Digging roots is easier with AI

The scale of root quantification in research is often limited by the time required for sampling, measurement and processing samples. Recent developments in Convolutional Neural Networks (CNN) have made faster and more accurate plant image analysis possible which may significantly reduce the time required for root measurement, but challenges remain in making these methods accessible to researchers without an in-depth knowledge of Machine Learning. We analyzed root images acquired from three destructive root samplings using the RootPainter CNN-software that features an interface for corrective annotation for easier use. Root scans with and without non-root debris were used to test if training a model, i.e., learning from labeled examples, can effectively exclude the debris by comparing the end-results with measurements from clean images. Root images acquired from soil profile walls and the cross-section of soil cores were also used for training and the derived measurements were compared with manual measurements. After 200 minutes of training on each dataset, significant relationships between manual measurements and RootPainter-derived data were noted for monolith (R 2=0.99), profile wall (R 2=0.76) and core-break (R 2=0.57). The rooting density derived from images with debris was not significantly different from that derived from clean images after processing with RootPainter. Rooting density was also successfully calculated from both profile wall and soil core images, and in each case the gradient of root density with depth was not significantly different from manual counts. Differences in root-length density (RLD: cm cm -3) between crops with contrasting root systems were captured using automatic segmentation at soil profiles with high RLD (1 to 5 cm cm -3) as well as at low RLD (0.1 to 0.3 cm cm -3). Our results demonstrate that the proposed approach using CNN can lead to substantial reductions in root sample processing workloads, increasing the potential scale of future root investigations.

Comparative Pharmacognostical Evaluation of Five Different Market Samples of Piper Longum Linn.

Pippalimoola (root of Piper longum.linn) is one of most important drug in Ayurveda used as single drug and in combination with other herbs ,minerals or metallic preparations for poly herbo-mineral formulations.. In Ancient literature we found that in the name of ‘Moola’(means firmly fixed a root) we must practice root but now a days instead of Pippali moola most of market samples are substituted with stem of same plant, so it is essential to check the botanical source of market samples.In this study,different five market samples of Pippalimoola were procured all over India and one sample (control) was collected after authentication of botanical source of plant.Pharmacognostical study was undertaken to observe morphological characters of market samples and compared with the collected sample. It was observed that out of five market samples; macroscopic and microscopic characters of one sample was matched with the characters of control root sample. While other four samples were found to be stem of the plant. Hence there is lots of variation in raw material of the plant in Indian market.

Does the rhythm and appliance type of rapid maxillary expansion have an effect on root resorption?: A comparative clinical study using micro–computed tomography

ABSTRACT Objectives To evaluate the volume, amount, and localization of root resorption in the upper first premolars by micro–computed tomography (micro-CT) after three different rapid maxillary expansion appliances and two different activation rhythms. Materials and Methods The patients were divided into three groups; Hyrax, acrylic cap splint (ACS), and full coverage acrylic bonded (FCAB) appliances. Each group was then divided into the following two subgroups: rapid maxillary expansion (RME) and semirapid maxillary expansion (SRME). After expansion was completed, the appliances were stabilized for 12 weeks during the retention period. For each group, 10 premolars (for a total of 60 premolars) were scanned with the micro-CT (SkyScan). The reconstructed 3D images of each root sample were divided into six regions. The resorption craters on these six different root surfaces were analyzed by special CTAn (SkyScan) software for direct volumetric measurements. Kruskal-Wallis one-way analysis of variance and Mann-Whitney U tests were used for statistical analysis. Results The total volume of root resorption was less with FCAB than with ACS and Hyrax (P < .001). In all groups, a greater volume of resorption was found on the buccal surface than on the lingual surface (P < .001). No significant differences were found between the RME and SRME groups (P > .05). Conclusions All expansion appliances caused root resorption in the upper first premolar teeth, but FCAB may be safer in terms of root resorption. The resorption craters were generally concentrated on the buccal surface. There was no effect of activation rhythm on root resorption.

UPLC-ESI-MRM/MS for Absolute Quantification and MS/MS Structural Elucidation of Six Specialized Pyranonaphthoquinone Metabolites From Ventilago harmandiana

