull over the somatosensory cortex is utilized to map the spatiotemporal characteristics of local cerebral blood flow (CBF) in anesthetized rats during sciatic nerve stimulation. The time course of signals from all spatial loci among the massive dataset is hard to analyze, especially for the thousands of images, each of which composes millions of pixels. We introduce a temporal clustering analysis (TCA) method, which is proven as an efficient method to analyze functional magnetic resonance imaging (fMRI) data in the temporal domain. The timing and location of CBF activation shows that contralateral hindlimb sensory cortical microflow is activated to increase promptly in less than 1 s after the onset of 2-s electrical stimulation and is evolved in different discrete regions. This pattern is similar but slightly elaborated from the results obtained from laser Doppler flowmetry (LDF) and fMRI. We present this combination to investigate interacting brain regions, which might lead to a better understanding of the nature of brain parcellation and effective connectivity.

Animals↗
PubMed2004

Canal-otolith interactions after off-vertical axis rotations. II. Spatiotemporal properties of roll and pitch postrotatory vestibuloocular reflexes.

We have examined the spatiotemporal characteristics of postrotatory eye velocity after roll and pitch off-vertical axis rotations (OVAR). Three rhesus monkeys were placed in one of 3 orientations on a 3-dimensional (3D) turntable: upright (90 degrees roll or pitch OVAR), 45 degrees nose-up (45 degrees roll OVAR), and 45 degrees left ear-down (45 degrees pitch OVAR). Subjects were then rotated at +/-60 degrees /s around the naso-occipital or interaural axis and stopped after 10 turns, in one of 7 final head orientations, each separated by 30 degrees . We found that postrotatory eye velocity showed horizontal-vertical components after roll OVAR and horizontal-torsional components after pitch OVAR that varied systematically as a function of final head orientation. The quantitative analysis suggests that, in contrast to the analogous yaw OVAR paradigm, a system of up to 3 real, gravity-dependent eigenvectors and eigenvalues determines the spatiotemporal characteristics of the residual eye velocities after roll and pitch OVAR. One of these eigenvectors closely aligned with gravity, whereas the other 2 determined the orientation of the earth horizontal plane. We propose that the spatial characteristics of eye velocity after roll and pitch OVAR follow the physical constraints of stationary orientation in a gravitational field and reflect the brain's best estimate of head-in-space orientation within an internal representation of 3D space.

Animals↗
PubMedDate not supplied

Spatiotemporal visualization of the tongue surface using ultrasound and Kriging (SURFACES).

Analyzing the motion of the human tongue surface provides valuable information about speech and swallowing. One method to analyse this motion is to acquire two-dimensional ultrasound images and extract the tongue surface contours from them. Quantitative and statistical analysis of these extracted contours is made difficult because of the absence of physical fleshpoint markers on them. In this research, this problem is overcome by pre-processing the contours using Kriging. Pre-processing includes extrapolating and resampling the contours on a regular spatial grid. The preprocessed contours can then be visualized as spatiotemporal surfaces. A dedicated user interface called SURFACES is designed to aid in the generation, visualization and quantitative comparisons of these spatiotemporal surfaces.

Algorithms↗
PubMed1993

Spatiotemporal expression of SCIP and myelin genes in rat brain during early postnatal development.

The expression of the SCIP and myelin genes (PLP, BP and MAG) was quantitated by Northern blot analysis during early postnatal rat brain development. The SCIP gene was already profoundly upregulated on day 1 postpartum. The SCIP message level in the forebrain was 4- and 17-fold higher than the message level in the cerebellum and brainstem, respectively. By day 20, the SCIP gene expression declined in the forebrain to approximately 5% of the day-1 level, and became undetectable in the brainstem and cerebellum. The myelin gene expression sharply upregulated at approximately day 7-8, and in general, was highest in the brainstem, and lowest in the forebrain. The results demonstrate that the expression of the SCIP gene in the oligodendrocytic lineage cells is relatively low, whereas other cellular elements feature very active expression of the gene during the early postnatal development. Additionally, the variation in the relative ratios of the myelin messages among the brain regions indicates that the levels of expression of the myelin genes are not tightly synchronized.

Animals↗
PubMed2006

Predictability analysis for an automated seizure prediction algorithm.

