Possible calculations with temperature, humidity, images and VIS spectrum of a plant in an Integrating sphere

Possible calculations with temperature, humidity, images and VIS spectrum of a plant in an Integrating sphere

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I am currently working on a project which involves growing some plants in a integrating sphere made of foam. I have added temperature, humidity and soil moisture sensors as well as a Spectrometer (350 - 800nm) and a webcam which takes images of the plant every 30 minutes.

I thought of calculating the LAI (Leaf area index) from the webcam images.

Does anyone have any other suggestions/ideas on what I could calculate with the given data from these sensors?

With the images you could, perhaps, assess growth rate of the plant which can be plotted against spectral content of light to investigate effects of light quality on growth. Using moist and water and temperature the same can be done. Multivariate analysis can help to implement all the values, while ANCOVA may may help to correct for covariance.

A detailed experimental set up may help to answer this question. Not specifically the hardware, but how the effect of water stress is measured. E.g., are multiple plants tested under different watering conditions? In that case all the other measures (temperature, light) are probably used to check whether everything is constant across all specimens except water availability. This may limit the usefulness of analysis of these additional measures. I think the other parameters (light, water, temperature) may be not so interesting other than covariates for water stress as they are either not controlled or deliberately kept constant. Moreover, probably their effects on plants are pretty obvious too.

Super hygroscopic nanofibrous membrane-based moisture pump for solar-driven indoor dehumidification

Desiccants play vital roles in dehumidification and atmospheric water harvesting however, current desiccants have mediocre hygroscopicity, limited recyclability, and high energy consumption. Herein, we report a wood-inspired moisture pump based on electrospun nanofibrous membrane for solar-driven continuous indoor dehumidification. The developed moisture pump with multilayer wood-like cellular networks and interconnected open channels is composed of a desiccant layer and a photothermal layer. The desiccant layer exhibits an unprecedented moisture absorption capacity of 3.01 g g −1 at 90% relative humidity (RH), fast moisture absorption and transport rates, enabling atmospheric water harvesting. The photothermal layer shows a high solar absorption of 93%, efficient solar thermal conversion, and good moisture permeability, thus promoting water evaporation. The moisture pump efficiently reduces the indoor relative humidity to a comfort level (40‒60% RH) under one-sun illumination. This work opens the way to develop new-generation, high-performance nanofibrous membrane-based desiccants for energy-efficient humidity control and atmospheric water harvesting.

Detection of downy mildew of opium poppy using high-resolution multi-spectral and thermal imagery acquired with an unmanned aerial vehicle

Downy mildew (DM) caused by the biotrophic obligate oomycete Peronospora arborescens (Berk.) is one of the most economically limiting diseases of opium poppy (Papaver somniferum L.) worldwide. The first symptoms appear as small chlorotic leaf lesions, which can evolve to curled and thickened tissues that become deformed and necrotic as the disease develops. The present study explored the use of high-resolution thermal and multi-spectral imagery as an indicator of DM infection. Work was conducted in two opium poppy field plots artificially infected by P. arborescens. Airborne thermal and multi-spectral imagery were acquired at 200 mm resolution on three dates in spring of 2009 using an unmanned aerial vehicle (UAV). Leaf reflectance and transmittance spectra of DM asymptomatic and symptomatic opium poppy leaves were measured using an integrating sphere. Simulation work was conducted with the coupled PROSPECT + SAILH radiative transfer model to assess the effects of the variability found in an opium poppy plot developing a DM epidemic on the normalized difference vegetation index (NDVI) and the green/red index (R550/R670) calculated from the multi-spectral imagery. The airborne flights enabled DM detection by using image-derived canopy temperature (Tc) normalized by air temperature (Tc − Ta) and the green/red index (R550/R670). Tmin for each grid unit was calculated to estimate pure-vegetation temperature removing background and soil effects. Tmin − Ta and R550/R670 were assessed as a function of aggregated NDVI clusters to compare asymptomatic and symptomatic plants normalized by similar growth levels. Results demonstrated that Tc − Ta and the R550/R670 index were related to physiological stress caused by DM infection. In addition, Tmin − Ta was found to decrease as the NDVI increased and symptomatic plants reached significantly higher (P < 0.05) temperatures for an NDVI ≥0.6. The R550/R670 index was positively correlated with the NDVI, showing significantly higher values (P < 0.05) in symptomatic plants with an NDVI ≥0.5. These results demonstrate the feasibility of detecting P. arborescens infection in opium poppy plants using high-resolution thermal and multi-spectral imagery acquired with an UAV.

