Sessions, Sharing and Downloads

Sessions, Sharing and Downloads | Website Update

Now you can save and share your analysis as sessions or download your data as a spreadsheet.

The data viewer on PhotosynQ is the tool to analyze your collected data. You can filter the data set and create sub-sets (Series), you can Plot parameters in various ways, view the data on a map based of the geo-location attached to each measurement, do simple statistics, or dive into every value using the spreadsheet. We are introducing a few new functions, we hope you will give you a better experience.

Sessions

Now you can save your results as sessions when analyzing the data. Every session will save your current dashboard, plot, map, filter settings/series and thresholds. They are a great way of saving interesting observations, compare different filters, thresholds, without having to repeat all the steps to get there.

Sharing a Session

When you save a session, you will notice a checkbox labeled shareable, making the session available to others when checked. After you saved your session, just click on the copy button in the list of available sessions, to save the link to your clipboard. Use the link, to share your findings with collaborators, in the forums or for presenting them in the Project results section. You can also un-share the session at any time. The link will still be pointing to the Project’s data, but your session is no longer available. In case you make up your mind, just re-share it and the link works again.

Auto-Save

When you have been been analyzing your data, you might have noticed, that the filters and thresholds you were applying got saved and re-applied the next time you opened the dataset. This was only saved locally, so opening your project on a different computer, would mean you have to start all over again. Now it gets saved to the cloud, so you can continue working where you have left off, even when you are using different computer.


Downloads

We developed the Data Viewer so you can analyze the measurements you have collected for a project, online. But we do understand, that downloading the data and using it in spreadsheets like Excel, Origin or others can be necessary. To this point, we have offered libraries for Python and R to get data from PhotosynQ into an easy to use format to work with. Now we also offer a download* of the data in a spreadsheet (xlsx) or in the JSON format right from the project page.

Yet, we strongly recommend you view your data using the data viewer, since there you can flag measurements that were not taken correctly, you can look at raw traces, etc. That way you can ensure the best data quality, when it comes to your final analysis.

*The downloads are only available for the project lead and project collaborators


Statistics – Summary

The data viewer is offering simple statistic functions as well as a summery for a selected parameter. The histogram in the summary has been extended and is showing now the normal distribution for the sample as well.

Please be aware, that all functions are currently at a beta stadium, so you might experience some issues and the functionality might be different in the final version.

New PhotosynQ Related Publication

Check out the new publication in the journal Front. Plant Sci., using the MultispeQ and PhotosynQ Platform (10.3389/fpls.2018.00767)

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)

Soltani A, MafiMoghaddam S, Oladzad-Abbasabadi A, Walter K, Kearns PJ, Vasquez-Guzman J, Mamidi S, Lee R, Shade AL, Jacobs JL, Chilivers MI, Lowry DB, McClean P and Osorno JM

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the Biocontrol Science and Technology, using the MultispeQ and PhotosynQ Platform (10.1080/09583157.2017.1376035)

Genotype-specific responses to the effects of commercial Trichoderma formulations in lentil (Lens culinaris ssp. culinaris) in the presence and absence of the oomycete pathogen Aphanomyces euteiches

Pratibha Prashar & Albert Vandenberg

Members of the endophytic fungal genus Trichoderma have been established as plant-beneficial microbes and are most successful commercial biologicals in the form of bio-fertilisers, biocontrol agents, and growth stimulators. We report the variable interactions among different lentil genotypes and Trichoderma strains in both the presence and absence of biotic stress (root-rot pathogen Aphanomyces euteiches). Two commercial Trichoderma formulations, namely RootShield® (RS) and RootShield® Plus (RSP) based on T. harzianum T22 and T. virens G41, respectively, were evaluated for control of Aphanomyces root rot and plant growth promotion in 23 wild and cultivated lentil genotypes. No significant disease control was recorded with either formulation in any lentil genotype. Significant genotype-specific plant growth promotion was observed in terms of root and shoot development and leaf parameters in a genotype-specific manner. Genotypes of Lens culinaris and Lens tomentosus, both in the primary lentil gene pool, demonstrated the maximum response. The overall effect of Trichoderma treatment was markedly higher under biotically stressed conditions in comparison to unstressed conditions. In many cases, negative responses were recorded, particularly in the absence of root-rot disease. L. tomentosus PI 572390 exhibited positive responses for most of the tested parameters. Our findings clearly indicate that, in the case of lentil, plant genotype plays a major role in interactions among the tested Trichoderma strains and the plant. Moreover, the influence of Trichoderma was greater and more favourable under conditions of biotic stress vs. the absence of stress.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the Journal of Plant Breeding and Crop Sciences, using the MultispeQ and PhotosynQ Platform (10.5897/JPBCS2017.0679 )

Evaluation of Cowpea Genotypes for Resistance to Fusarium redolens in Uganda

Namasaka Roy Wanjala, Geoffrey Tusiime, Orawu Martin, Paul Gibson, Symphorien Agbahoungba, Alladassi Mahule Elyse Boris, Richard Edema

