Image reconstruction of optical attenuation coefficient variation in biological tissues

A procedure for non-invasive imaging of the optical attenuation coefficient variation of in vivo thick organs/tissues is developed. The laser back-scattered surface profiles at various locations of human forearm, by multi-probe reflectometer, are measured. These profiles are matched by iterative procedure, with that as obtained by Monte Carlo simulation and the corresponding values of attenuation coefficient (equal to the sum of absorption and reduced scattering coefficients) are determined. By interpolation of this data a 100 x 100 grid is constructed and after median filtering of this data a color-coded image of the variability of the optical attenuation coefficient of the forearm is obtained. These images in different subjects show variation due to change in overall tissue composition and blood pooling. This non-invasive imaging procedure may help in identifying the diseased affected regions in healthy tissues and in application of photodynamic therapy.     

Localization and characterization of tissue changes by laser backscattering imaging and Monte Carlo simulation

Laser backscattering from biological tissues depends on their composition and blood flow. The onset of the tissue abnormalities is associated with the change in composition at a specific location which may affect laser backscattering. The objective of the present work is to detect the compositional changes in tissue-equivalent phantom of fat, prepared by mixing paraffin wax with wax colors, and to characterize these in terms of their optical parameters. For this purpose these phantoms are scanned by a multi-probe non-contact automatic laser scanning system and images of the normalized backscattered intensity (NBI) are constructed. By scanning the background subtracted image of the phantom the location of the abnormality and its size from the full width at half maximum (FWHM) are determined. The data obtained by ultrasonic technique for localization of the abnormalities are in agreement with that as obtained by the present method. The optical parameters of the abnormality are obtained by matching the measured surface profiles of the abnormality with that of the profile obtained by Monte Carlo simulation. This analysis shows the possibility of detection of changes at the onset stage in tissues as required for planning of the photodynamic therapy.     

Development of biological tissue-equivalent phantoms for optical imaging

Optical characteristics of freshly isolated tissues depend on their color and composition. The surface backscattered profile, which account for the tissue compositional variation in fresh excised sheep's heart, lungs, bone and muscle, were measured by multi-probe reflectometer. Optical phantoms were prepared from paraffin wax by mixing a specific combination of wax color materials till the surface backscattered profile of these matched with that of the biological tissues. The optical parameters absorption coefficient (micro(a)), reduced scattering coefficient (micro(s)) and anisotropy factor (g) of these phantoms, are the same as that of biological tissues and are obtained by matching their surface backscattered profiles with that as simulated by Monte Carlo procedure. The maximum and minimum values of absorption coefficient are for the phantoms of lungs (1.0 cm(-1)) and muscle (0.02 cm(-1)), whereas, for scattering coefficient these values are for muscle (21.2 cm(-1)) and bone (13.08 cm(-1)).     

Optical parameters of embedded abnormalities in tissues as determined by Monte Carlo simulation

Photon propagation through tissue phantoms, made of heart, adipose, and spleen tissues was simulated by Monte Carlo procedure. To detect the presence of deep-seated abnormalities, phantoms of heart with adipose and spleen tissues embedded into it were created and simulations were performed to scan the tissue surface with a source and four detector model. Profiles drawn showed variation in parameters such as backscattered intensity in regions where adipose and spleen tissues were embedded. This study shows that depending on the type of embedded tissue the backscattered fraction as measured at 2 mm from the input fiber is altered. This is enhanced for adipose and decreased for spleen tissue. This is not only shown in scanned profiles on the surface but also in constructed images.     

Vibrotactile thresholds at the sole of the foot: Effect of vibration frequency and contact location

Studies of vibration perception in the glabrous skin of the human hand have identified four mechanoreceptor channels, with each channel showing characteristic variations in thresholds with variations in the frequency of vibration and the area of vibration excitation. To advance understanding of the channels mediating vibration perception on the sole of the foot, this study determined how thresholds depend on the frequency of vibration, the location on the foot (the big toe, the ball of the foot, and the heel), and the gap between a vibrating probe and a fixed surround. Thresholds at the three locations were obtained at the 12 preferred one-third octave centre frequencies from 20 to 250?Hz using a 6-mm diameter probe with both a 10-mm and a 20-mm diameter surround. With the 10-mm surround, the displacement thresholds at all three locations showed flat responses from 20 to 40?Hz. With both the 10-mm and the 20-mm surround, the displacement thresholds at the three locations showed “U-shaped” responses from 40 to 250?Hz. Relative to thresholds obtained with the 20-mm surround, thresholds obtained with the 10-mm surround were lower at the toe and the heel with 20- and 25-Hz vibration, but higher at the ball of the foot with 31.5- to 250-Hz vibration. It is concluded that absolute thresholds for the perception of vibration at the sole of the foot show important variations with location and with contact conditions and tend to be mediated by the NP I channel in the range from about 20 to 40?Hz and the P channel from about 40 to 250?Hz.     