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Light distribution

Fibre-optic microprobe measurements showed that scalar irradiance of both red (636 nm) and near-infrared (785 nm) light was enhanced in the coral tissue as far as 14–20 mm away from the tissue area directly illuminated by the incident laser beam (Figs 1, 2). The lateral attenuation of near-infrared radiation (NIR) scalar irradiance occurred homogeneously within the tissue of an intact coral and was almost identical to the lateral attenuation observed on the bare skeleton (compare Fig. 1A and 1B and see ratio of 785 nm light in 1E). However, for 636 nm light there were clear differences in the lateral scalar irradiance distribution around the incident laser beam between the intact coral and the bare skeleton (Fig. 1C–E). Lateral attenuation of 636 nm scalar irradiance was more rapid on an intact coral compared with the bare skeleton (see ratio in Fig. 1E). Additionally, we found that on a vertical scale there was a clear tendency for an increase in 636 nm scalar irradiance from the skeleton surface towards the tissue surface for an intact coral but not in measurements above the bare skeleton. For instance, at

Diffractive hygrochromic effect in the cuticle of the hercules beetle Dynastes hercules

The elytra from dry specimens of the hercules beetle, Dynastes hercules appear khaki-green in a dry atmosphere and turn black passively under high humidity levels. New scanning electron images, spectrophotometric measurements and physical modelling are used to unveil the mechanism of this colouration switch. The visible dry-state greenish colouration originates from a widely open porous layer located 3 μm below the cuticle surface. The structure of this layer is three-dimensional, with a network of filamentary strings, arranged in layers parallel to the cuticle surface and stiffening an array of strong cylindrical pillars oriented normal to the surface. Unexpectedly, diffraction plays a significant role in the broadband colouration of the cuticle in the dry state. The backscattering caused by this layer disappears when water infiltrates the structure and weakens the refractive index differences.

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GENERAL SCIENTIFIC SUMMARY Introduction and background. Hygrochromic materials have recently raised the attention of part of the scientific community. They consist of a porous structure which can be infiltrated with a liquid or a gas. This infiltration induces a change of colour due to the variation of the refractive index when the liquid replaces air in the medium, or to swelling effects. Such a phenomenon is observed on the cuticle (i.e. the carapace) of the beetle Dynastes hercules due to penetration of water vapor when humidity rises above 80%.

Main results. Scanning electron microscopy gave access to the structure responsible for the greenish colouration of the beetle, changing to black when infiltrated with water. The change of colour has been described in detail from spectrophotometry data. Finally numerical simulation showed that, in contrast to current belief, diffraction is involved in the colouration mechanism. A noticeable fact about this research is that nature has developed such a hygrochromic material through thousands of years of evolution and, in order to engineer the same function, one does not have to repeat the long trial and error sequence followed by natural selection.

Wider implications. X-chromic (meaning changing colour due to X, such as hygrometry hygro, temperature thermo, electric voltage electro. ) materials are highly attractive today. A visible change of colour, easily observed by a human eye or a spectrophotometer, gives information about some environmental change. This could be useful for example in food processing to monitor parameters such as the moisture level.

Figure. The Dynastes hercules is greenish under normal humidity conditions (left). It becomes black when the humidity level is above 80% (right).


The field of integrative biology, combining data from various “omics” disciplines, is expanding at a fast pace [1]. A particularly promising combination is genomics linked with phenomics [2]. The latter approach is understood as a way to trace causal links between genotypes, environmental factors and phenotypes. This type of analysis is a complex task usually involving the handling of multidimensional datasets. In human health and plant science, complex and costly data collection and evaluation are frequently performed [3–6]. However, there has been difficulty in employing this strategy in the field of insect integrative biology [7].