Epileptic seizures of mesial temporal origin are preceded by changes in signal properties detectable in the intracranial EEG. A series of computer algorithms designed to detect the changes in spatiotemporal dynamics of the EEG signals and to warn of impending seizures have been developed. In this study, we evaluated the performance of a novel adaptive threshold seizure warning algorithm (ATSWA), which detects the convergence in Short-Term Maximum Lyapunov Exponent (STLmax) values among critical intracranial EEG electrode sites, as a function of different seizure warning horizons (SWHs). The ATSWA algorithm was compared to two statistical based naïve prediction algorithms (periodic and random) that do not employ EEG information. For comparison purposes, three performance indices "area above ROC curve" (AAC), "predictability power" (PP) and "fraction of time under false warnings" (FTF) were defined and the effect of SWHs on these indices was evaluated. The results demonstrate that this EEG based seizure warning method performed significantly better (P < 0.05) than both naïve prediction schemes. Our results also show that the performance indexes are dependent on the length of the SWH. These results suggest that the EEG based analysis has the potential to be a useful tool for seizure warning.

Adult↗
PubMed1994

Transcriptional regulation of string (cdc25): a link between developmental programming and the cell cycle.

During postblastoderm embryogenesis in Drosophila, cell cycles progress in an invariant spatiotemporal pattern. Most of these cycles are differentially timed by bursts of transcription of string (cdc25), a gene encoding a phosphatase that triggers mitosis by activating the Cdc2 kinase. An analysis of string expression in 36 pattern-formation mutants shows that known patterning genes act locally to influence string transcription. Embryonic expression of string gene fragments shows that the complete pattern of string transcription requires extensive cis-acting regulatory sequences (> 15.3 kb), but that smaller segments of this regulatory region can drive proper temporal expression in defined spatial domains. We infer that string upstream sequences integrate many local signals to direct string's transcriptional program. Finally, we show that the spatiotemporal progression of string transcription is largely unaffected in mutant embryos specifically arrested in G2 of cycles 14, 15, or 16, or G1 of cycle 17. Thus, there is a regulatory hierarchy in which developmental inputs, not cell cycle inputs, control the timing of string transcription and hence cell cycle progression.

Animals↗
PubMed2005

Quantitative gait analysis in Parkinson's disease: comparison with a healthy control group.

OBJECTIVE: To compare gait parameters in Parkinson's disease (PD) during the on-phase of medication cycle with those of healthy elderly control subjects. DESIGN: A group-comparison study. SETTING: Gait analysis laboratory of a university hospital. PARTICIPANTS: Fifteen patients with PD and 9 healthy elderly controls. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Spatiotemporal, kinematic, and kinetic gait parameters. RESULTS: The PD spatiotemporal results showed a significant reduction in step length and walking velocity compared with controls. In the kinematics, the major feature of the PD group was a markedly reduced ankle plantarflexion excursion (at 50%-60% of the gait cycle). Most important, the kinetics showed reduced ankle push-off power and hip pull-off power. Unlike the control subjects, the patients with PD did not show any correlation between ankle generation (push-off) power and stride length ( r =.19) or with gait speed ( r =.29). Correction for walking velocity did not result in significant changes in the kinetics between the groups. CONCLUSIONS: Reduced ankle (push-off) power generation and reduced hip flexion (pull-off) power persisted in PD gait despite being tested in the on-phase of the medication cycle. Lack of a correlation between ankle and hip power generation and walking velocity suggests that peripheral and central factors contribute to lack of forward progression. Patients with PD may benefit from intervention strategies that correct the kinematic and the kinetic gait components.

Aged↗
PubMed2005

Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling.