Vibrotactile thresholds at the sole of the foot: effect of vibration frequency and contact location

Studies of vibration perception in the glabrous skin of the human hand have identified four mechanoreceptor channels, with each channel showing characteristic variations in thresholds with variations in the frequency of vibration and the area of vibration excitation. To advance understanding of the channels mediating vibration perception on the sole of the foot, this study determined how thresholds depend on the frequency of vibration, the location on the foot (the big toe, the ball of the foot, and the heel), and the gap between a vibrating probe and a fixed surround. Thresholds at the three locations were obtained at the 12 preferred one-third octave centre frequencies from 20 to 250 Hz using a 6-mm diameter probe with both a 10-mm and a 20-mm diameter surround. With the 10-mm surround, the displacement thresholds at all three locations showed flat responses from 20 to 40 Hz. With both the 10-mm and the 20-mm surround, the displacement thresholds at the three locations showed "U-shaped" responses from 40 to 250 Hz. Relative to thresholds obtained with the 20-mm surround, thresholds obtained with the 10-mm surround were lower at the toe and the heel with 20- and 25-Hz vibration, but higher at the ball of the foot with 31.5- to 250-Hz vibration. It is concluded that absolute thresholds for the perception of vibration at the sole of the foot show important variations with location and with contact conditions and tend to be mediated by the NP I channel in the range from about 20 to 40 Hz and the P channel from about 40 to 250 Hz.     

Optical parameters of embedded abnormalities in tissues as determined by Monte Carlo simulation

Photon propagation through tissue phantoms, made of heart, adipose, and spleen tissues was simulated by Monte Carlo procedure. To detect the presence of deep-seated abnormalities, phantoms of heart with adipose and spleen tissues embedded into it were created and simulations were performed to scan the tissue surface with a source and four detector model. Profiles drawn showed variation in parameters such as backscattered intensity in regions where adipose and spleen tissues were embedded. This study shows that depending on the type of embedded tissue the backscattered fraction as measured at 2?mm from the input fiber is altered. This is enhanced for adipose and decreased for spleen tissue. This is not only shown in scanned profiles on the surface but also in constructed images.     

Development of thermodynamic models for simulating probe dissociation profiles in fluorescence in situ hybridization

Stringency in ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH) is typically adjusted with formamide, and the optimum formamide concentration at which the probe can hybridize with the target rRNA, but not with rRNAs with mismatches, is to be found experimentally. This is a difficult task when target or closest non-target organisms are not available in pure culture, or when there are numerous non-targets of concern. The objective of this work was to formulate mechanistic models capable of simulating the effect of formamide on probe dissociation. Using a previously described equilibrium model of FISH [Yilmaz and Noguera (2004) Applied and Environmental Microbiology 70(12):7126-7139] as the basis, the effect of formamide on free energy changes of probe-target duplex formation (DeltaG(1)(0)) and folding of target region (DeltaG(3)(0)) was simulated to be linear, and models differing in the definitions of the slopes of these relationships (m(1) and m(3)) were calibrated using experimental dissociation profiles for 27 probes targeting the 16S rRNA of Escherichia coli (E. coli). A good level of predictive power was obtained when m(1) was linearly related to probe length and when m(3) was made proportional to DeltaG(3)(0). The effect of single mismatches on probe dissociation with formamide was also studied, although at a preliminary level. The expected changes in DeltaG(1)(0) with the introduction of mismatches were not sufficient to capture the overall trends of mismatched dissociation profiles. In conclusion, this study offers the first theoretical method to calculate dissociation profiles for perfectly matched probes, and suggests a direction to systematically evaluate the effect of formamide on mismatched probes.     

In vivo evidence against a role for adenosine in the exercise pressor reflex in humans.