Phenotypic plasticity describes the capacity of a single genotype to exhibit a variety of phenotypes as well as the mechanisms that translate environmental variation into reproducible phenotypic modifications [8]. If “phenotype” is understood in a broad sense, including all aspects of an organism other than the genotype, from the enzyme products of the genes to learned behaviors and the “environment” to include both the external surroundings of an organism and the internal conditions affecting gene expression, “phenotypic plasticity” is seen to encompass an enormous diversity of kinds of variability [9]. Distinction should be made between phenotypic plasticity and polyphenism, the latter being understood as the existence of environmentally cued alternative phenotypes in a population. Recently a comprehensive work has investigated the polyphenism and phenotypic plasticity in five related species of mycalesine butterflies from the Old World tropics, exhibiting seasonal polyphenism. For example, the differences between wet and dry season form of Bicyclus anynana, and those of many other mycalesines, are the color patterns on the ventral wing surfaces strongly associated with the alternative seasonal strategies to avoid predation. In the laboratory, the seasonal forms of B. anynana can be induced by the temperature control during the critical period of pre-adult development [10].

An interesting point is made in a focus paper tentatively applying IBM Watson to pathology: “Remember, from the whole genome sequence perspective, there is no difference between a caterpillar and a butterfly.” [3]. Indeed, despite exhibiting distinct body structures, diets, behavior, survival strategies, etc., the caterpillar and the butterfly represent the expression of the same genetic information. In a certain sense, they can be regarded as two different phenotypes of the same genetic information. The switchover between the larval form and the imaginal form takes place in the pupa, which takes only slightly longer than one week in many species. Furthermore, as concisely formulated by Nijhout: “With (genetic) dominance, a particular phenotype can be produced by several different genotypes. The uncertainty works in the other direction as well: a single genotype can produce many different phenotypes, depending on various contingencies encountered during development. That is, the phenotype is the outcome of a complex series of developmental processes that are influenced by environmental factors as well as by genes” [11]. It is worth noting that for insects with complete metamorphosis (for butterflies in particular), there is an opportunity to induce species-specific changes in the pupal stage–when transformation from larva to imagine takes place–at a well-defined developmental time [12–14]. Some of these phenotypic changes induced by targeted interventions can be perceived by the naked eye. For example, we recently showed that for Polyommatus icarus butterflies (both males and females), the extent of the induced phenotypic alterations in pigment-based patterns on the ventral wing surface is proportional to the duration of cooling applied to the pupa immediately after pupation [14].

We also found that the blue structural coloration of the dorsal wing surface of P. icarus males showed a much smaller magnitude of change upon cooling than the pigmented pattern on the ventral wing surfaces [14]. The observed change was not proportional to the duration of cooling, indicating that only hidden genetic variations were revealed by the stress [15,16]. In contrast to pigment-based colors, structural colors arise from particular interactions between chitin-based nanoarchitectures in wing scales and electromagnetic radiation [17]. These nanoarchitectures are self-assembled during scale formation. Despite some insight to these special nanoarchitectures [18–22], their formation is not yet fully understood, nor is the mechanism that causes P. icarus males to exhibit structurally colored blue dorsal cover scales while females exhibit brown dorsal cover scales colored by pigment.

In the case of structural colors, the characteristic dimensions–in the tens of nanometers range–and the periodicity of the nanoarchitecture determine which wavelength ranges cannot propagate in the nanostructure and are reflected towards the eye of the observer [17]. Changes of the characteristic nanostructures in the range of a few tens of nanometers can produce a significant shift in the spectral reflectance maximum [23].

Surprisingly, all cooled P. icarus females exhibit a number of blue scales with a similar structure in their lumen to that of the males [14]. The number of these scales varies from individual to individual, with the general trend of longer cooling yielding an increasing number of blue scales. In natural populations in Central Europe, females exhibit pigment-based brown coloration on the dorsal wing surface, and the frequency of bluish females in museum collections is usually below 10% [14]. Here, one must take into account that collectors tend to keep those individuals that are “unusual” therefore, bluish females are overrepresented in these collections.

