Hasil untuk "Botany"

Simeon Adebola, Chung Min Kim, Justin Kerr et al.

Commercial plant phenotyping systems using fixed cameras cannot perceive many plant details due to leaf occlusion. In this paper, we present Botany-Bot, a system for building detailed "annotated digital twins" of living plants using two stereo cameras, a digital turntable inside a lightbox, an industrial robot arm, and 3D segmentated Gaussian Splat models. We also present robot algorithms for manipulating leaves to take high-resolution indexable images of occluded details such as stem buds and the underside/topside of leaves. Results from experiments suggest that Botany-Bot can segment leaves with 90.8% accuracy, detect leaves with 86.2% accuracy, lift/push leaves with 77.9% accuracy, and take detailed overside/underside images with 77.3% accuracy. Code, videos, and datasets are available at https://berkeleyautomation.github.io/Botany-Bot/.

Davide De Benedittis, Giovanni Di Lorenzo, Franco Angelini et al.

According to the European Union's Habitat Directive, habitat monitoring plays a critical role in response to the escalating problems posed by biodiversity loss and environmental degradation. Scree habitats, hosting unique and often endangered species, face severe threats from climate change due to their high-altitude nature. Traditionally, their monitoring has required highly skilled scientists to conduct extensive fieldwork in remote, potentially hazardous locations, making the process resource-intensive and time-consuming. This paper presents a novel approach for scree habitat monitoring using a legged robot to assist botanists in data collection and species identification. Specifically, we deployed the ANYmal C robot in the Italian Alpine bio-region in two field campaigns spanning two years and leveraged deep learning to detect and classify key plant species of interest. Our results demonstrate that agile legged robots can navigate challenging terrains and increase the frequency and efficiency of scree monitoring. When paired with traditional phytosociological surveys performed by botanists, this robotics-assisted protocol not only streamlines field operations but also enhances data acquisition, storage, and usage. The outcomes of this research contribute to the evolving landscape of robotics in environmental science, paving the way for a more comprehensive and sustainable approach to habitat monitoring and preservation.

Fraser Binns

Li-Xie-Zhang classified instanton Floer minimal knots in balanced sutured manifolds subject to a condition on the fundamental group. In this paper, we give a similar classification in the Heegaard Floer homology setting. Since our classifications agree when they are both applicable, this provides further evidence for the conjecture of Kronheimer-Mrowka that instanton Floer homology and Heegaard Floer homology are isomorphic. We also study link Floer homology botany question in $S^1\times S^2$, showing that link Floer homology detects spherical braid closures among homologically nontrivial links.

Ipsita Datta, Tanushree Shah

We present new families of examples of non-simple prime Legendrian and transversal knots in tight Lens spaces, which demonstrate that the botany of Legendrians in Lens space is rich. In fact, there are more non-isotopic Legendrians that are topologically isotopic to the $n$-twist knot in a Lens space $L(α, β)$ than in $S^3$. We also include connect sum formulas for rational variants of classical invariants, $\mathrm{tb}_\mathbb{Q}$, $\mathrm{rot}_\mathbb{Q}$, and $\mathrm{sl}_\mathbb{Q}$, which indicate that prime knots are the right playground to look for exotic behaviour.

Fatema S. Mohamed, Rim Hamdy, Essam M. Abd-Elkhader

Hui Wu, Jia-Jie Yang, Chao-Qun Li et al.

Elliptic Fourier analysis (EFA) is a powerful tool for shape analysis, which is often employed in geometric morphometrics. However, the normalization of elliptic Fourier descriptors has persistently posed challenges in obtaining unique results in basic contour transformations, requiring extensive manual alignment. Additionally, contemporary contour/outline extraction methods often struggle to handle complex digital images. Here, we reformulated the procedure of EFDs calculation to improve computational efficiency and introduced a novel approach for EFD normalization, termed true EFD normalization, which remains invariant under all basic contour transformations. These improvements are crucial for processing large sets of contour curves collected from different platforms with varying transformations. Based on these improvements, we developed ElliShape, a user-friendly software. Particularly, the improved contour/outline extraction employs an interactive approach that combines automatic contour generation for efficiency with manual correction for essential modifications and refinements. We evaluated ElliShape's stability, robustness, and ease of use by comparing it with existing software using standard datasets. ElliShape consistently produced reliable reconstructed shapes and normalized EFD values across different contours and transformations, and it demonstrated superior performance in visualization and efficient processing of various digital images for contour analysis.The output annotated images and EFDs could be utilized in deep learning-based data training, thereby advancing artificial intelligence in botany and offering innovative solutions for critical challenges in biodiversity conservation, species classification, ecosystem function assessment, and related critical issues.