The pressor response to exercise is of great importance in both physiology and pathophysiology. Whether endogenous adenosine is a trigger for this reflex remains controversial. Muscle interstitial adenosine concentration can be determined by microdialysis. However, there are indications that local muscle cell damage by the microdialysis probe confounds these measurements in exercising muscle. Therefore, we used the nucleoside uptake inhibitor dipyridamole as pharmacological tool to bypass this confounding. We used microdialysis probes to measure endogenous adenosine in forearm skeletal muscle of healthy volunteers during two cycles of 15 min of intermittent isometric handgripping. During the second contraction, dipyridamole (12 microg.min(-1).dl forearm(-1)) was administered into the brachial artery. Dipyridamole potentiated the exercise-induced increase in dialysate adenosine from 0.30 +/- 0.08 to 0.48 +/- 0.10 micromol/l (n = 9, P < 0.05), but it did not potentiate the exercise-induced increase in blood pressure. A time-control study without dipyridamole revealed no difference in exercise-induced increase in adenosine between both contractions (n = 8). To exclude the possibility that the dipyridamole-induced increase in dialysate adenosine originates from extravasation of increased circulating adenosine, we simultaneously measured adenosine with microdialysis probes in forearm muscle and antecubital vein. In a separate group of nine volunteers, simultaneous intrabrachial infusion of 100 microg.min(-1).dl(-1) dipyridamole and 5 microg.min(-1).dl(-1) adenosine increased dialysate adenosine from the intravenous but not the interstitial probe, indicating preserved endothelial barrier function for adenosine. We conclude that dipyridamole significantly inhibits uptake of interstitial adenosine without affecting the pressor response to exercise, suggesting that interstitial adenosine is not involved in the pressor response to rhythmic isometric exercise.     

Multiple components in restriction enzyme digests of mammalian (insectivore), avian and reptilian genomic DNA hybridize with murine immunoglobulin VH probes.

High molecular weight genomic DNAs isolated from an insectivore, Tupaia, and a representative reptilian, Caiman, and avian, Gallus, were digested with restriction endonucleases transferred to nitrocellulose and hybridized with nick-translated probes of murine VH genes. The derivations of the probes designated S107V (1) and mu 107V (2,3) have been described previously. Under conditions of reduced stringency, multiple hybridizing components were observed with Tupaia and Caiman; only mu mu 107V exhibited significant hybridization with the separated fragments of Gallus DNA. The nick-translated S107V probe was digested with Fnu4H1 and subinserts corresponding to the 5' and 3' regions both detected multiple hybridizing components in Tupaia and Caiman DNA. A 5' probe lacking the leader sequence identified the same components as the intact 5' probe, suggesting that VH coding regions distant as the reptilians may possess multiple genetic components which exhibit significant homology with murine immunoglobulin in VH regions.     

Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.     

Muscle temperature transients before, during, and after exercise measured using an intramuscular multisensor probe.

Seven subjects (1 woman) performed an incremental isotonic test on a Kin-Com isokinetic apparatus to determine their maximal oxygen consumption during bilateral knee extensions (Vo(2 sp)). A multisensor thermal probe was inserted into the left vastus medialis (middiaphysis) under ultrasound guidance. The deepest sensor (tip) was located approximately 10 mm from the femur and deep femoral artery (T(mu 10)), with additional sensors located 15 (T(mu 25)) and 30 mm (T(mu 40)) from the tip. Esophageal temperature (T(es)) was measured as an index of core temperature. Subjects rested in an upright seated position for 60 min in an ambient condition of 22 degrees C. They then performed 15 min of isolated bilateral knee extensions (60% of Vo(2 sp)) on a Kin-Com, followed by 60 min of recovery. Resting T(es) was 36.80 degrees C, whereas T(mu 10), T(mu 25), and T(mu 40) were 36.14, 35.86, and 35.01 degrees C, respectively. Exercise resulted in a T(es) increase of 0.55 degrees C above preexercise resting, whereas muscle temperature of the exercising leg increased by 2.00, 2.37, and 3.20 degrees C for T(mu 10), T(mu 25), and T(mu 40), respectively. Postexercise T(es) showed a rapid decrease followed by a prolonged sustained elevation approximately 0.3 degrees C above resting. Muscle temperature decreased gradually over the course of recovery, with values remaining significantly elevated by 0.92, 1.05, and 1.77 degrees C for T(mu 10), T(mu 25), and T(mu 40), respectively, at end of recovery (P < 0.05). These results suggest that the transfer of residual heat from previously active musculature may contribute to the sustained elevation in postexercise T(es).     

Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.     

