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PubMed2002

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.

Animals↗
PubMed2006

Fluorescence imaging of cardiac propagation: spectral properties and filtering of optical action potentials.

Fluorescence imaging using voltage-sensitive dyes is an important tool for studying electrical propagation in the heart. Yet, the low amplitude of the voltage-sensitive component in the fluorescence signal and high acquisition rates dictated by the rapid propagation of the excitation wave front make it difficult to achieve recordings with high signal-to-noise ratios. Although spatially and temporally filtering the acquired signals has become de facto one of the key elements of optical mapping, there is no consensus regarding their use. Here we characterize the spatiotemporal spectra of optically recorded action potentials and determine the distortion produced by conical filters of different sizes. On the basis of these findings, we formulate the criteria for rational selection of filter characteristics. We studied the evolution of the spatial spectra of the propagating wave front after epicardial point stimulation of the isolated, perfused right ventricular free wall of the pig heart stained with di-4-ANEPPS. We found that short-wavelength (<3 mm) spectral components represent primarily noise and surface features of the preparation (coronary vessels, fat, and connective tissue). The time domain of the optical action potential spectrum also lacks high-frequency components (>100 Hz). Both findings are consistent with the reported effect of intrinsic blurring caused by light scattering inside the myocardial wall. The absence of high-frequency spectral components allows the use of aggressive low-pass spatial and temporal filters without affecting the optical action potential morphology. We show examples where the signal-to-noise ratio increased up to 150 with <3% distortion. A generalization of our approach to the rational filter selection in various applications is discussed.

Action Potentials↗
PubMed2005

Acceleration of functional reentry by rapid pacing in anisotropic cardiac monolayers: formation of multi-wave functional reentries.

OBJECTIVE: Attempts to cardiovert tachycardia by rapid point pacing can sometimes result in transient or stable increase of the heart rate (acceleration), changed ECG morphology, and/or fibrillation. The goal of this study was to investigate the effect of rapid pacing on the dynamics of functional reentry in monolayer cultures of cardiac cells. METHODS: Fully confluent, uniformly anisotropic monolayers of neonatal rat ventricular myocytes were prepared using methods of microabrasion. Cells were paced by a point electrode at rest and during functional reentry, and membrane voltages were optically mapped. RESULTS: Point pacing readily induced single loop anisotropic functional reentry with monomorphic optical pseudo-ECG (pECG) and average rotation period of 193+/-52 ms (n=71 monolayers). Attempts to cardiovert reentry by rapid pacing at rates 10-50% faster than the reentry rate were successful in 57/71 monolayers. In 14/71 monolayers, the number of rotating waves was stably increased by 1 to 4, yielding a 10-70% acceleration of pECG rate and change to a different monomorphic or polymorphic pECG. The resulting multi-wave functional reentries were classified based on the number and direction of their rotating waves. The higher the number of waves in the multi-wave reentry, the more accelerated was the rate of cell firing in the monolayer. Importantly, stable acceleration was only inducible in monolayers with relatively deep and broad conduction velocity restitution relationships. Reapplication of point pacing further accelerated, decelerated, or eventually terminated the reentrant activity. CONCLUSIONS: These results suggest that stable multiplication of rotating waves in conjunction with a deep and broad conduction velocity restitution relationship is a possible mechanism for stable acceleration of functional reentry by rapid pacing.

Animals↗
PubMed2000

Stable microreentrant sources as a mechanism of atrial fibrillation in the isolated sheep heart.

BACKGROUND: Atrial fibrillation (AF) has traditionally been described as aperiodic or random. Yet, ongoing sources of high-frequency periodic activity have recently been suggested to underlie AF in the sheep heart. Our objective was to use a combination of optical and bipolar electrode recordings to identify sites of periodic activity during AF and elucidate their mechanism. METHODS AND RESULTS: AF was induced by rapid pacing in the presence of 0.1 to 0.5 micromol/L acetylcholine in 7 Langendorff-perfused sheep hearts. We used simultaneous optical mapping of the right and left atria (RA and LA) and frequency sampling of optical and bipolar electrode recordings (including a roving electrode) to identify sites having the highest dominant frequency (DF). Rotors were identified from optical recordings, and their rotation period, core area, and perimeter were measured. In all, 35 AF episodes were analyzed. Mean LA and RA DFs were 14.7+/-3.8 and 10.3+/-2.1 Hz, respectively. Spatiotemporal periodicity was seen in the LA during all episodes. In 5 of 7 experiments, a single site having periodic activity at the highest DF was localized. The highest DF was most often (80%) localized to the posterior LA, near or at the pulmonary vein ostium. Rotors (n=14) were localized on the LA. The mean core perimeter and area were 10.4+/-2.8 mm and 3.8+/-2.8 mm(2), respectively. CONCLUSIONS: Frequency sampling allows rapid identification of discrete sites of high-frequency periodic activity during AF. Stable microreentrant sources are the most likely underlying mechanism of AF in this model.