Pyranonaphthoquinones (PNQs) are important structural scaffolds found in numerous natural products. Research interest in these specialized metabolites lies in their natural occurrence and therapeutic activities. Nonetheless, research progress has thus far been hindered by the lack of analytical standards and analytical methods for both qualitative and quantitative analysis. We report here that various parts of Ventilago harmandiana are rich sources of PNQs. We developed an ultraperformance liquid chromatography–electrospray ionization multiple reaction monitoring/mass spectrometry method to quantitatively determine six PNQs from leaves, root, bark, wood, and heartwood. The addition of standards in combination with a stable isotope of salicylic acid-D6 was used to overcome the matrix effect with average recovery of 82% ± 1% (n = 15). The highest concentration of the total PNQs was found in the root (11,902 μg/g dry weight), whereas the lowest concentration was found in the leaves (28 μg/g dry weight). Except for the root, PNQ-332 was found to be the major compound in all parts of V. harmandiana, accounting for ∼48% of the total PNQs quantified in this study. However, PNQ-318A was the most abundant PNQ in the root sample, accounting for 27% of the total PNQs. Finally, we provide novel MS/MS spectra of the PNQs at different collision induction energies: 10, 20, and 40 eV (POS and NEG). For structural elucidation purposes, we propose complete MS/MS fragmentation pathways of PNQs using MS/MS spectra at collision energies of 20 and 40 eV. The MS/MS spectra along with our discussion on structural elucidation of these PNQs should be very useful to the natural products community to further exploring PNQs in V. harmandiana and various other sources.

Digging roots is easier with AI

The scale of root quantification in research is often limited by the time required for sampling, measurement and processing samples. Recent developments in Convolutional Neural Networks (CNN) have made faster and more accurate plant image analysis possible which may significantly reduce the time required for root measurement, but challenges remain in making these methods accessible to researchers without an in-depth knowledge of Machine Learning. We analyzed root images acquired from three destructive root samplings using the RootPainter CNN-software that features an interface for corrective annotation for easier use. Root scans with and without non-root debris were used to test if training a model, i.e., learning from labeled examples, can effectively exclude the debris by comparing the end-results with measurements from clean images. Root images acquired from soil profile walls and the cross-section of soil cores were also used for training and the derived measurements were compared with manual measurements. After 200 minutes of training on each dataset, significant relationships between manual measurements and RootPainter-derived data were noted for monolith (R2=0.99), profile wall (R2=0.76) and core-break (R2=0.57). The rooting density derived from images with debris was not significantly different from that derived from clean images after processing with RootPainter. Rooting density was also successfully calculated from both profile wall and soil core images, and in each case the gradient of root density with depth was not significantly different from manual counts. Our results demonstrate that the proposed approach using CNN can lead to substantial reductions in root sample processing workloads, increasing the potential scale of future root investigations.

Assessment of Heavy Metals Contamination of Water and Cupscale Grass (Sacciolepisafricana) along the Epie Creek in Bayelsa State, Nigeria

This study was conducted to investigate the concentration of three heavy metals; iron, chromium and lead in surface water and plant (Sacciolepisafricana) tissues along the Epie creek. This was aimed at determining the heavy metal loading of surface waters and the extent of bioaccumulation in the most prevalent grass species found growing within the river course. Metals were determined using atomic absorption spectrophotometer. Result of water analysis recorded the least and most significant iron concentrations of 3.42 ± 0.06 mg/L and 12.06 ± 0.06 mg/L for Agudama and Edepie axis respectively. Contrastingly, water samples showed chromium and lead levels which were below their instrument measurable limits. Consequently, lead (Pb) and chromium (Cr) levels were within WHO permissible limits, while iron (Fe) exceeded regulatory standard for water samples collected from all field locations. Similarly, iron recorded elevated iron concentrations in plant (cupscale grass) with the least amount being revealed for Igbogene stem (196.63 ± 5.21 mg/kg), and the most concentration been reflected for Edepie root sample (9,423.17 ± 48.55 mg/kg). Even though iron levels prevalently exceeded recommended threshold in plants, the stem were mostly within limit for iron. The only grass sample depicting significant lead amount (0.34 mg/kg) was the stem section collected at Akenfa location. Evidently, metals were least stored in plant stems and most bioaccumulated in plant roots. Furthermore, Cr and Fe are the only significantly correlating metals in plants (r = 0.700, p < 0.01). Overall, the increasing level of Fe in the water environment is further indication of the impact of unregulated dumping of scraps and domestic waste along the creeks embankment.

Efficacy of e-beam irradiation on shelf-life and accompanied changes in major metabolites of Desmodium gangeticum (L.) DC., an Ayurveda medicinal plant

The effects of electron beam irradiation (5, 10 and 15 kGy) on shelf-life and major plant metabolites of an Ayurvedic medicinal plant Desmodium gangeticum was evaluated. Its root possesses incredible medicinal effects; hence powdered root sample (choorna) was subjected to radiation processing and thereby shelf-life extension. The root sample was found to possess an appreciable amount of phenolic and flavonoid compounds. Processing with radiation did not produce prominent changes in the phenolic content of samples even after storage for up to 12 months. In contrast, Calcium content was increased significantly (p < 0.05) on radiation processing wit 5 kGy and 15 kGy. Microbial status revealed that the untreated sample was acceptable only up to 4 months. A dose-dependent reduction in the microbial count resulted in all the radiation processed samples. Treatment with doses of 10 kGy and 15 kGy reduced the colony count to nil immediately after irradiation. Irradiation with 15 kGy kept the sample completely sterilized up to 2 months of storage and was acceptable even 12th month of storage. GC-MS analyses identified compounds with pharmacological importance such as methyl palmitate, mome-inositol, Neophytadiene, etc. Although, a slight change in mineral composition and phytochemicals were observed it could effectively decontaminate the medicinal herb and increase the shelf-life with minimum loss of major metabolites compared to other conventional methods of processing.