Fusarium related root rots have been associated with reduced cowpea productivity in Uganda. Sources of genetic resistance to Fusarium redolens which was found to be the most virulent have been identified but the mode of inheritance of the genes conferring the resistance is unknown. This study aims to investigate how the genes for resistance to F. redolens are inherited in cowpea. Four F. redolens root rot resistant cowpea genotypes were crossed with four intermediately resistant and 2 susceptible cowpea genotypes using North Carolina mating design II. The F1 and the parents were evaluated and data were collected on resistance to seed rot, leaf chlorophyll amount, produced lateral roots, response to plant mortality and root rot severity. Results revealed that additive gene effects were significant for all evaluated traits and non-additive genetic effects were significant in resistance to seed rot and chlorophyll amount. General combining ability (GCA) effects showed that the Asontem genotype was a good combiner for increased lateral roots production and resistance to root rot. Degree of dominance estimates revealed that response to plant mortality, root rots and increased lateral root production traits were recessively inherited while seed rot and amount of leaf chlorophyll were dominantly inherited.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in Photosynthesis Research, using the MultispeQ and PhotosynQ Platform (10.1007/s11120-017-0449-9)

Faster photosynthetic induction in tobacco by expressing cyanobacterial flavodiiron proteins in chloroplasts

Rodrigo Gómez, Néstor Carrillo, María P. Morelli, Suresh Tula, Fahimeh Shahinnia, Mohammad-Reza Hajirezaei, Anabella F. Lodeyro

Plants grown in the field experience sharp changes in irradiation due to shading effects caused by clouds, other leaves, etc. The excess of absorbed light energy is dissipated by a number of mechanisms including cyclic electron transport, photorespiration, and Mehler-type reactions. This protection is essential for survival but decreases photosynthetic efficiency. All phototrophs except angiosperms harbor flavodiiron proteins (Flvs) which relieve the excess of excitation energy on the photosynthetic electron transport chain by reducing oxygen directly to water. Introduction of cyanobacterial Flv1/Flv3 in tobacco chloroplasts resulted in transgenic plants that showed similar photosynthetic performance under steady-state illumination, but displayed faster recovery of various photosynthetic parameters, including electron transport and non-photochemical quenching during dark–light transitions. They also kept the electron transport chain in a more oxidized state and enhanced the proton motive force of dark-adapted leaves. The results indicate that, by acting as electron sinks during light transitions, Flvs contribute to increase photosynthesis protection and efficiency under changing environmental conditions as those found by plants in the field.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in Plant Physiology, using the MultispeQ and PhotosynQ Platform (10.1104/pp.17.01624)

The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain

Andreas Carstensen, Andrei Herdean, Sidsel Birkelund Schmidt, Anurag Sharma, Cornelia Spetea, Mathias Pribil, Søren Husted

Phosphorus (P) is an essential macronutrient, and P deficiency limits plant productivity. Recent work showed that P deficiency affects electron transport to photosystem I (PSI), but the underlying mechanisms are unknown. Here, we present a comprehensive biological model describing how P deficiency disrupts the photosynthetic machinery and the electron transport chain through a series of sequential events in barley (Hordeum vulgare). P deficiency reduces the orthophosphate concentration in the chloroplast stroma to levels that inhibit ATP synthase activity. Consequently, protons accumulate in the thylakoids and cause lumen acidification, which inhibits linear electron flow. Limited plastoquinol oxidation retards electron transport to the cytochrome b6f complex, yet the electron transfer rate of PSI is increased under steady-state growth light and is limited under high-light conditions. Under P deficiency, the enhanced electron flow through PSI increases the levels of NADPH, whereas ATP production remains restricted and, hence, reduces CO2 fixation. In parallel, lumen acidification activates the energy-dependent quenching component of the nonphotochemical quenching mechanism and prevents the overexcitation of photosystem II and damage to the leaf tissue. Consequently, plants can be severely affected by P deficiency for weeks without displaying any visual leaf symptoms. All of the processes in the photosynthetic machinery influenced by P deficiency appear to be fully reversible and can be restored in less than 60 min after resupply of orthophosphate to the leaf tissue.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

 

Check out the new publication in the American Journal of Plant Sciences, using the MultispeQ and PhotosynQ Platform (10.4236/ajps.2017.89154)

Evaluation of Cowpea Genotypes for Resistance to Fusarium redolens in Uganda

Roy Wanjala Namasaka, Geoffrey Tusiime, Martin Orawu, Paul Gibson, Josiane Nyiramugisha, Richard Edema

Fusarium redolens, a virulent fungus which causes damping off, leaf yellowing, wilting and root rots has recently been devastating cowpea fields in Uganda. This study aimed at identifying cowpea genotypes that are resistant to Fusarium redolens. Therefore, ninety cowpea genotypes were evaluated two times against a highly virulent Fusarium redolens (isolate from Zombo in Paidha district) in the screen house in 2016. Genotype effect was highly significant (P < 0.001) for root rot severity. Based on the Index of Susceptibility (IS), three genotypes (Asontem, Dan1 LA and IT89KD-88) remained resistant (IS < 3.5) over the two screening periods, 72 moderately resistant (3.5 ≤ IS < 6.5) and 11 susceptible (IS ≥ 6.5). Resistance was found to be enhanced by presence of lateral roots above or at the ground level. Further results suggested a difference in genetic control of resistance to root rots and seed rots caused by Fusarium redolens. All the released varieties tested (SECOW 1 T, SECOW 2 W, SECOW 3 B, SECOW 4 W and SECOW 5 T) had moderate resistance to Fusarium redolens. Correlation analysis revealed root rot severity was strongly correlated to disease incidence (+0.64, P < 0.001), to proportion of plants with lateral roots (−0.56, P < 0.001), to amount of leaf chlorophyll (−0.53, P < 0.001) and to proportion of plants that died prematurely due to Fusarium redolens infection (+0.45, P < 0.001). No significant correlation was detected between root rot severity and proportion of plants that germinated. The established resistance could be exploited for improvement of farmer preferred cowpea varieties towards Fusarium redolens resistance in Uganda.


More PhotosynQ related publications are available here