Animals↗
PubMed1980

Segregation of optic fibre projections into eye-specific bands in dually innervated tecta in Xenopus.

The restoration of the retinotectal projections following metamorphic bilateral optic nerve sections was studied in Xenopus 20 weeks after operation, using [3H]proline autoradiography and electrophysiological mapping. Optic fibre projections from each eye to both tecta segregated into eye-specific termination bands with some overlap at the borders. The bands were arranged rostrocaudally in the tecta such that each eye had an alternating representation. Despite the segregation of the optic fibres, each eye had a complete visual (retinal) projection with the normal nasotemporal and dorsoventral polarities of the visual field maintained. The results suggest competition for preferred terminal sites between the two sets of optic fibres in dually innervated tecta.

Animals↗
PubMed1999

Direct mapping of bioelectric activity.

Much can be learned about physiological function in heart, brain, and other tissues from measuring the electrical activity that mediates mechanical or neural phenomena. The study of electrophysiology has progressed from acquisition of a single or a few channels to hundreds of signals acquired simultaneously. Data acquisition, signal processing, and visualization in electrophysiology have benefitted from the parallel advances in electronics and computing hardware and software. The two primary technologies for mapping electrical activity at many sites are electrical, using electrodes directly placed on tissue, and optical, using voltage sensitive dyes to estimate membrane parameters. Each is valuable and provides information that is complementary to the other. This article is a description of the current state of electrical and optical mapping.

Animals↗
PubMed1998

Demonstration of a founder effect and fine mapping of dominant optic atrophy locus on 3q28-qter by linkage disequilibrium method: a study of 38 British Isles pedigrees.

Dominant optic atrophy, a hereditary optic neuropathy causing decreased visual acuity, colour vision deficits, a centro-caecal scotoma and optic nerve pallor, has been mapped to a genetic interval of 1.4 cM between loci D3S3669 and D3S3562 on chromosome 3q28-qter. In order to further refine the critical disease interval, and to test the power of haplotype analysis and linkage disequilibrium mapping, we identified a total of 38 families with dominant optic atrophy, unrelated on the basis of genealogy, from a data base of genetic eye disease families originating from the British Isles. They were studied with 12 highly polymorphic microsatellite markers spanning a region of 12 cM around the dominant optic atrophy locus (OPA1). Allelic frequency analysis [chi-squared test, likelihood ratio test (LRT) and P values] and haplotype parsimony analysis showed evidence of a founder effect in 36 of the 38 pedigrees. Six markers (D3S3669, D3S1523, D3S3642, D3S2305, D3S3590 and D3S3562), spanning 1.4 cM across the disease-associated region, demonstrated significant linkage disequilibrium by LRT (P < 0.05). A peak LRT value of 10.86 (P < 0.0005, lambda = 0.4) occurred at D3S3669. On linkage disequilibrium multipoint analysis the maximum lod score of 8.01 is achieved at D3S1523, and 95% confidence intervals suggest that OPA1 lies within ca. 400 kb of D3S1523.

Alleles↗
PubMed2006

Optical force field mapping in microdevices.

We present a method for characterizing microscopic optical force fields. Two dimensional vector force maps are generated by measuring the optical force applied to a probe particle for a grid of particle positions. The method is used to map out the force field created by the beam from a lensed fiber inside a liquid filled microdevice. We find transverse gradient forces and axial scattering forces on the order of 2 pN per 10 mW laser power which are constant over a considerable axial range (>35 microm). These findings suggest future useful applications of lensed fibers for particle guiding/sorting. The propulsion of a small particle at a constant velocity of 200 microm s(-1) is shown.

Lasers↗
PubMed2006

Optical images of dose distributions in Gel-Fricke: dosimetric performances of the gel.

