Optical sensors combined with machine learning algorithms have led to significant advances in seed science. These advances have facilitated the development of robust approaches, providing ...decision-making support in the seed industry related to the marketing of seed lots. In this study, a novel approach for seed quality classification is presented. We developed classifier models using Fourier transform near-infrared (FT-NIR) spectroscopy and X-ray imaging techniques to predict seed germination and vigor. A forage grass (Urochloa brizantha) was used as a model species. FT-NIR spectroscopy data and radiographic images were obtained from individual seeds, and the models were created based on the following algorithms: linear discriminant analysis (LDA), partial least squares discriminant analysis (PLS-DA), random forest (RF), naive Bayes (NB), and support vector machine with radial basis (SVM-r) kernel. In the germination prediction, the models individually reached an accuracy of 82% using FT-NIR data, and 90% using X-ray data. For seed vigor, the models achieved 61% and 68% accuracy using FT-NIR and X-ray data, respectively. Combining the FT-NIR and X-ray data, the performance of the classification model reached an accuracy of 85% to predict germination, and 62% for seed vigor. Overall, the models developed using both NIR spectra and X-ray imaging data in machine learning algorithms are efficient in quickly, non-destructively, and accurately identifying the capacity of seed to germinate. The use of X-ray data and the LDA algorithm showed great potential to be used as a viable alternative to assist in the quality classification of U. brizantha seeds.
Abstract
Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and ...physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: a RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.
Graphical Abstract
Graphical Abstract
KVFinder-web: A web-based application for cavity detection and characterization of any type of biomolecular structure.
Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from ...the increasing availability of biostructural data due to advances in structural determination and computational methods. In this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated data structures. To fulfill this need, we developed pyKVFinder, a Python package to detect and characterize cavities in biomolecular structures for data science and automated pipelines.
pyKVFinder efficiently detects cavities in biomolecular structures and computes their volume, area, depth and hydropathy, storing these cavity properties in NumPy arrays. Benefited from Python ecosystem interoperability and data structures, pyKVFinder can be integrated with third-party scientific packages and libraries for mathematical calculations, machine learning and 3D visualization in automated workflows. As proof of pyKVFinder's capabilities, we successfully identified and compared ADRP substrate-binding site of SARS-CoV-2 and a set of homologous proteins with pyKVFinder, showing its integrability with data science packages such as matplotlib, NGL Viewer, SciPy and Jupyter notebook.
We introduce an efficient, highly versatile and easily integrable software for detecting and characterizing biomolecular cavities in data science applications and automated protocols. pyKVFinder facilitates biostructural data analysis with scripting routines in the Python ecosystem and can be building blocks for data science and drug design applications.
Q-CEP (Qualificação dos Comitês de Ética em Pesquisa que compõem o Sistema CEP/Conep) is a nationwide project resulting from a partnership between the Brazilian National Research Ethics Commission ...(Conep), the Ministry of Health and Hospital Moinhos de Vento (HMV). It was developed to consolidate policy for ethical review of research with human beings in all members of the CEP/Conep System, Brazil's national system of institutional review boards. The aim of this study was therefore to report on the experience and results of the Q-CEP project. An observational, retrospective study includes data from the Q-CEP, obtained from visits to all the institutional research ethics committees (RECs) in the country. The actions implemented by Q-CEP were part of a two-step process: (i) training visits to each REC; (ii) development of distance learning modules on strategic topics pertaining to research ethics evaluation. The data presented herein cover step one (training visits), defined by Q-CEP as the diagnostic stage of the project. For a country with social and economics inequalities such as Brazil, this is a particularly important stage; an accurate picture of reality is needed to inform planning of quality improvement strategies. In 2019-2021, Q-CEP visited 832 RECs and trained 11,197 people. This sample covered almost all active RECs in the country; only 4 (0.5%) were not evaluated. Of the 94 items evaluated, 62% did not reach the target of at least 80% compliance and around 1/4 (26%) were below 50% compliance. The diagnostic stage of the process revealed inadequacies on the part of the RECs in their ethical reviews. The analysis of informed consent forms showed compliance in only 131 RECs (15.74%). The description of pending issues made by RECs in their reports was compliant in 19.33% (n = 161). Administrative and operational aspects were also considered inadequate by more than half of the RECs. Overall, Brazilian RECs showed poor compliance in several aspects of their operation, both in ethics evaluation and in other processes, which justifies additional training. The Q-CEP project is part of a quality improvement policy promoted by the Brazilian Ministry of Health. The data obtained in the diagnostic step of the project have contributed to the qualification and consolidation of one of the world's largest research ethics evaluation systems.
