Classification of rhizosphere components using visible–near infrared spectral images

To establish new techniques for automatic classification of rhizosphere components, we investigated the utility of visible (VIS) and near–infrared (NIR) spectral images of the rhizosphere under two soil moisture conditions (mean volumetric water content: 0.39 and 0.16 cm³ cm^?3). Spectral reflectance images of the belowground parts of hybrid poplar cuttings (Populus deltoides × P. euramericana, I45/51) grown in a rhizobox were recorded at 120 spectral bands ranging from 480 to 972 nm. We examined which wavelengths were suitable and the number of spectral bands needed to accurately classify live roots of four age classes, dead roots, leaf mold, and soil. VIS reflectance (<700 nm) of live roots first increased and then decreased with age, whereas NIR reflectance (≥700 nm) was stable in mature roots. The reflectance of dead roots was lower than that of mature roots in both the VIS and NIR spectral regions. VIS reflectance did not differ among dead roots, leaf mold, and soil, but the NIR reflectance was clearly lower in soil than in the other materials. The reflectance of leaf mold and soil increased mainly in the NIR spectral region with reducing soil moisture, but this increase did not affect the order of reflectance intensity among the rhizosphere components in general. Although the most suitable spectral bands statistically selected for classifying rhizosphere components differed somewhat between moist and dry conditions, the spectral bands 580–679 nm (VIS) and 848–894 nm (NIR) provided high reliability under both conditions. Classification accuracy was higher when using two to five VIS–NIR images (overall accuracy ≥87.8%) than three VIS images (red, green, and blue; accuracy <67.1%). The high accuracy with VIS–NIR was mainly due to successful separation of leaf mold and soil. Irrespective of soil moisture condition, the overall accuracy tended to be stable at 92–94% with use of four VIS–NIR images. The spectral bands effective in wet soil conditions could also be used for classification in dry conditions, with overall accuracies >86.9%. These results suggest that automatic image analysis using VIS–NIR images at four spectral bands, including red and NIR, allows for accurate classification of the growth stage or live/dead status of roots and distinguishes between leaf mold and soil.     

Long Fluorescence Lifetime Molecular Probes Based on Near Infrared Pyrrolopyrrole Cyanine Fluorophores for In Vivo Imaging

Fluorescence lifetime (FLT) properties of organic molecules provide a new reporting strategy for molecular imaging in the near infrared (NIR) spectral region. Unfortunately, most of the NIR fluorescent dyes have short FLT typically clustered below 1.5 ns. In this study, we demonstrate that a new class of NIR fluorescent dyes, pyrrolopyrrole cyanine dyes, have exceptionally long FLTs ranging from 3 to 4 ns, both in vitro (dimethyl sulfoxide and albumin/water solutions) and in vivo (mice). These results provide a new window for imaging molecular processes, rejecting backscattered light and autofluorescence, and multiplexing imaging information with conventional NIR fluorescent dyes that absorb and emit light at similar wavelengths.     

Automated Reconstruction of Three-Dimensional Fish Motion,Forces, and Torques

Fish can move freely through the water column and make complex three-dimensional motions to explore their environment, escape or feed. Nevertheless, the majority of swimming studies is currently limited to two-dimensional analyses. Accurate experimental quantification of changes in body shape, position and orientation (swimming kinematics) in three dimensions is therefore essential to advance biomechanical research of fish swimming. Here, we present a validated method that automatically tracks a swimming fish in three dimensions from multi-camera high-speed video. We use an optimisation procedure to fit a parameterised, morphology-based fish model to each set of video images. This results in a time sequence of position, orientation and body curvature. We post-process this data to derive additional kinematic parameters (e.g. velocities, accelerations) and propose an inverse-dynamics method to compute the resultant forces and torques during swimming. The presented method for quantifying 3D fish motion paves the way for future analyses of swimming biomechanics.     