The purpose of this work was to examine the dosimetric performances of the radiochromic Fricke-Agarose-Xylenol Orange gel by optical measurements in order to perform dose reconstructions, in view of a future development for 3-D maps. Optical images and dose-response curves of the gel were obtained by a CCD-based device, originally designed for reading radiochromic films, that was modified to meet the optical properties of the dosemeter. With a resolution of 0.18 x 0.18 mm the optimum range of doses in which per cent uncertainty is lower than 2% was 3-10 Gy. The minimum detectable dose, estimated as the absorbed dose corresponding to 3 SD above background, was 0.1 Gy. With a resolution of 1.98 x 1.98 mm the optimum range of doses in which per cent uncertainty is lower than 2% was 0.3-10 Gy. The minimum detectable dose, estimated as the absorbed dose corresponding to 3 SD above background, was 0.015 Gy. The comparison with alanine dosemeters in the dose range 7-10 Gy showed agreement within a few per cent and the same agreement was observed for the comparison with TLD in the range 1-3 Gy.

Dose-Response Relationship, Radiation↗
PubMed1995

Optical imaging of intrinsic signals as a tool to visualize the functional architecture of adult and developing visual cortex.

One of the most common principles of cortical organization is that neurons with similar response properties are clustered together in space. Thereby the environment is represented in an orderly fashion on the cortical surface in a so-called "cortical map". In primary visual cortex, for instance, neurons with similar orientation preferences are grouped together, forming the orientation preference map. Optical imaging of intrinsic signals allows to investigate the organization of such maps in vivo. Neuronal activity was measured utilizing the fact that the transition from oxy-hemoglobin to hemoglobin in active brain areas can be detected optically by recording changes in light reflectance with a high resolution CCD-camera. When using this technique to look at the exact patterning of orientation preference maps in cat visual cortex a novel principle for the organization of cortical maps was observed: orientation was not organized in parallel bands as had previously been thought but iso-orientation domains were organized radially; orientations from 0 to 180 degrees were laid out in a pinwheel-like fashion around singularities which we termed "orientation-centers". After observing pinwheel patterns in orientation preference maps in adult cat visual cortex it was also investigated how these meticulously arranged maps develop in the cortex of young kittens. Performing chronical recordings in kittens from the age of postnatal day 17 on we were able to observe how orientation maps form already during the third week of life and--under normal conditions--remain largely unchanged thereafter.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2006

Mechanisms of atrial tachyarrhythmia induction in a canine model of autonomic tone fluctuation.

BACKGROUND: The purpose of this study was to investigate the effect of cholinergic modulation in the presence of increased adrenergic tone (i. e., autonomic fluctuation) on atrial tachyarrhythmia (AT) induction. METHODS AND RESULTS: High-resolution optical mapping was used to measure action potentials from the left atrium in isolated arterially perfused canine atrial preparations. Optical recordings were made in the presence of isoproterenol during electrical stimulation of a fat pad at the right pulmonary veinatrial junction (Group I, n = 6), during electrical stimulation of a fat pad locating the superior vena cava contacted by the right pulmonary artery (Group II, n = 4), and during acetylcholine (ACh; Group III, n = 4) infusion. In the presence of isoproterenol,each of the three different transitory cholinergic interventions induced spontaneous AT in all preparations. In Group I, AT induced from the right atrium was sustained. However, AT induced from the left atrium was not sustained (RRB) in Group I. In Groups II and III, AT induced from the left atrium as well as the right atrium were also sustained (BAF-AT). The A1A2 coupling interval was shorter when BAF-AT was induced than it was when RRB was induced. Mean cycle length of repetitive focal excitation was shorter during the initiation of BAF-AT compared to RRB. Isochrone maps during the initiation of AT demonstrated a macroreentry with lines of conduction block following a single extrasystole (27 %) and focal repetitive excitation (73 %). CONCLUSIONS: These results suggest that transitory cholinergic activation in the presence of increased adrenergic drive in the left atrium causes a single premature extrasystole with a short coupling interval and a focal repetitive excitation with a short cycle length, which favors the generation of AT originating from the left atrium.

Adrenergic Fibers↗
PubMed2002

Frequency analysis of ventricular fibrillation in Swine ventricles.