Catarina Leal, Ales Eichmeier, Kateřina Štůsková et al.

With a reduction in available chemical treatments, there is an increased interest in biological control of grapevine trunk diseases. Few studies have investigated the impact of introducing beneficial microorganisms in the rhizosphere on the existing indigenous soil microbiome. In this study, we explored the effect of two biocontrol agents (BCAs), Trichoderma atroviride SC1 (Ta SC1) (Vintec; Certis Belchim) and Bacillus subtilis PTA-271 (Bs PTA-271), on the grapevine rhizosphere bacterial and fungal microbiome as well as plant defense expression using high-throughput amplicon sequencing and quantitative real-time polymerase chain reaction (PCR), respectively. Additionally, we quantified both Ta SC1 and Bs PTA-271 in the rhizosphere over time using droplet digital PCR. The fungal microbiome was more affected by factors such as soil type, BCA treatment, and sampling time compared with the bacterial microbiome. Specifically, Ta SC1 application produced negative impacts on fungal diversity, whereas application of BCAs did not affect bacterial diversity. Interestingly, the survival and establishment of both BCAs showed opposite trends depending on the soil type, indicating that the physicochemical properties of soils have a role in BCA establishment. Fungal co-occurrence networks were less complex than bacterial networks but highly impacted by Ta SC1 application. Soils treated with Ta SC1 presented more complex and stable co-occurrence networks, with a higher number of positive correlations. Induced grapevine defenses also differed according to the soil, being more affected by BCA inoculation on sandy soil. The findings of this research emphasize the complex relationships among microorganisms in the rhizosphere and highlight the significance of taking into account various factors, such as soil type, sampling time, and BCA treatment, and their influence on the structure and dynamics of microbial communities.

L Medrano-González, K Audley, CS Baker et al.

Here, we describe variation in mtDNA haplotypes among 22 individual humpback whales off the Guerrero coast in southern Mexico and compare this to other wintering regions in the eastern North Pacific Ocean using published data. After correcting for different sample sizes, Guerrero humpback whales fit the cline in the eastern North Pacific in which A types are more abundant northwards, while E and F types are more abundant southwards. Whales observed around Guerrero in early winter exhibited a greater frequency of F types that are also observed earlier in winter at Bahía de Banderas in the mainland region, suggesting a seasonal passage of whales from Mexico to Central America. Four diversity indices were higher in different wintering regions between Nayarit and Guerrero. Departures from neutrality were observed in the bordering wintering grounds of the region. Four measures of differentiation by distance indicated boundaries between Nayarit and Southern Jalisco, and between Guerrero and Oaxaca, suggesting a transitional region between wintering regions of Mexico and Central America from 17.5° to 19.5°N.

Rekha Boora, Neelam Rani, Santosh Kumari et al.

Climate change is now evident and severe water shortage due to unpredictable raining season along with extended summers is expected to hamper crop production across the globe. Application of nanoparticle based formulations is one of the most sought after approach that is being explored currently to alleviate drought stress impact on plants. The present study was aimed to evaluate the potential of biosynthesized silica nanoparticles (silica NPs) in improving the drought tolerance of wheat. Four different concentrations of silica NPs (30, 60, 90, and 120 ppm) were used to treat wheat plants grown under two irrigation regimes- 50% soil moisture content (drought) and 100% soil moisture content (well-watered). The induced drought caused a prominent reduction in both - the crop yield and the morphological parameters of the crop. Foliar application of silica NPs at all concentrations, increased the plant's tolerance towards water stress but 60 ppm concentration was found to be most effective amongst all. After treatment with silica NPs at 60 ppm concentration, the plant height increased by 8.28%, spikes per plant by 98%, seeds per spike by 12.4%, and thousand seed weight by 37.5% as compared to the control. Besides this, expression levels of four drought-stress responsive genes-ABC1, Wdhn13, CHP, and EXP2 was also studied. We observed an enhanced expression of all the stress genes after treatment with silica nanoparticles in wheat plants grown under water deficient conditions, clearly supporting the influence of NP treatment at gene/molecular level. In nutshell, we conclude that silica nanoparticles have the potential to significantly ameliorate the negative impact of drought stress by reviving plant growth and modulating gene expression.