As discussed in detail by Houle et al. [2], the multiple ways in which genotypic information influences the phenotype of an organism can be best represented in a genotype-phenotype (G-P) map (Box 1 in [2]). This approach extends back to Richard Levontin’s work stating that evolution takes place in the space of all possible genotypes (G space) and the space of all possible phenotypes (P space) [24]. A central point under this approach is the decomposition of evolution into two processes taking place in two distinct “spaces”: G space and P space. There are four key components of this evolutionary process: (1) the epigenetic process generates the phenotype using genotypic information (2) natural selection acts in P space to shift the average phenotype of the parents away from the average phenotype of all individuals (3) the identity of successful parents determines which genotypes are preserved and (4) genetic processes such as mutation and recombination alter the position in G space [2]. Convincing examples of this process are provided by the numerous varieties of fruits, such as apples, and of dogs, cats and other domestic animals that have been generated by targeted human selection from essentially the same genotypes, which has been achieved in only the last two thousand years in many cases.

Under the above approach, it is tempting to examine whether a given “environmental factor”, such as prolonged cooling of the pupae, may have reproducible effects on the resulting phenotypes of a certain genotype. Our test species of butterfly, P. icarus, is particularly well suited for this type of experiment, as the blue structural coloration on the dorsal wing surface of this species used for sexual communication [23] exhibits a high degree of stability [14,25], while the alteration of the pigment-based pattern on the ventral wing surface exhibits fairly linear dependence on the duration of cooling at 5 °C to which freshly formed pupae are subjected. Therefore, we repeated our earlier cooling experiments using 200 pupae resulting from 220 larvae reared under controlled conditions as described previously [14].

To get further insights in the phenotypic modification induced by prolonged cooling of the freshly formed pupae of P. icarus butterflies [14] we wanted to answer a number of questions:

  • The linear dependence and the slope, characterizing quantitatively the magnitude of the modifications on the ventral wing patterns versus the cooling time, is the same between different experiments?
  • Our previous results indicated that the genes governing the production of the photonic nanoarchitecture responsible for the blue coloration of the dorsal wing surface of the males must be present in the genome of both sexes [14]. Linked to this: if all the progenitors originate from the same population, and were collected at the same time, how large is the deviation in the position of the blue reflectance maxima of the females with induced blue coloration?
  • Is there a limit in the number of brown pigmented scales converted to blue colored by nanoarchitectures, or is it possible to convert most, or all? This conversion process implies a fundamental modification of the cellular processes as the two coloration mechanisms are radically different.
  • The common origin and the number of the reared larvae together were sufficient to allow the investigation of the relation of eclosed individuals and that of individuals eclosed with defects. This aspect was not discussed in our previous work.

We found that the alteration of the pigment-based pattern of the ventral wings induced by controlled cooling exhibited a remarkably high degree of reproducibility. Additionally, the blue coloration on the dorsal wings of the cooled females showed significantly greater deviation from the color of the wild males than did the spectral deviation of the cooled males. The fraction of butterflies that eclosed from cooled pupae showing defects after the termination of cooling indicated three stages in the duration of cooling: 0 to 4 weeks, 4 to 8 weeks, and 8 to 12 weeks. The changes in the arrangement of the scales and the micron-scale morphology of the blue scales of females support this division of the cooling time into three stages.

How do plants sense light?

Since the 19th century, it has been known that a plant's response to light can be sensitive to wavelength. Hunt ( 1844 , 1854 ) identified that the extreme red portion of the spectrum was associated with flowering and that blue light induced germination of seed, independently of the broad spectral range of light associated with the ‘decomposition of carbonic acid’ (photosynthesis). During the 20th century, several plant pigments involved in these and other responses were identified, and action spectra for several such photoreceptor pigments have been defined for example cryptochrome has been shown to respond to light between 390 to 530 nm (violet to blue/green Ahmad et al. 2002 ) phototropins respond primarily to blue light (Christie 2007 ) and phytochrome primarily to red and/or far-red light, depending on the form (Casal, Candia & Sellaro 2014 ). In algae, a wide range of pigments spanning the visible spectrum have been identified (Rockwell et al. 2014 ).