It has been suggested from frequency analysis that cardiac fibrillation is driven by stable intramural reentry, with wavebreak occurring due to failure of 1:1 propagation. We tested this hypothesis with a combined experimental and theoretical approach. Optical mapping was performed on epicardial, endocardial, and transmural cut surfaces of fibrillating swine ventricles. Wavelets were characterized, the frequency content of optical signals analyzed, and space-time plots (STPs) constructed to detect Wenckebach-like conduction. The findings were compared with simulations in 2D and 3D cardiac tissue using the Luo-Rudy action potential model. The incidence of reentry in the cut transmural surface (11.8% in right ventricle, 14.3% in left ventricle) was similar to that on the endocardial surface (13.1%, P=NS) but greater than on the epicardial surface (7.7%, P<0.01). Frequency spectra of optically recorded membrane voltage were organized into spatial domains with the same dominant frequency, but these domains were nonstationary. In STPs, pseudo-2:1 conduction block was caused by double potentials arising when reentry occurred on the recording site rather than true Wenckebach conduction. The latter was observed in 11 of 166 STPs but did not occur at borders of high-to-low frequency domains. In simulations, similar findings were obtained when action potential duration (APD) restitution slope was steep. Stationary dominant frequency domains with Wenckebach conduction patterns were observed only in the presence of shallow APD restitution slope and marked nonuniform tissue heterogeneity. In conclusion, stable intramural reentry as the engine of fibrillation was not observed. Our findings support the idea that dynamic wavebreak plays a fundamental role in the generation and maintenance of ventricular fibrillation.

Action Potentials↗
PubMed2019

The 22q11 low copy repeats are characterized by unprecedented size and structural variability.

Low copy repeats (LCRs) are recognized as a significant source of genomic instability, driving genome variability and evolution. The Chromosome 22 LCRs (LCR22s) mediate nonallelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS). However, LCR22s are among the most complex regions in the genome, and their structure remains unresolved. The difficulty in generating accurate maps of LCR22s has also hindered localization of the deletion end points in 22q11DS patients. Using fiber FISH and Bionano optical mapping, we assembled LCR22 alleles in 187 cell lines. Our analysis uncovered an unprecedented level of variation in LCR22s, including LCR22A alleles ranging in size from 250 to 2000 kb. Further, the incidence of various LCR22 alleles varied within different populations. Additionally, the analysis of LCR22s in 22q11DS patients and their parents enabled further refinement of the rearrangement site within LCR22A and -D, which flank the 22q11 deletion. The NAHR site was localized to a 160-kb paralog shared between the LCR22A and -D in seven 22q11DS patients. Thus, we present the most comprehensive map of LCR22 variation to date. This will greatly facilitate the investigation of the role of LCR variation as a driver of 22q11 rearrangements and the phenotypic variability among 22q11DS patients.

22q11 Deletion Syndrome↗
PubMed2001

Dynamics of intramural and transmural reentry during ventricular fibrillation in isolated swine ventricles.

The intramural dynamics of ventricular fibrillation (VF) remain poorly understood. Recent investigations have suggested that stable intramural reentry may underlie the mechanisms of VF. We performed optical mapping studies of VF in isolated swine right ventricles (RVs) and left ventricles (LVs). Nine RV walls were cut obliquely in their distal edge exposing the transmural surface. Six LV wedge preparations were also studied. Results showed that intramural reentry was present. In RV, 28 of 44 VF episodes showed reentry; 15% of the activation pathways were reentrant. Except for 4 episodes, reentry was transmural, involving subendocardial structures as the papillary muscle (PM) or trabeculae. In LV, reentry was observed in 27 of 27 VF episodes; 23% of the activations were part of reentrant pathways (P<0.05 compared with RV). All LV reentrant pathways were truly intramural (confined to the wall) and were frequently located at the PM insertion. In both ventricles, reentry was spatially and temporally unstable. Histological studies showed abrupt changes in fiber orientation at sites of reentry and wave splitting. Connexin 40 immunostaining demonstrated intramyocardial Purkinje fibers at sites of reentry in the PM root and around endocardial trabeculae. Our results confirm that reentry is frequent-but unstable-in the myocardial wall during VF. In RV, reentry is mostly transmural and requires participation of subendocardial structures. The LV has a greater incidence of reentry and is intramural. Anisotropic anatomic structures played key roles in the generation of wave splitting and in the maintenance of reentry.

Animals↗
PubMed2006

Quantitative analysis of brain optical images with 2D C0 complexity measure.