Diurnal Variations in Swimming Activity of Rutilus rutilus (Cyprinidae) in a Group under Tank Conditions

Measurements of the swimming activity of a group of roach (12–19 cm TL, average) in a circular swimming chamber revealed two distinct activity patterns: a diurnal and a nocturnal one. The experiments showed that, having the choice, two factors stimulated the rhythmicity of the swimming behaviour of the fish, i.e. light intensity and the presence of a current field in the proximity of the fish. During daytime (bright light conditions) the fish moved into the current field and swam on average at 0.4 BL/s (resting swimming). The roach remained swimming at this speed even if no current field was established, however, then distributed evenly in the basin. By contrast, during night (dim light conditions) the fish predominantly chose the still water section but swam on average with a cruising speed of 1.6 BL/s (night swimming). Accordingly, they did not seek the still water section for night swimming if the light was kept on. Then again, the fish distributed more or less evenly in the basin. The results support the hypothesis that the fish migrate during night-time and do this preferably in still water.     

Light effects on the multicellular magnetotactic prokaryote ‘<Emphasis Type="Italic">Candidatus</Emphasis> Magnetoglobus multicellularis’ are cancelled by radiofrequency fields: the involvement of radical pair mechanisms

‘Candidatus Magnetoglobus multicellularis’ is the most studied multicellular magnetotactic prokaryote. It presents a light-dependent photokinesis: green light decreases the translation velocity whereas red light increases it, in comparison to blue and white light. The present article shows that radio-frequency electromagnetic fields cancel the light effect on photokinesis. The frequency to cancel the light effect corresponds to the Zeeman resonance frequency (DC magnetic field of 4 Oe and radio-frequency of 11.5 MHz), indicating the involvement of a radical pair mechanism. An analysis of the orientation angle relative to the magnetic field direction shows that radio-frequency electromagnetic fields disturb the swimming orientation when the microorganisms are illuminated with red light. The analysis also shows that at low magnetic fields (1.6 Oe) the swimming orientation angles are well scattered around the magnetic field direction, showing that magnetotaxis is not efficiently in the swimming orientation to the geomagnetic field. The results do not support cryptochrome as being the responsible chromophore for the radical pair mechanism and perhaps two different chromophores are necessary to explain the radio-frequency effects.     

Comparative photobehavior of marine cercariae with differing secondary host preferences

Light may serve as an important exogenous cue for parasitic larvae that have multi-host lifecycles and need to locate specific microhabitats, thereby increasing the probability of encountering their next host. We studied light as an initiating and orienting cue for swimming in two species of marine cercariae (Trematoda), Euhaplorchis sp. and Probolocoryphe lanceolata, which initially parasitize the same species of benthic snail, but then utilize different second intermediate hosts located in pelagic and benthic habitats, respectively. When tested in a laboratory simulation of underwater angular light distribution, dark-adapted Euhaplorchis cercariae swam slowly in darkness but ascended quickly toward downwelling light at quantal intensities over 4.0 × 10(15) photons m(-2) s(-1). They oriented toward a directional light source in a horizontal trough, confirming that light plays both an initiating and an orienting role in phototactic behavior that results in ascent in the water column to locate a fish host. In contrast, Probolocoryphe lanceolata cercariae exhibited haphazard vertical swimming in darkness, with downward swimming upon exposure to angular light at lower quantal intensities (>4.0 × 10(14) photons m(-2) s(-1)) than initiated swimming in Euhaplorchis. However, P. lanceolata cercariae did not swim in response to a directional light source, suggesting that while light initiated descent behavior, its orientation was controlled by another factor. These differences in photobehavior support the idea that trematode cercariae use light in selecting for microhabitats frequented by potential hosts: an adaptive benefit that optimizes their contact and transmission to the next host.     