The best known action spectrum for plants is that of photosynthesis photosynthetically active radiation (PAR), usually defined as light between 400 and 700 nm, has an action spectrum defined by the absorbance spectra of chlorophyll and carotenoids. Because photosynthesis is a quantum process, the flux of photons, rather than energy is appropriate, and it is usually quantified as a photosynthetic photon flux density (PPFD) with units of μmol photons m −2 s −1 . As short-wavelength photons carry more energy than those at longer wavelengths, and both the sensitivity of human vision and that of photosynthetic pigments vary considerably in their absorption at different wavelengths, the relationship between irradiance, illuminance and PPFD is strongly sensitive to the spectral distribution of the light source. The effect of artificial light at night on net photosynthesis in the environment is limited due to the low quantum flux densities associated with outdoor lighting when compared to daylight. While theoretically urban skyglow may be sufficient to induce a small photosynthetic response (Raven & Cockell 2006 ), in practice measureable effects on carbon fixation are likely to be limited to situations where leaves are in very close proximity to light sources (such as the canopies of trees around street lights), or when artificial lighting is introduced into naturally dark situations such as cave systems. In the latter case, the installation of lighting in caves for tourism is often sufficient to support Lampenflora, communities of algae, bryophytes and vascular plants solely reliant on electric lighting as an energy source (Lefèvre 1974 Johnson 1979 ) .

In addition to the use of light as an energy source for photosynthesis, plants utilize a suite of other photoreceptors in order to sense information about their environment, the time of day and season of the year. The photosynthetic system itself is sensitive to light at night, providing a set of secondary pathways through which artificial light could influence carbon fixation. Poulin et al. ( 2014 ) showed that low levels of light from a high-pressure sodium street light, at an illuminance equivalent to that observed at the shore of an urban lakeside (6.6 lux), significantly changed several aspects of the photobiology of phytoplankton, including decreasing the intracellular chlorophyll a concentration and the number of Rubisco molecules per cell. In higher plants, light quality, even at low fluence rates, is known to affect physical characteristics of the photosystem, such as leaf stomatal density, as well as the opening of stomata (Smith 1982 ).

Detection of photoperiod in plants is not always, if ever, a simple function of the photoreversible forms of phytochrome, however. In the facultative long-day plant Arabidopsis thaliana, night interruptions from red, far-red or blue light are all effective in inducing flowering (Goto, Kumagai & Koornneef 1991 ). Cryptochromes, sensitive to light in the UV-A, violet and blue portions of the spectrum, act together with phytochromes to regulate the circadian clock, keeping daily rhythms set to a 24-h cycle of light and darkness. Photoperiodic control of flowering integrates both the circadian clock, and sensing of the length of the dark period thus, there is an interaction between the detection of daily and seasonal cycles, and between photoreceptor systems. The cryptochrome/photolyase family of photoreceptors also plays critical roles in controlling a wide range of light-induced responses in germination, growth and development, and shade avoidance (Kami et al. 2010 ), as well as DNA repair (Fortunato et al. 2015 ). A further blue light-sensitive receptor protein, phototropin, is responsible for phototropism, the growth of plant organs towards a light source.

Figure 3 shows the spectral power distribution of five types of lighting frequently used in outdoor street lighting, along with the relationship between PPFD (photosynthesis), the PSS (phytochrome) and the relative amount of blue light between 350 and 500 nm (cryptochrome and phototropins).

The detection of light in plants is complex, often relies on more than one physiological pathway and may have partial redundancy, so that processes induced by one photoreceptor system may also be induced or repressed by another system (Song, Ito & Imazuimi 2010 ). Furthermore, processes that rely on light-induced responses such as photoperiodism in one species or phenotype may be linked to other environmental cues in others (Basler & Körner 2012 ).

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JCM conceived the project JCM performed qPCR experiments JCM and SK performed biomass experiments SA and JCM performed carotenoid extraction, UPLC measurements and data analysis MAS and WT performed photosynthetic measurements and analysis JM and SA performed apocarotenoid profiling and data analysis VT and DT performed hormone measurements and analysis JCM wrote the article with input from MAS and RB.

All relevant data can be found within the manuscript and its supporting materials.

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