Optical imaging based on intrinsic signals is a powerful method to visualize the activities of neural assembly in the cortex of animals in vivo, especially the detailed functional architecture of the visual cortex. Here, a new index, two-dimensional (2D) C0 complexity has been used to give a quantitative measure of the spatial pattern of the neural activity in orientation maps optically recorded from the visual cortex of cats globally. Results show that 2D C0 complexity could be employed to reveal the dynamic process of generating an orientation map in the visual cortex, and describe the variance of the neural responses in cortical area 17 under high and normal intraocular pressure. This suggests that 2D C0 could be used as a new quantitative measure for analyzing the intrinsic signal optical images.

Algorithms↗
PubMed2006

Orientation selectivity in the common marmoset (Callithrix jacchus): the periodicity of orientation columns in V1 and V2.

Orientation selectivity is a ubiquitous property of the primary visual cortex of mammals. Within the primate, orientation selectivity is arranged into vertical columns that are organized into a regular patchy pattern. Previous studies, in old world primates, have noted an anisotropy in this arrangement that appears to be due to the presence of ocular dominance columns within the same tissue. In addition, orientation selective responses appear to be arranged into bands of activity within the adjoining extrastriate region V2. Little is known about the precise arrangement of orientation columns within V2. In this study, we examined the layout of orientation columns within both V1 and V2 of a new world primate, the common marmoset, using optical imaging. New world primates have the advantage that, unlike the macaque, V2 exists on the cortical surface, a requirement for this form of optical mapping. We found the arrangement of orientation columns to be isotropic within marmoset V1 with an average repeat distance of around 575 mum, smaller than the repeat distance previously reported for the macaque. We found no evidence of ocular dominance within the animals tested supporting the claim that ocular dominance columns when present distort the mapping of orientation in V1. In V2 we found that orientation columns were larger and as in other primates were represented in discrete bands throughout V2. Orientation columns were spaced on average around 1 mm apart. This suggests that, at least in the marmoset, the visual system maps orientation at a different scale within V1 and V2.

Animals↗
PubMed1991

Early visual deprivation results in a degraded motor map in the optic tectum of barn owls.

The optic tectum contains a precise map of orienting movements: the size and direction of movements of the eyes, head, and/or body vary systematically with the locus of neural activation within the tectum. In adult animals, this motor map aligns closely with the tectal map of visual space. This study addressed the question of whether the motor map develops entirely independently of visual experience. We found that in barn owls (Tyto alba) raised without vision, although a tectal map of head movement develops, its topography and alignment with the map of visual (and auditory) space are abnormal. The results demonstrate that during early life vision is necessary either to maintain or to guide the development of a normal tectal motor map.

Animals↗
PubMed2003

Effects of electroporation on optically recorded transmembrane potential responses to high-intensity electrical shocks.

The outcome of defibrillation shocks is determined by the nonlinear transmembrane potential (DeltaVm) response induced by a strong external electrical field in cardiac cells. We investigated the contribution of electroporation to DeltaVm transients during high-intensity shocks using optical mapping. Rectangular and ramp stimuli (10-20 ms) of different polarities and intensities were applied to the rabbit heart epicardium during the plateau phase of the action potential (AP). DeltaVm were optically recorded under a custom 6-mm-diameter electrode using a voltage-sensitive dye. A gradual increase of cathodal and well as anodal stimulus strength was associated with 1) saturation and subsequent reduction of DeltaVm; 2) postshock diastolic resting potential (RP) elevation; and 3) postshock AP amplitude (APA) reduction. Weak stimuli induced a monotonic DeltaVm response and did not affect the RP level. Strong shocks produced a nonmonotonic DeltaVm response and caused RP elevation and a reduction of postshock APA. The maximum positive and maximum negative DeltaVm were recorded at 170 +/- 20 mA/cm2 for cathodal stimuli and at 240 +/- 30 mA/cm2 for anodal stimuli, respectively (means +/- SE, n = 8, P = 0.003). RP elevation reached 10% of APA at a stimulus strength of 320 +/- 40 mA/cm2 for both polarities. Strong ramp stimuli (20 ms, 600 mA/cm2) induced a nonmonotonic DeltaVm response, reaching the same largest positive and negative values as for rectangular shocks. The transition from monotonic to nonmonotonic morphology correlates with RP elevation and APA reduction, which is consistent with cell membrane electroporation. Strong shocks resulted in propidium iodide uptake, suggesting sarcolemma electroporation. In conclusion, electroporation is a likely explanation of the saturation and nonmonotonic nature of cellular responses reported for strong electric stimuli.

Action Potentials↗