Speleothem fluorescence can provide insights into past vegetation dynamics and stalagmite chronology. However, its origin and especially the formation of fluorescent laminations in stalagmites are poorly understood. We conducted a year-long monthly monitoring of drip water fluorescence in La Vallina Cave (northern Iberian Peninsula) and compared the results to drip water chemistry and active speleothems from the same sites. Drip waters were analyzed using fluorescence spectroscopy and parallel factor analysis (PARAFAC). The resulting five-component model indicates contributions from vegetation, microbial activity, and bedrock. Intra-site fluorescence variability is mainly influenced by changes in overlying vegetation, water reservoir time, and respiration rates. Contrary to prevailing views, we find no systematic increase in drip water fluorescence during rainy conditions across drip sites and seasonal variations in drip water fluorescence are absent at a location where present-day speleothem layers form. Our findings challenge the notion of a higher abundance of humic-like fluorescence during the rainy season as the primary cause for layer formation and suggest additional controls on drip water fluorescence, such as bedrock interaction and microbial reprocessing. We also propose that growth rate may control the dilation of the fluorescence signal in stalagmites, indicating other potential mechanisms for fluorescent layer formation.

Two rapid, nondestructive assays were developed and tested for their potential in differentiating glyphosate-resistant from glyphosate-susceptible biotypes of horseweed. In one assay, leaves of glyphosate-resistant and -susceptible corn, cotton, and soybean plants as well as glyphosate-resistant and -susceptible horseweed plants were dipped in solutions of 0, 300, 600, and 1200 mg ae L−1 glyphosate for 3 d and subsequent injury was evaluated. In the second assay, plant sensitivity to glyphosate was evaluated in vivo by incubating excised leaf disc tissue from the same plants used in the first assay in 0.7, 1.3, 2.6, 5.3, 10.6, 21.1, 42.3, and 84.5 mg ae L−1 glyphosate solutions for 16 h and measuring shikimate levels with a spectrophotometer. The leaf-dip assay differentiated between glyphosate-resistant and -susceptible crops and horseweed biotypes. The 600 mg L−1 rate of glyphosate was more consistent in differentiating resistant and susceptible plants compared with the 300 and 1,200 mg L−1 rates. The in vivo assay detected significant differences between susceptible and glyphosate-resistant plants of all species. Shikimate accumulated in a glyphosate dose-dependent manner in leaf discs from susceptible crops, but shikimate did not accumulate in leaf discs from resistant crops and levels were similar to nontreated leaf discs. Shikimate accumulated at high (≥ 21.1 mg ae L−1) concentrations of glyphosate in leaf discs from all horseweed biotypes. Shikimate accumulated at low glyphosate concentrations (≤ 10.6 mg L−1) in leaf discs from susceptible horseweed biotypes but not in resistant biotypes. Both assays were able to differentiate resistant from susceptible biotypes of horseweed and might have utility for screening other weed populations for resistance to glyphosate.

Two rapid, nondestructive assays were developed and tested for their potential in differentiating glyphosate-resistant from glyphosate-susceptible biotypes of horseweed. In one assay, leaves of glyphosate-resistant and -susceptible corn, cotton, and soybean plants, as well as glyphosate-resistant and -susceptible horseweed plants, were dipped in solutions of 0, 300, 600, and 1,200 mg ae L−1 glyphosate for 3 d, and subsequent injury was evaluated. In the second assay, plant sensitivity to glyphosate was evaluated in vivo by incubating excised leaf disc tissue from the same plants used in the first assay in 0.7, 1.3, 2.6, 5.3, 10.6, 21.1, 42.3, and 84.5 mg ae L−1 glyphosate solutions for 16 h and measuring shikimate levels with a spectrophotometer. The leaf dip assay differentiated between glyphosate-resistant and -susceptible crops and horseweed biotypes. The 600 mg L−1 rate of glyphosate was more consistent in differentiating resistant and susceptible plants compared with the 300 and 1,200 mg L−1 rates. The in vivo assay detected significant differences between susceptible and glyphosate-resistant plants of all species. Shikimate accumulated in a glyphosate dose–dependent manner in leaf discs from susceptible crops, but shikimate did not accumulate in leaf discs from resistant crops, and levels were similar to nontreated leaf discs. Shikimate accumulated at high (≥ 21.1 mg ae L−1) concentrations of glyphosate in leaf discs from all horseweed biotypes. Shikimate accumulated at low glyphosate concentrations (≤ 10.6 mg L−1) in leaf discs from susceptible horseweed biotypes but not in resistant biotypes. Both assays were able to differentiate resistant from susceptible biotypes of horseweed and could have utility for screening other weed populations for resistance to glyphosate.