How much interactivity is in a seed‐seedling transition system? We hypothesize that seed‐seed, seed‐seedling, and seedling‐seedling interactions can drive the early plant development in artificial ...growth systems directly due to mutual stimulation phenomena. To test the hypothesis, we performed seed germination measurements, gene expression in germination sensu stricto, water dynamics in germinating seeds, and information theory. For a biological model, we used Solanum lycocarpum A. St.‐Hil. seeds. This is a neotropical species with high intraspecific variability in the seed sample. Our findings demonstrate that the dynamic and transient seed‐seedling transition system is influenced by the number of individuals (seed or seedling) in the artificial system. In addition, we also discuss that: (1) the information entropy enables the quantification of system disturbance relative to individuals at the same physiological stage (seed‐seed or seedling‐seedling), which may be determinant for embryo growth during germination and (2) the intraspecific communication in seed‐seedling transition systems formed by germinating seeds has the potential to alter the expression pattern of key genes for embryo development. Therefore, the phenomenon of mutual stimulation during the germination process can be an important aspect of seed‐seedling transition, especially in laboratory conditions.
We hypothesize that by simulating the natural priming in seeds of a species that forms transient seed banks it is possible to clarify molecular aspects of germination that lead to the recruitment of ...seedlings when the next rainy season begins. We used seeds of Solanum lycocarpum as a biological model. Our findings support the idea that the increment of seed germination kinetics when the rainy season returns is mainly based on the metabolism and embryonic growth, and that the hydropriming, at the end of seed dispersion, increases the germination window time of these seeds by mainly increasing the degradation of galactomannan of the cell wall. This can improve the energy supply (based on carbon metabolism) for seedling growth in post-germination, which improves the seedling's survival chances. From these findings, we promote a hypothetical model about how the priming at the end of the rainy season acts on mRNA synthesis in the germination of seeds from transient banks and the consequence of this priming at the beginning of the following rainy season. This model predicts that besides the Gibberellin and Abscisic Acid balance (content and sensitivity), Auxin would be a key component for the seed-seedling transition in Neotropical areas. Seed collection was performed under authorization number SISGEN AB0EB45.
Breeding for drought tolerance is a challenging task that requires costly, extensive, and precise phenotyping. Genomic selection (GS) can be used to maximize selection efficiency and the genetic ...gains in maize (Zea mays L.) breeding programs for drought tolerance. Here, we evaluated the accuracy of genomic selection (GS) using additive (A) and additive + dominance (AD) models to predict the performance of untested maize single-cross hybrids for drought tolerance in multi-environment trials. Phenotypic data of five drought tolerance traits were measured in 308 hybrids along eight trials under water-stressed (WS) and well-watered (WW) conditions over two years and two locations in Brazil. Hybrids' genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GS analyses were performed using genomic best linear unbiased prediction by fitting a factor analytic (FA) multiplicative mixed model. Two cross-validation (CV) schemes were tested: CV1 and CV2. The FA framework allowed for investigating the stability of additive and dominance effects across environments, as well as the additive-by-environment and the dominance-by-environment interactions, with interesting applications for parental and hybrid selection. Results showed differences in the predictive accuracy between A and AD models, using both CV1 and CV2, for the five traits in both water conditions. For grain yield (GY) under WS and using CV1, the AD model doubled the predictive accuracy in comparison to the A model. Through CV2, GS models benefit from borrowing information of correlated trials, resulting in an increase of 40% and 9% in the predictive accuracy of GY under WS for A and AD models, respectively. These results highlight the importance of multi-environment trial analyses using GS models that incorporate additive and dominance effects for genomic predictions of GY under drought in maize single-cross hybrids.