Water temperature, light intensity and zooplankton density and the feeding activity of juvenile brook charr (Salvelinus fontinalis)

SUMMARY 1. The objective of this study was to evaluate the effects of zooplankton biomass (as a measure of density), fish biomass, light intensity and water temperature on the attack rate and swimming characteristics (i.e. swimming speed and angle of turn) of juvenile (1+) brook charr (Salvelinus fontinalis) in field enclosures. We used a portable underwater camera system in a series of pelagic enclosures to quantify the feeding behaviour of brook charr over a gradient of natural conditions. 2. In simple linear or non‐linear regression models we found (i) that attack rate and angle of turn were positively related to water temperature, (ii) that attack rate and swimming speed were positively related to zooplankton biomass and light intensity and (iii) that attack rate was positively related to swimming speed. In multiple regression models, fish biomass, light intensity and variance of the angle of turn accounted for 87% of the variation in attack rate. Light intensity and water temperature accounted for 86% of the variation in swimming speed. Fish gut fullness and attack rate accounted for 83% of the variation in the variance of the angle of turn executed by fish. 3. The increase in the number of attacks as zooplankton biomass increases conforms to the general positive functional response observed in other fish species. Our results also support the hypothesis that swimming speed increases with prey biomass. We did not observe a plateau in attack rate as zooplankton biomass increased. As our experiments were performed under natural biotic and abiotic conditions, factors other than zooplankton biomass might affect or limit this response, such as water temperature and light intensity. 4. Because zooplankton biomass was correlated with water temperature and light intensity, it was not possible to evaluate the independent contribution of these factors on the attack rate and swimming characteristics (swimming speeds and angle of turn) of brook charr. However, this study highlighted the impact of these factors on the feeding behaviour of juvenile brook charr when feeding in the pelagic habitat under natural conditions, and their importance in future models of optimal foraging and fish habitat quality.     

Migration speeds and orientation of Atlantic salmon and sea trout post-smolts in a Norwegian fjord system

We recorded the observed and actual swimming speeds of Atlantic salmon and sea trout post-smolts in a Norwegian fjord system, and initiated studies on the orientation mechanisms of the post-smolts. We tracked Atlantic salmon and sea trout with acoustic transmitters for up to 14 h after release. The actual swimming speed and direction of a fish relative to the ground is the vector sum of the observed movements of the fish and the movements of the water. We determined actual swimming speeds and directions of the post-smolts, which reflect their real swimming capacities and orientation, by corrections for the speed and direction of the water current. The post-smolts were actively swimming. The observed direction of movement was dependent on the actual movement of the fish and not the water current. Water currents were not systematically used as an orientation cue either in Atlantic salmon or sea trout, as the actual movements were random compared to the direction of the water current. The actual movement of sea trout were in all compass directions, with no systematic pattern. The Atlantic salmon also moved in all compass directions, but with the lowest frequency of actual movement towards the fjord.     

Multivariate Calibration Using Covariance Adjustment

In this paper we treat linear calibration of multivariate chemical measurement instruments. Two new calibration methods for multicollinear spectral data are proposed. The methods are compared with established predictors on a set of data. The data consists of measurements of fat in fish meat and near infrared (NIR) reflectance measurements. The new methods give improvements compared with the established ones.     

The roles of vision and the lateral-line system in Sacramento splittail’s fish-screen avoidance behaviors: Evaluating vibrating screens as potential fish deterrents

The roles of vision and the lateral-line system in fish-screen avoidance behaviors were investigated in Sacramento splittail (Pogonichthys macrolepidotus). Fish were viewed swimming in front of water-diversion-type fish screens in a laboratory flume during the day (lit condition) and night (darkened condition, using infrared equipment). Streptomycin-sulfate treatments were used to block the fish’s lateral-line systems. Lateral line neuromasts were labeled with 2-(4-(dimethylamino)styryl)-N-ethylpyridinium iodide (DASPEI) to assess the streptomycin treatment’s effectiveness. Splittail contacted the screens infrequently during the day, but contacted the screens significantly more often during the night. Also, in darkened conditions, streptomycin-treated splittail contacted the screens significantly more often than did control fish. Furthermore 60 % of the streptomycin-treated fish became impinged (stuck) to the screens during night experiments, compared to 15 % of the untreated fish. These findings suggest that splittail use their lateral-line system to detect and avoid objects (screens) in the absence of vision. Splittail displayed no response to stimuli generated from a piston-driven vibrator mounted to the center of the screens. Our findings are the first to show how fish can use different sensory systems to detect and avoid fish screens in the presence or absence of light, and they should benefit fisheries and water resources managers, regarding the timing of water extractions through screened water diversions.     