Luis E. Nieto-Barajas

In the biology field of botany, leaf shape recognition is an important task. One way of characterising the leaf shape is through the centroid contour distances (CCD). Each CCD path might have different resolution, so normalisation is done by associating each contour to a circular density. Densities are rotated by subtracting the mean or mode preferred direction. Distance measures between densities are used to produce a hierarchical clustering method to cluster the leaves. We illustrate our approach with a motivating small dataset as well as a larger dataset.

Giuliano Vitali

The present study is aimed at analysing the benefits of an ontological approach in Functional Structural Plant Modelling. The ontological approach has been used at two levels, to refine the conceptual modelling approach, and to define the nomenclature of the plant. To the scope available domain-specific ontologies describing plant entities and their relations have been analysed to verify how they support botanical and phenological descriptions at different scales. The analysis put in evidence how ontologies have a large number of shared terms and also host a large number of structural and dynamical relations among entities, however, they still lack semantic annotation useful for a complete and consistent Conceptual Modelling, as put in evidence by Foundation Ontologies. Nonetheless, the analysis also put in evidence the potential of the approach and the basis for designing a bridged ontology to be used to produce tools for learning botany, growing techniques, and supporting precision Agriculture.

Katarzyna Szajko, Jarosław Ciekot, Iwona Wasilewicz-Flis et al.

Tarek Hamel, Noelia Hidalgo Triana, Amel Meddad-Hamza et al.

The identification of priority conservation areas (PCA) plays an important role in biodiversity conservation, but uncertainties create challenges for conservation planning. The objective was to test a method based on 'taxonomic distinctness' (TD) and to identify PCA to quantify the heritage value of a territory and establish the most appropriate conservation measures. The researchers performed a systematic and phytogeographical analysis of ten islands in northeastern Algeria, a biological hotspot with heterogeneous ecosystem types and subject to socio-economic pressures. The biological diversity represented by 223 species in these environments reflects a high rate of endemicity (13%).

Marcelo Augusto Pereira Coelho Dias, Eduarda Melo de Abreu Vieira, Clodoaldo Lopes de Assis et al.

Reptiles can be on the diet of some bird species, and the glass lizard Ophiodes fragilis seems to be no exception. Although predation events are not easily recorded, in this work we document a new record of predation by C. cristata upon O. fragilis. The event occurredin November 2017 in the municipality of Viçosa, state of Minas Gerais, Brazil, and helps to fill a gap in trophic relationships between the lizard and its predators.

Hai-Xiang Jin, Ming Jiang, Jian-Feng Yang et al.

<i>Zoysia japonica</i> is a warm-season turfgrass that is extensively used in landscaping, sports fields, and golf courses worldwide. Uncovering the low-temperature response mechanism of <i>Z. japonica</i> can help to accelerate the development of new cold-tolerant cultivars, which could be used to prolong the ornamental and usage duration of turf. A novel <i>Z. japonica</i> biotype, YueNong-9 (YN-9), was collected from northeastern China for this study. Phenotypic measurements, cold-tolerance investigation, and whole-transcriptome surveys were performed on YN-9 and LanYin-3 (LY-3), the most popular <i>Z. japonica</i> cultivar in Southern China. The results indicated the following: YN-9 has longer second and third leaves than LY-3; when exposed to the natural low temperature during winter in Guangzhou, YN-9 accumulated 4.74 times more anthocyanin than LY-3; after cold acclimation and freezing treatment, 83.25 ± 9.55% of YN-9 survived while all LY-3 leaves died, and the dark green color index (DGCI) value of YN-9 was 1.78 times that of LY-3; in YN-9, there was a unique up-regulation of <i>Phenylalanine ammonia-lyase</i> (<i>PAL</i>), <i>Homeobox-leucine Zipper IV</i> (<i>HD-ZIP</i>), and <i>ATP-Binding Cassette transporter B8</i> (<i>ABCB8</i>) expressions, as well as a unique down-regulation of <i>zinc-regulated transporters and iron-regulated transporter-like proteins</i> (<i>ZIPs</i>) expression, which may promote anthocyanin biosynthesis, transport, and accumulation. In conclusion, YN-9 exhibited enhanced cold tolerance and is thus an excellent candidate for breeding cold-tolerant <i>Z. japonica</i> variety, and its unique low-temperature-induced anthocyanin accumulation and gene responses provide ideas and candidate genes for the study of low-temperature tolerance mechanisms and genetic engineering breeding.