Anthropogenic and soil environmental drivers of arbuscular mycorrhizal community composition differ between grassland ecosystems

Interactions between arbuscular mycorrhizal fungi (AMF) and plants are sensitive to a myriad of underlying factors, including soil chemistry and land-use disturbances. Here we address how two grassland ecosystems (Ozark glades vs. tallgrass prairies) in south-central USA have been impacted by legacy effects from land-use disturbances (e.g., fire suppression in glades and tillage, fertilizer, row cropping, and grazing in prairies) and geological substrate (acidic versus calcareous bedrock). We surveyed AMF on the roots of two native generalist host species [Ruellia humilis Nutt. and Schizachyrium scoparium (Michx.) Nash] as well as plants randomly selected from the plant community. Glades on calcareous bedrock had a higher pH than those on acidic bedrock, and AMF communities on all three root sample types varied between acidic and calcareous bedrock locations. In prairies, both bedrock types had a similar soil pH, and AMF communities on all three root sample types varied across remnant and disturbed prairies. Shifts in AMF composition across land-use history included shifts in dominant AMF genera, and some unique rare AMF taxa were restricted to only calcareous glades or remnant prairies. Our findings suggest that reseeding prairie plant communities on cultivated lands does not restore AMF communities. Restoration projects need to address the soil environment and community.

The composition and diversity of arbuscular mycorrhizal fungi in karst soils and roots collected from mulberry of different ages

ABSTRACT: Arbuscular mycorrhizal fungi (AMF) have been attracted more scientific attentions due to its critical role in enhancement of drought tolerance of plants for growth and vegetation restoration in karst fragile ecosystem. However, scientists know little about the AMF composition and diversity occurring in root systems of mulberry (Morus sp.), and in karst habitats which return land use from mulberry forestry, as well as the effects of soil environment change on the diversity of the AMF communities. To understand: (1) the AMF community composition and diversity at different stage of returning cropland to forest; and (2) the effects of soil environment change on the diversity of the AMF communities, soil and mulberry root samples were collected from Bijie and Libo sites, China, which experienced one and ten years, respectively, after returning croplands to forest. With the high throughput 454-sequencing technology, 8 known genera including 83 virtual species were distinguished and the genera Glomus, Paraglomus, Archaeospora and Diversispora were found to be dominant in soil and root sample. Compared to the samples in Libo, the genera Glomus, Paraglomus, Acaulospora and Claroideoglomus in root samples at Bijie site had a relatively abundance of species indicating that the returning cropland to forest is benefit to the AMF diversity and abundance, which was attribute to the variation of soil physiochemical properties. This conclusion is of great significance for guiding the return of farmland to forests.

Arbuscular Mycorrhizal Fungi Associated with Wati (Piper methysticum), a Medicinal Plant from Merauke Lowland, Papua, Indonesia

Indonesia is rich of natural resources, including the diversity of agricultural crops and other valuable plants. Many plant species used by local people for traditional herbal medicine and some other species used by drug industries. Among these, Wati (Piper methysticum, Piperaceae) is one of the medicinal plant found in Merauke lowland, Papua. It has been cultivated by local people because of it high value as medicinal and cultural uses. Wati plant is used to treat anti-stress, rheumatism, respiratory tract infections, tuberculosis, gonorrhea, headache etc. The habitat, including the microorganism in the soil plays an important role in the growth of this plant. Therefore, this study was conducted to identify the arbuscular mycorrhizal fungi (AMF) associated with the rhizosphere of Wati from Merauke lowland. Soil and root samples were collected from different locations and the colonization percentage on the root sample were determined. Our results showed that the number of the spores in the soil samples was 45-89 spores/50 g soil, while the colonization percentage on the root was 38.46-83.3%. Among 13 AMF morphospecies that found on the soil samples, 10 were identified to genus level such as Glomus, Clariodeoglomus, Acaulospora and Scutellospora, while the other were unidentified. Further work will be needed such as trap-plant culture method to get more information on the diversity of AMF associated with Wati.