Major components of the flux density of global photosynthetically active radiation (PAR) were measured above and within canopies in a tropical deciduous forest on the Pacific coast of Mexico. At each of 69 locations grouped along a topographic sequence the PAR reflected from the top of the canopy, the vertical profile of transmittance, and the reflectance from the ground, were measured as many as four times in the year, including the extremes of the wet and dry seasons. With these observations an annual balance of the portion of PAR radiation reflected and absorbed by the canopy and ground was assembled and the detailed spatial and temporal dynamics of PAR within canopy layers were estimated. Canopy stature declined along the topographic sequence and the shape of the transmittance profiles reflected this. In locations of declining moisture availability the fraction of PAR absorbed by the ground increased and the fraction absorbed by non-foliar tissues decreased. Seasonal variation in canopy structure was the dominant influence on the partitioning of radiation – spatial variation was less important. Of a total annual PAR input of 15 200 mol m−2, about 95% of incident PAR was absorbed, 50% by leaves, 25% by non-foliar tissues and 20% by the ground. The remaining 5% was reflected by the top of the canopy.

Temperature effects on spectral properties of the two types of rod photoreceptors in toad retina, “red” and “green” rods, were studied in the range 0–38°C. Absorbance spectra of the visual pigments were recorded by single-cell microspectrophotometry (MSP) and spectral sensitivities of red rods were measured by electroretinogram (ERG) recording across the isolated retina. The red-rod visual pigment is a usual rhodopsin (λmax = 503.6 nm and 502.3 nm at room temperature (21°C) in, respectively, Bufo marinus and Bufo bufo), that of green rods (λmax = 432.6 nm in Bufo marinus) belongs to the “blue” cone pigment family. In red rods, λmax depended inversely and monotonically on temperature, shifting by −2.3 nm when temperature was raised from 0°C to 38°C. Green-rod λmax showed no measurable dependence on temperature. In red rods, warming caused a relative increase of sensitivity in the long-wavelength range. This effect can be used for estimating the energy needed for photoexcitation, giving Ea = 44.3 ± 0.6 kcal/mol for Bufo marinus rhodopsin and 48.8 ± 0.5 kcal/mol for Bufo bufo rhodopsin. The values are significantly different (P < 0.001), although the two rhodopsins have very similar absorption spectra and thermal isomerization rates. Our recording techniques did not allow measurement of the corresponding effect at long wavelengths in green rods. Although spectral effects of temperature changes in the physiological range are small and of little significance for visual function, they reveal information about the energy states and different spectral tuning mechanisms of the visual pigments.

The utility of absorbance and fluorescence-emission spectra for discriminating among microalgal phylogenetic groups, selected species, and phycobilin- and non-phycobilin-containing algae was examined using laboratory cultures. A similarity index algorithm, in conjunction with fourth-derivative transformation of absorbance spectra, provided discrimination among the chlorophyll [Chl] a/phycobilin (cyanobacteria), Chl a/Chl c/phycobilin (cryptophytes), Chl a/Chl b (chlorophytes, euglenophytes, prasinophytes), Chl a/Chl c/fucoxanthin (diatoms, chrysophytes, raphidophytes) and Chl a/Chl c/peridinin (dinoflagellates) spectral classes, and often between/among closely related phylogenetic groups within a class. Spectra for phylogenetic groups within the Chl a/Chl c/fucoxanthin, Chl a/Chl c/peridinin, Chl a/phycobilins and Chl a/Chl c/phycobilin classes were most distinguishable from spectra for groups within the Chl a/Chl b spectral class. Chrysophytes/diatoms/raphidophytes and dinoflagellates (groups within the comparable spectral classes, Chl a/Chl c/fucoxanthin and Chl a/Chl c/peridinin, respectively) displayed the greatest similarity between/among groups. Spectra for phylogenetic groups within the Chl a/Chl c classes displayed limited similarity with spectra for groups within the Chl/phycobilin classes. Among the cyanobacteria and chlorophytes surveyed, absorbance spectra of species possessing dissimilar cell morphologies were discriminated, with the greatest range of differentiation occurring among cyanobacteria. Among the cyanobacteria, spectra for selected problematic species were easily discriminated from spectra from each other and from other cyanobacteria. Fluorescence-emission spectra were distinct among spectral classes and the similarity comparisons involving fourth-derivative transformation of spectra discriminated the increasing contribution of distinct cyanobacterial species and between phycobilin- and non-phycobilin-containing species within a hypothetical mixed assemblage. These results were used to elucidate the application for in situ moored instrumentation incorporating such approaches in water quality monitoring programmes, particularly those targeting problematic cyanobacterial blooms.