Andrea Loddo, Cecilia Di Ruberto, A. M. P. G. Vale et al.

Image analysis is an essential field for several topics in the life sciences, such as biology or botany. In particular, the analysis of seeds (e.g. fossil research) can provide significant information on their evolution, the history of agriculture, plant domestication and knowledge of diets in ancient times. This work aims to present software that performs image analysis for feature extraction and classification from images containing seeds through a novel and unique framework. In detail, we propose two plugins \emph{ImageJ}, one able to extract morphological, textual and colour features from seed images, and another to classify seeds into categories using the extracted features. The experimental results demonstrated the correctness and validity of both the extracted features and the classification predictions. The proposed tool is easily extendable to other fields of image analysis.

Sergei Esipov, Clara Salueña

Spatio-temporal analysis typically performed in botany and in statistical physics reveals persistent correlations of olive yields which range depend on the size of the averaging region. Mapping spatially correlated regions reveals areas which mimic historical spread of Olea europaea. These yield patterns are remarkable given the intensive nature of modern agriculture, and cannot be attributed to weather due to inability of weather variables to predict yields. Long-range correlations between olive trees may indicate long-range communications.

Lu Yu, Yuan Chen, Jie Shi et al.

Background: Ginsenosides are known as the principal pharmacological active constituents in Panax medicinal plants such as Asian ginseng, American ginseng, and Notoginseng. Some ginsenosides, especially the 20(R) isomers, are found in trace amounts in natural sources and are difficult to chemically synthesize. The present study provides an approach to produce such trace ginsenosides applying biotransformation through Escherichia coli modified with relevant genes. Methods: Seven uridine diphosphate glycosyltransferase (UGT) genes originating from Panax notoginseng, Medicago sativa, and Bacillus subtilis were synthesized or cloned and constructed into pETM6, an ePathBrick vector, which were then introduced into E. coli BL21star (DE3) separately. 20(R)-Protopanaxadiol (PPD), 20(R)-protopanaxatriol (PPT), and 20(R)-type ginsenosides were used as substrates for biotransformation with recombinant E. coli modified with those UGT genes. Results: E. coli engineered with GT95syn selectively transfers a glucose moiety to the C20 hydroxyl of 20(R)-PPD and 20(R)-PPT to produce 20(R)-CK and 20(R)-F1, respectively. GTK1- and GTC1-modified E. coli glycosylated the C3OH of 20(R)-PPD to form 20(R)-Rh2. Moreover, E. coli containing p2GT95synK1, a recreated two-step glycosylation pathway via the ePathBrich, implemented the successive glycosylation at C20OH and C3OH of 20(R)-PPD and yielded 20(R)-F2 in the biotransformation broth. Conclusion: This study demonstrates that rare 20(R)-ginsenosides can be produced through E. coli engineered with UTG genes. Keywords: biosynthesis, 20(R)-ginsenosides, ginsenoside, UDP-glycosyltransferase

Sohaib Younis, Claus Weiland, Robert Hoehndorf et al.

Herbaria worldwide are housing a treasure of 100s of millions of herbarium specimens, which are increasingly being digitized in recent years and thereby made more easily accessible to the scientific community. At the same time, deep learning algorithms are rapidly improving pattern recognition from images and these techniques are more and more being applied to biological objects. We are using digital images of herbarium specimens in order to identify taxa and traits of these collection objects by applying convolutional neural networks (CNN). Images of the 1000 species most frequently documented by herbarium specimens on GBIF have been downloaded and combined with morphological trait data, preprocessed and divided into training and test datasets for species and trait recognition. Good performance in both domains is promising to use this approach in future tools supporting taxonomy and natural history collection management.

Sara Hosseinzadeh Kassani, Peyman Hosseinzadeh Kassani

Due to the rapid development of technology, large amounts of heterogeneous data generated every day. Biological data is also growing in terms of the quantity and quality of data considerably. Despite the attempts for building a uniform platform to handle data management in Plant Science, researchers are facing the challenge of not only accessing and integrating data stored in heterogeneous data sources but also representing the implicit and explicit domain knowledge based on the available plant genomic and phenomic data. Ontologies provide a framework for describing the structures and vocabularies to support the semantics of information and facilitate automated reasoning and knowledge discovery. In this paper, we focus on building an ontology for Arabidopsis Thaliana in Plant Science domain. The aim of this study is to provide a conceptual model of Arabidopsis Thaliana as a reference plant for botany and other plant sciences, including concepts and their relationships.