不同水氮条件下水稻冠层反射光谱与植株含水率的定量关系

研究了不同土壤水氮条件下水稻 (Oryzasativa) 冠层光谱反射特征和植株水分状况的量化关系。结果表明, 水稻冠层近红外光谱反射率随土壤含水量的降低而降低, 短波红外光谱反射率随土壤含水量的降低而升高。相同土壤水分条件下, 高氮水稻的冠层含水率高于低氮水稻的冠层含水率 ;同一水分条件下, 高氮处理的可见光区和短波红外波段光谱反射率低于低氮处理, 近红外波段光谱反射率高于低氮处理。发现拔节后比值植被指数 (R810 /R460 ) 与水稻叶片含水率和植株含水率呈极显著的线性相关, 模型的检验误差 (RootmeansquareError, RMSE) 分别为 0.93和 1.5 0。表明比值植被指数R810 /R460 可以较好地监测不同生育期水稻叶片和植株含水率。     

Effects of light wavelength on growth and survival rate in juvenile Pacific bluefin tuna, Thunnus orientalis

The spectral sensitivity of the fish and the suitable light wavelength range for survival and growth performance of juvenile Pacific bluefin tuna (PBT) were investigated. The spectral sensitivity peak of PBT under photopic condition was observed between 449 and 503 nm, which corresponded to their natural habitat. The fish were reared in tanks irradiated continuously with 4 kinds of light emitting diodes (LEDs). The maximum wavelength of LEDs used for the rearing experiment were 460 nm (blue), 520 nm (green), 630 nm (red), and 450–680 nm (white). There was no notable difference in survival rate among fish in the four LED groups. However, the growth of juvenile PBT was lesser under red light compared to the green and white light wavelengths. These results suggest that PBT juveniles have low sensitivity to red light because the fish are rarely exposed to the red light wavelengths under natural ocean conditions. Thus, low sensitivity to red light negatively influenced the feeding behavior and growth of PBT juveniles.     

Characterization of Light Lesion Paradigms and Optical Coherence Tomography as Tools to Study Adult Retina Regeneration in Zebrafish

Light-induced lesions are a powerful tool to study the amazing ability of photoreceptors to regenerate in the adult zebrafish retina. However, the specificity of the lesion towards photoreceptors or regional differences within the retina are still incompletely understood. We therefore characterized the process of degeneration and regeneration in an established paradigm, using intense white light from a fluorescence lamp on swimming fish (diffuse light lesion). We also designed a new light lesion paradigm where light is focused through a microscope onto the retina of an immobilized fish (focused light lesion). Focused light lesion has the advantage of creating a locally restricted area of damage, with the additional benefit of an untreated control eye in the same animal. In both paradigms, cell death is observed as an immediate early response, and proliferation is initiated around 2 days post lesion (dpl), peaking at 3 dpl. We furthermore find that two photoreceptor subtypes (UV and blue sensitive cones) are more susceptible towards intense white light than red/green double cones and rods. We also observed specific differences within light lesioned areas with respect to the process of photoreceptor degeneration: UV cone debris is removed later than any other type of photoreceptor in light lesions. Unspecific damage to retinal neurons occurs at the center of a focused light lesion territory, but not in the diffuse light lesion areas. We simulated the fish eye optical properties using software simulation, and show that the optical properties may explain the light lesion patterns that we observe. Furthermore, as a new tool to study retinal degeneration and regeneration in individual fish in vivo, we use spectral domain optical coherence tomography. Collectively, the light lesion and imaging assays described here represent powerful tools for studying degeneration and regeneration processes in the adult zebrafish retina.     