The visual pigment from the ultraviolet (UV) cone photoreceptor of the tiger salamander has been cloned, expressed, and characterized. The cDNA contains a full-length open reading frame encoding 347 amino acids. The phylogenetic analysis indicates that the highest sequence homology is to the visual pigments in the S group. The UV opsin was tagged at the carboxy-terminus with the sequence for the 1D4 epitope. This fusion opsin was expressed in COS-1 cells, regenerated with 11-cis retinal (A1) and immuno-purified, yielding a pigment with an absorbance maximum (λmax) of 356 nm which is blue shifted from the absorption of retinal itself. The transducin activation assay demonstrated that this pigment is able to activate rod transducin in a light-dependent manner. Regeneration with 11-cis 3,4-dehydroretinal (A2) yielded a pigment with a λmax of 360 nm, only 4 nm red shifted from that of the A1 pigment, while bovine rhodopsin generated with A2 showed a 16-nm red shift from the corresponding A1 pigment. These results demonstrate that the trend for a shorter wavelength pigment to have a smaller shift of λmax between the A1 and A2 pigments also fits UV pigments. We hypothesize that the small red shift with A2 could be due to a twist in the chromophore that essentially isolates the ring double bond(s) from conjugation with the rest of the polyene chain.

Absorbance spectra were recorded by microspectrophotometry from 39 different rod and cone types representing amphibians, reptiles, and fishes, with A1- or A2-based visual pigments and λmax ranging from 357 to 620 nm. The purpose was to investigate accuracy limits of putative universal templates for visual pigment absorbance spectra, and if possible to amend the templates to overcome the limitations. It was found that (1) the absorbance spectrum of frog rhodopsin extract very precisely parallels that of rod outer segments from the same individual, with only a slight hypsochromic shift in λmax, hence templates based on extracts are valid for absorbance in situ; (2) a template based on the bovine rhodopsin extract data of Partridge and De Grip (1991) describes the absorbance of amphibian rod outer segments excellently, contrary to recent electrophysiological results; (3) the λmax/λ invariance of spectral shape fails for A1 pigments with small λmax and for A2 pigments with large λmax, but the deviations are systematic and can be readily incorporated into, for example, the Lamb (1995) template. We thus propose modified templates for the main “α-band” of A1 and A2 pigments and show that these describe both absorbance and spectral sensitivities of photoreceptors over the whole range of λmax. Subtraction of the α-band from the full absorbance spectrum leaves a “β-band” described by a λmax-dependent Gaussian. We conclude that the idea of universal templates (one for A1- and one for A2-based visual pigments) remains valid and useful at the present level of accuracy of data on photoreceptor absorbance and sensitivity. The sum of our expressions for the α- and β-band gives a good description for visual pigment spectra with λmax > 350 nm.

The photoreceptor layer of F. heteroclitus was examined by light and electron microscopy. We identified four cone visual pigments with maximum absorbance (λmax) in the UV (363 nm), short (400 nm), middle (463 nm), and long (563 nm) wavelength regions of the spectrum and a rod visual pigment that peaked in the middle wavelengths (503 nm). Electron-dense bodies, ellipsosomes and pseudoellipsosomes, were present in the distal ellipsoids of long/middle (L/M) and long/long (L/L) wavelength double cones and in single short wavelength (S) cones, respectively. The light absorption of ellipsosomes indicated the presence of reduced cytochrome-c with the highest optical densities found in the M members of L/M double cones. By contrast, S cones contained pseudo-ellipsosomes which had very low optical density. UV cones were present everywhere as part of square or row mosaics in the retina of F. heteroclitus. Cone packing was on average higher for locations in the upper half of the retina while the highest cone density was found in the centro-ventral retina. An analysis of potential quantum catches for each cone type as a function of retinal sector and underwater irradiance characteristics revealed higher overall quantum catches for cones in the upper retina when the light field was assumed homogeneous, and higher quantum catches for cones in the lower retina when downwelling, horizontal, and upwelling irradiances were considered separately. At dusk, quantum catch was highest for M cones and the contribution to the overall retinal quantum catch by UV and S cones was much greater than during daylight hours. We propose that UV and S cones may be used to detect targets of interest against the background irradiance sensed by double cones.