Vasculogenesis, the de novo growth of the primary vascular network from initially dispersed endothelial cells, is the first step in the development of the circulatory system in vertebrates. In the first stages of vasculogenesis, endothelial cells elongate and form a network-like structure, called the primary capillary plexus, which subsequently remodels, with the size of the vacancies between ribbons of endothelial cells coarsening over time. To isolate such intrinsic morphogenetic ability of endothelial cells from its regulation by long-range guidance cues and additional cell types, we use an in vitro model of human umbilical vein endothelial cells (HUVEC) in Matrigel. This quasi-two-dimensional endothelial cell culture model would most closely correspond to vasculogenesis in flat areas of the embryo like the yolk sac. Several studies have used continuum mathematical models to explore in vitro vasculogenesis: such models describe cell ensembles but ignore the endothelial cells' shapes and active surface fluctuations. While these models initially reproduce vascular-like morphologies, they eventually stabilize into a disconnected pattern of vascular "islands." Also, they fail to reproduce temporally correct network coarsening. Using a cell-centered computational model, we show that the endothelial cells' elongated shape is key to correct spatiotemporal in silico replication of stable vascular network growth. We validate our simulation results against HUVEC cultures using time-resolved image analysis and find that our simulations quantitatively reproduce in vitro vasculogenesis and subsequent in vitro remodeling.

Blood Vessels↗
PubMed2002

Isolation and characterization of runxa and runxb, zebrafish members of the runt family of transcriptional regulators.

OBJECTIVE: The AML/RUNX family of transcription factors plays important roles in hematopoiesis, neurogenesis, bone development, and segmentation in vertebrate embryos. The aim of this study was to isolate runt-related genes in a genetically and embryologically exploitable system, the zebrafish, and characterize their function during hematopoietic development. MATERIALS AND METHODS: Two runt-related genes were isolated by degenerate PCR and standard library screening, and a radiation hybrid panel, T51 RH, was used to resolve their chromosomal localization. In situ hybridization demonstrated their expression whereas their transcriptional activity was assessed using an AML1-responsive reporter gene in the MLA 144 T-cell line. RESULTS: We isolated the zebrafish runxa and runxb cDNAs, which encode proteins highly homologous to the human and murine Runx1 (AML1) and Runx3 (AML2) proteins. In contrast to a recent report, we detected runxa expression in both hematopoietic and neural tissues of the developing zebrafish. runxa transcripts first appear during segmentation in bilateral mesodermal cells that coexpress one of the earliest blood and endothelial cell markers, scl/tal-1. By 24 hours postfertilization (hpf), runxa transcripts are seen in the ventral wall of the dorsal aorta. Hematopoietic runxa expression is lost in cloche mutants, which are defective in blood and endothelial cell formation. runxb transcripts are seen in nonhematopoietic domains. Both Runxa and Runxb transactivate an AML1-responsive human promoter in hematopoietic cells. Genomic localization studies demonstrate that runxa is located on linkage group 1 (LG1), and the runxb gene is located on LG13. CONCLUSIONS: Our gene expression analysis strongly suggests that both the functional and spatial aorta-gonad-mesonephros (AGM) region has been conserved throughout evolution. Our runxa spatiotemporal expression data shed light on the role of vertebrate Runx1/AML1 in primitive vs definitive hematopoietic development.

Amino Acid Sequence↗
PubMed2006

Imaging diacylglycerol dynamics at organelle membranes.

Fluorescence imaging is a powerful technique to visualize spatiotemporal dynamics of biomolecules in living cells. We describe fluorescent indicators for a lipid second messenger, diacylglycerol (DAG), which allow the localized analysis of DAG dynamics at subcellular membranes. We have thus pinpointed that DAG concentrations increase and/or decrease at not only the plasma membrane but also organelle membranes such as endomembranes and mitochondrial outer membranes.

Animals↗
PubMed1999

Characterization of the Shank family of synaptic proteins. Multiple genes, alternative splicing, and differential expression in brain and development.