Reactions in individual fish to strobe light. Field and aquarium experiments performed on whitefish (Coregonus lavaretus)

This study describes how individual whitefish Coregonus lavaretusreact to strobe light. Field experiments were performed in a net enclosure on fish tagged with ultrasonic transmitters. A strobe light array was switched on near the tagged fish. The fish moved away from the light and increased their swimming speed. Aquarium experiments under controlled conditions were carried out in rearing tanks at Saimaa Fisheries and Aquaculture Station in Finland. A strobe light was directed from the side of the basin just ahead of, directly at, and behind the fish at a close range. In the first two cases fish responded by a distinct turn and a change in swimming direction away from the light. The fish did not change its swimming direction when light was aimed from behind. It is concluded that strobe light may be used to prevent fish from swimming into a specific area. Implications for development of new fishing equipment and research concerning fishes in areas with water power stations is briefly discussed.     

Oriented swimming at an angle to light in a schooling characid, Moenkhausia dichrowa Kner

Two groups each of approximately 100 Moenkhausia dichroua , a schooling characid, showed a long–lasting, constant–oriented swimming when placed in a light–centred circular channel. This apparatus consists of a 1–m diameter circular channel illuminated by either a central or a peripheral light system, so that the light angle is constant all around the channel. With the central light at a fixed angle, fish swam for several months in one direction and reversed direction at a certain date. When the light angle was increased by 10° every other day between 0° (horizontal) and 90° (vertical), swimming direction was reversed at a particular angle in each experiment. This response to artificial light suggests that this small schooling fish uses the sun as an orientation clue in its seasonal migrations.     

The time course and frequency content of hydrodynamic events caused by moving fish,frogs, and crustaceans

Summary In the present study the time course and spectral-amplitude distribution of hydrodynamic flow fields caused by moving fish, frogs, and crustaceans were investigated with the aid of laser-Doppler-anemometry. In the vicinity of a hovering fish sinusoidal water movements can be recorded whose velocity spectra peak below 10 Hz (Fig. 2). Single strokes during startle responses or during steady swimming of fish, frogs, and crustaceans cause short-lasting, low-frequency (<10 Hz), transient water movements (Fig. 3). Low-frequency transients also occur if a frog approaches and passes a velocity-sensitive hydrodynamic sensor. In contrast, transient water movements caused by a rapidly struggling or startled fish or water motions measured in the wake of a slowly swimming (47 cm/s) trout can be broadbanded, i.e., these water movements can contain frequency components up to at least 100 Hz (Figs. 4, 5A, 6). High-frequency hydrodynamic events can also be measured behind obstacles submerged in running water (Fig. 5C). The possible biological advantage of the ability to detect high-frequency hydroynamic events is discussed with respect to the natural occurrence of high frequencies and its potential role in orientation and predator-prey interactions of aquatic animals.Abbreviations LDA laser Doppler anemometer     

Wide Dynamic Range Vegetation Index for remote quantification of biophysical characteristics of vegetation

The Normalized Difference Vegetation Index (NDVI) is widely used for monitoring, analyzing, and mapping temporal and spatial distributions of physiological and biophysical characteristics of vegetation. It is well documented that the NDVI approaches saturation asymptotically under conditions of moderate-to-high aboveground biomass. While reflectance in the red region (rho(red)) exhibits a nearly flat response once the leaf area index (LAI) exceeds 2, the near infrared (NIR) reflectance (PNIR) continue to respond significantly to changes in moderate-to-high vegetation density (LAI from 2 to 6) in crops. However, this higher sensitivity of the rho(NIR) has little effect on NDVI values once the rho(NIR) exceeds 30%. In this paper a simple modification of the NDVI was proposed. The Wide Dynamic Range Vegetation Index, WDRVI = (a * rho(NIR-rho(red))/(a * rho(NIR) + rho(red)), where the weighting coefficient a has a value of 0.1-0.2, increases correlation with vegetation fraction by linearizing the relationship for typical wheat, soybean, and maize canopies. The sensitivity of the WDRVI to moderate-to-high LAI (between 2 and 6) was at least three times greater than that of the NDVI. By enhancing the dynamic range while using the same bands as the NDVI, the WDRVI enables a more robust characterization of crop physiological and phenological characteristics. Although this index needs further evaluation, the linear relationship with vegetation fraction and much higher sensitivity to change in LAI will be especially valuable for precision agriculture and monitoring vegetation status under conditions of moderate-to-high density. It is anticipated that the new index will complement the NDVI and other vegetation indices that are based on the red and NIR spectral bands.     