A Comparison of the Use of In Vitro-Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment

Abstract Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro-transcribed and native rRNA indicated that, when in vitro-transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro-transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.     

Identification of cells by backscattered electron imaging of silver stained bulk tissues in scanning electron microscopy

Anuran tadpole tail muscle was stained en bloc by a modified light microscope silver stain for light microscopy and freeze-fractured in liquid nitrogen after partial dehydration with ethanol. The fractured specimens were observed in both secondary electron and backscattered electron modes in a scanning electron microscope. Since the cell nuclei specifically stained with silver provided high contrast against the unstained background due to atomic number contrast of backscattered electron image, various cells were easily identified by a comparison of secondary electron images and compositional images of backscattered electron signals.     

Validation of a model for prediction of skin temperatures in footwear

A model for foot skin temperature prediction was evaluated on the basis of 2 experiments on subjects at various environmental temperatures (light seated manual work at -10.7 degrees C (Study 1), and a short walking period in combination with standing and sitting at +2.8 degrees C, -11.8 degrees C and -24.6 degrees C (Study 2), with boots of 3 insulation levels. Insulation of the footwear was measured on a thermal foot model. Predicted and measured data showed a relatively good correlation (r = 0.87) at the 2 colder conditions in Study 2. The environmental temperature of 2.8 degrees C was not low enough at the chosen activity for a considerable foot skin temperature drop. In Study 1 the predicted temperature stayed higher for the whole exposure period and the difference between the predicted and the measured foot skin temperatures grew proportionally with time, while subsequent warm-up curves at room temperature were almost parallel. In Study 1 the correlation was 0.95. However, the paired t-test showed usually significant differences between measured and predicted foot skin temperatures. The insulation values from thermal foot measurements can be used in the model calculations. Lotens' foot model is lacking activity as direct input parameter, however, the blood flow is used instead (effect through Tcore). The Lotens foot model can give reasonable foot skin temperature values if the model limitations are considered. Due to the lack of activity level input, it will be difficult to make any good estimation of foot skin temperature during intermittent exercise. The rate of the foot temperature recovery after cold exposure was somewhat overestimated in the model--the warm-up of the feet of the subjects started later and was slower in the beginning of the warm-up than in the prediction. It could be useful to develop the model further by taking into consideration various wetness and activity levels.     

Effect of Voltage Sensitive Fluorescent Proteins on Neuronal Excitability

Fluorescent protein voltage sensors are recombinant proteins that are designed as genetically encoded cellular probes of membrane potential using mechanisms of voltage-dependent modulation of fluorescence. Several such proteins, including VSFP2.3 and VSFP3.1, were recently reported with reliable function in mammalian cells. They were designed as molecular fusions of the voltage sensor of Ciona intestinalis voltage sensor containing phosphatase with a fluorescence reporter domain. Expression of these proteins in cell membranes is accompanied by additional dynamic membrane capacitance, or “sensing capacitance”, with feedback effect on the native electro-responsiveness of targeted cells. We used recordings of sensing currents and fluorescence responses of VSFP2.3 and of VSFP3.1 to derive kinetic models of the voltage-dependent signaling of these proteins. Using computational neuron simulations, we quantitatively investigated the perturbing effects of sensing capacitance on the input/output relationship in two central neuron models, a cerebellar Purkinje and a layer 5 pyramidal neuron. Probe-induced sensing capacitance manifested as time shifts of action potentials and increased synaptic input thresholds for somatic action potential initiation with linear dependence on the membrane density of the probe. Whereas the fluorescence signal/noise grows with the square root of the surface density of the probe, the growth of sensing capacitance is linear. We analyzed the trade-off between minimization of sensing capacitance and signal/noise of the optical read-out depending on kinetic properties and cellular distribution of the probe. The simulation results suggest ways to reduce capacitive effects at a given level of signal/noise. Yet, the simulations indicate that significant improvement of existing probes will still be required to report action potentials in individual neurons in mammalian brain tissue in single trials.     

Performance of Scanning Near-Field Optical Microscope Probes with Single Groove and Various Metal Coatings

We investigate the performance of a simple corrugated aperture scanning near-field optical microscope (SNOM) probe with various cladding metals. The probes have only one corrugation, however, they offer increased transmission over both uncorrugated probes and those with many grooves. Enhancement of light throughput results from excitation of surface plasmons at the corrugation at the core–cladding interface. We show how the choice of metal influences radiation properties of grooved probes.     

Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin

Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.