Shank1, Shank2, and Shank3 constitute a family of proteins that may function as molecular scaffolds in the postsynaptic density (PSD). Shank directly interacts with GKAP and Homer, thus potentially bridging the N-methyl-D-aspartate receptor-PSD-95-GKAP complex and the mGluR-Homer complex in synapses (Naisbitt, S., Kim, E., Tu, J. C. , Xiao, B., Sala, S., Valtschanoff, J., Weinberg, R. J., Worley, P. F., and Sheng, M. (1999) Neuron 23, 569-582; Tu, J. C., Xiao, B., Naisbitt, S., Yuan, J. P., Petralia, R. S., Brakeman, P., Doan, A., Aakalu, V. K., Lanahan, A. A., Sheng, M., and Worley, P. F. (1999) Neuron 23, 583-592). Shank contains multiple domains for protein-protein interaction including ankyrin repeats, an SH3 domain, a PSD-95/Dlg/ZO-1 domain, a sterile alpha motif domain, and a proline-rich region. By characterizing Shank cDNA clones and RT-PCR products, we found that there are four sites for alternative splicing in Shank1 and another four sites in Shank2, some of which result in deletion of specific domains of the Shank protein. In addition, the expression of the splice variants is differentially regulated in different regions of rat brain during development. Immunoblot analysis of Shank proteins in rat brain using five different Shank antibodies reveals marked heterogeneity in size (120-240 kDa) and differential spatiotemporal expression. Shank1 immunoreactivity is concentrated at excitatory synaptic sites in adult brain, and the punctate staining of Shank1 is seen in developing rat brains as early as postnatal day 7. These results suggest that alternative splicing in the Shank family may be a mechanism that regulates the molecular structure of Shank and the spectrum of Shank-interacting proteins in the PSDs of adult and developing brain.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Differential effects of interleukin-1beta and transforming growth factor-beta1 on the expression of the inflammation-associated protein, ADAMTS-1, in human decidual stromal cells in vitro.

BACKGROUND: The pro-inflammatory cytokine, interleukin-1 beta (IL-1beta) promotes the proteolytic degradation of the extracellular matrix (ECM) of maternal decidua, a critical step in pregnancy that is counterbalanced by the expression of the anti-inflammatory cytokine, transforming growth factor-beta 1 (TGF-beta1). Recently, the inflammation-associated protein, ADAMTS-1, a member of the ADAMTS (A Disintegrin And Metalloproteinase with ThromboSpondin repeats) gene family of metalloproteinases has been assigned a central role in the formation and organization of tissues. In view of these observations, we have hypothesized that ADAMTS-1 contributes to the cytokine-mediated remodelling of decidual ECM. METHODS: The spatiotemporal expression of ADAMTS-1 in human endometrium was examined by immunohistochemistry. A quantitative-competitive (QC)-PCR strategy and western blot analysis was then employed to determine whether IL-1beta and TGF-beta1 regulate ADAMTS-1 mRNA and protein expression levels in primary cultures of stromal cells isolated from first trimester decidua. RESULTS: ADAMTS-1 expression is associated with decidualization of the endometrial stroma in vivo. IL-1beta increased whereas TGF-beta1 decreased ADAMTS-1 mRNA and protein levels in decidual stromal cell cultures in a concentration- and time-dependent manner. These regulatory effects were attenuated by function-perturbing antibodies specific for either cytokine. CONCLUSION: IL-1beta and TGF-beta1 differentially regulate ADAMTS-1 expression in human decidual stromal cells.

ADAM Proteins↗
PubMed2006

Microscopic features of moving traffic jams.

Empirical and numerical microscopic features of moving traffic jams are presented. Based on a single vehicle data analysis, it is found that within wide moving jams, i.e., between the upstream and downstream jam fronts there is a complex microscopic spatiotemporal structure. This jam structure consists of alternations of regions in which traffic flow is interrupted and flow states of low speeds associated with "moving blanks" within the jam. Moving blanks within a wide moving jam resemble electron holes in the valence band of semiconductors: As the moving blanks that propagate upstream appear due to downstream vehicle motion within the jam, so appearance of electron holes moving with the electric field results from electron motion against the electric field in the valence band of semiconductors. Empirical features of moving blanks are found. Based on microscopic models in the context of the Kerner's three-phase traffic theory, physical reasons for moving blanks emergence within wide moving jams are disclosed. Microscopic nonlinear effects of moving jam emergence, propagation, and dissolution as well as a diverse variety of hysteresis effects in freeway traffic associated with phase transitions and congested traffic propagation are numerically investigated. Microscopic structure of moving jam fronts is numerically studied and compared with empirical results.

Journal Article↗
PubMed2004

Neuronal avalanches are diverse and precise activity patterns that are stable for many hours in cortical slice cultures.