Multispectral near infrared absorption imaging for histology of skin cancer

Multispectral imaging combines the spectral resolution of spectroscopy with the spatial resolution of imaging and is therefore very useful for biomedical applications. Currently, histological diagnostics use mainly stainings with standard dyes (eg, hematoxylin + eosin) to identify tumors. This method is not applicable in vivo and provides low amounts of chemical information. Biomolecules absorb near infrared light (NIR, 800‐1700 nm) at different wavelengths, which could be used to fingerprint tissue. Here, we built a NIR multispectral absorption imaging setup to study skin tissue samples. NIR light (900‐1500 nm) was used for homogenous wide‐field transmission illumination and detected by a cooled InGaAs camera. In this setup, images I(x, y, λ) from dermatological samples (melanoma, nodular basal‐cell carcinoma, squamous‐cell carcinoma) were acquired to distinguish healthy from diseased tissue regions. In summary, we show the potential of multispectral NIR imaging for cancer diagnostics.      

Red muscle function during steady swimming in brook trout, Salvelinus fontinalis.

Red muscle function during steady swimming in brook trout was studied through both in vivo swimming and in vitro muscle mechanics experiments. In the swimming experiments, red muscle activity was characterized through the use of electromyography and sonomicrometry, allowing the determination of several parameters such as tailbeat frequency, EMG burst duration, muscle length change patterns and relative phase of EMG activity and length change. Brook trout do show some shifts in these variables along their length during steady swimming, but the magnitude of these shifts is relatively small. In the muscle mechanics experiments, the in vivo muscle activity data were used to evaluate patterns of power production by red muscle during swimming. Unlike many fish species, the red muscle along the length of brook trout shows little change in isometric kinetic variables such as relaxation rate and twitch time. Furthermore, there is no rostral-caudal shift in red muscle mass-specific power output during steady swimming. This last result contrasts sharply with rainbow trout and with a variety of other fish species that power steady swimming primarily with the posterior red myotome.     

A study of the swimming performance of the Crucian carp Carassius carassius (L.) in relation to the effects of exercise and recovery on biochemical changes in the myotomal muscles and liver

A study has been made of the maximum sustained swimming speed of Crucian carp Carassius carassius (L.) using a fixed velocity technique. The data obtained from swimming tests on 214 carp have been analysed using the method of probit analysis. The 50% fatigue level for 13–16 cm fish acclimated to 9.5±0.6°C has been estimated to be 3.35 lengths/sec. Biochemical measurements have been made on the red and white myotomal muscles and liver of fish subjected to both varying intensities of sustained swimming and short periods of vigorous swimming. Free creatine was found to increase only during high speed swimming in the white muscle. Elevated lactate concentrations occurred at both low and high sustained swimming speeds in the red superficial muscle but not during short periods of strenuous exercise. Glycogen depletion from the red musculature also only took place at the sustained swimming speeds investigated. The reverse situation was operative in the white muscle, significant glycogen depletion occurring only at the highest swimming speed studied. Lactate levels were only significantly different from non-exercised fish in the fish swimming at the higher velocities. The effects of periods of recovery following 200 min of sustained swimming were also investigated. White muscle lactate was at a higher level than non-exercise fish 5 h post-exercise, while both red muscle glycogen and lactate rapidly returned to pre-exercise concentrations. Biochemical measurements on the myotomal muscle types have been discussed in relation to the swimming performance of the fish and the division of labour between red and white fibres.