A major goal of neuroscience is to elucidate mechanisms of cortical information processing and storage. Previous work from our laboratory (Beggs and Plenz, 2003) revealed that propagation of local field potentials (LFPs) in cortical circuits could be described by the same equations that govern avalanches. Whereas modeling studies suggested that these "neuronal avalanches" were optimal for information transmission, it was not clear what role they could play in information storage. Work from numerous other laboratories has shown that cortical structures can generate reproducible spatiotemporal patterns of activity that could be used as a substrate for memory. Here, we show that although neuronal avalanches lasted only a few milliseconds, their spatiotemporal patterns were also stable and significantly repeatable even many hours later. To investigate these issues, we cultured coronal slices of rat cortex for 4 weeks on 60-channel microelectrode arrays and recorded spontaneous extracellular LFPs continuously for 10 hr. Using correlation-based clustering and a global contrast function, we found that each cortical culture spontaneously produced 4736 +/- 2769 (mean +/- SD) neuronal avalanches per hour that clustered into 30 +/- 14 statistically significant families of spatiotemporal patterns. In 10 hr of recording, over 98% of the mutual information shared by these avalanche patterns were retained. Additionally, jittering analysis revealed that the correlations between avalanches were temporally precise to within +/-4 msec. The long-term stability, diversity, and temporal precision of these avalanches indicate that they fulfill many of the requirements expected of a substrate for memory and suggest that they play a central role in both information transmission and storage within cortical networks.

Action Potentials↗
PubMed2005

Brain signatures of meaning access in action word recognition.

The brain basis of action words may be neuron ensembles binding language- and action-related information that are dispersed over both language- and action-related cortical areas. This predicts fast spreading of neuronal activity from language areas to specific sensorimotor areas when action words semantically related to different parts of the body are being perceived. To test this, fast neurophysiological imaging was applied to reveal spatiotemporal activity patterns elicited by words with different action-related meaning. Spoken words referring to actions involving the face or leg were presented while subjects engaged in a distraction task and their brain activity was recorded using high-density magnetoencephalography. Shortly after the words could be recognized as unique lexical items, objective source localization using minimum norm current estimates revealed activation in superior temporal (130 msec) and inferior frontocentral areas (142-146 msec). Face-word stimuli activated inferior frontocentral areas more strongly than leg words, whereas the reverse was found at superior central sites (170 msec), thus reflecting the cortical somatotopy of motor actions signified by the words. Significant correlations were found between local source strengths in the frontocentral cortex calculated for all participants and their semantic ratings of the stimulus words, thus further establishing a close relationship between word meaning access and neurophysiology. These results show that meaning access in action word recognition is an early automatic process ref lected by spatiotemporal signatures of word-evoked activity. Word-related distributed neuronal assemblies with specific cortical topographies can explain the observed spatiotemporal dynamics reflecting word meaning access.

Acoustic Stimulation↗
PubMed2025

Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.

Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: &#x2022; Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. &#x2022; Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. &#x2022; Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.

Rhizosphere↗
PubMed2004

Molecular profiling: gene expression reveals discrete phases of lens induction and development in Xenopus laevis.

PURPOSE: Experimental tissue transplant studies reveal that lens development is directed by a series of early and late inductive interactions. These interactions impart a growing lens-forming bias within competent presumptive lens ectoderm that leads to specification and the commitment to lens fate. Relatively few genes are known which control these events. Identification of additional genes expressed during lens development may reveal key players in these processes and help to characterize these tissue properties. METHODS: A large suite of genes has been isolated that are expressed during the process of cornea-lens transdifferentiation (lens regeneration) in Xenopus laevis. Many of these genes are also expressed during embryonic lens development. Genes were selected for expression analysis via in situ hybridization. This group consisted of clones with possible roles in cell determination and differentiation as well as novel clones without previous identities. The spatiotemporal expression of these genes in conjunction with previously described genes were correlated with key events during embryonic lens formation. RESULTS: Eighteen of the thirty clones analyzed via in situ hybridization demonstrated observable expression in the developing lens. These genes were initially expressed in the presumptive lens ectoderm at a variety of timepoints throughout development. Expression is restricted to discrete time intervals during lens development. However, in most cases, expression was maintained throughout lens development after being initially upregulated. CONCLUSIONS: The expression of these genes suggests that a genetic hierarchy exists in which an increasing number of genes are upregulated and their expression is maintained throughout lens development. Suites of genes appear to be upregulated at specific timepoints during development, correlating with stages of lens induction, specification, commitment, lens placode formation, and lens differentiation, while suites at additional timepoints suggest that other, previously unreported stages exist as well. This analysis provides a genetic framework for characterizing these processes of lens development.

Animals↗