We are clarifying how the functional embryo growth occurs in germinating seeds of Solanum lycocarpum A. St.‐Hil., a nurse plant with a central role in forest dynamics in the Cerrado (a biodiversity ...hotspot). For that, we used classical seed germination measurements (germinability, mean germination time, mean germination rate, coefficient of variation of the germination time, synchronisation index and germination time range) and gene expression of mRNA codifying key proteins/enzymes for the success in the seed–seedling transition (Cyclin, Actin, Small Heat Shock Protein, Glutathione S‐transferase, Malate Dehydrogenase, Alcohol Dehydrogenase). Our findings demonstrate: (a) Although germination kinetics in S. lycocarpum seeds is slower than that in tomato seeds, the fold change of genes codifying key enzymes for the embryo development is similar in germinating seeds of both species. (b) The genes used here are useful, from a technical point of view, for classifying commercial seed samples of the species in relation to physiological quality. More notably, cyclin and malate dehydrogenase genes have a greater expression, both in germination sensu stricto and in immediate post‐germination. (c) A molecular framework for the embryo growth in germinating seeds of S. lycocarpum can be a functional explication for the species to be a nurse plant. Thus, the overlapping of classical and contemporary measurements is especially interesting to those species playing a central role in the environment, such as nurse plants, and may represent a new conservationist paradigm.
We demonstrate how the overlapping between molecular biology and classical germination measurements can be used for ecophysiological purposes.
ABSTRACT The immediate need for the increase in wheat production to meet the future world demand, associated with the occurrence of drastic climatic events, such as drought, makes it necessary to ...develop drought-resilient genotypes. The aims of this work were to evaluate the use of drought-tolerance indices for the selection of wheat genotypes, to compare the genetic gains in grain yield using different selection strategies by means of a multi-trait index, and to select superior drought-tolerant wheat genotypes. The total of 31 tropical wheat lines was evaluated in two experiments. Five agronomic traits were accessed. The grain yield data from the stress and nonstress experiments were used to obtain five drought-tolerance indices. The data were subjected to mixed model analysis, and four selection scenarios were designed. There was a significant effect of genotype for all traits. The inclusion of drought-tolerance indices in the selection index provided superior genetic gains in drought condition. Seven lines were selected due the high frequency of favorable alleles for drought-tolerance and other important agronomic traits. Drought-tolerance indices are appropriate for characterizing the response of wheat genotypes to drought-stress. The inclusion of drought-tolerance indices along with agronomic traits in multi-trait selection strategies provides for superior gains in grain yield compared to the non-inclusion of the indices.
Sample size fluctuation and the restriction of measurements that demonstrate kinetics (typical of physiological processes) are two of the largest inferential constraints in studies on embryonic ...development in vitro. Thus, we hypothesize that a practical and robust way of aggregating knowledge on aspects of embryonic development in vitro is to use measurements based on the binary counting component. These are typically used to measure the germination process (intraeminal embryonal development). Our biological model was Dragon’s blood (Croton lechleri Müll Arg.), a species native to the Amazon with great socioeconomic impact. Matrices originating from two populations (one native and another cultivated) were the source of biological material. From this material, we studied five sampling densities (5, 25, 50, and 100 embryos), forming a 2 × 4 factorial ANOVA. Among the measurements studied, the coefficient of variation of time, uncertainty, and the synchronization index were the most sensitive to sample-size fluctuation. The synchronization index, however, also proved to be an interesting measurement to detect the parental effect related to the place of occurrence of the matrices. The embryonic development ability, mean development time, and mean development rate were not affected by fluctuations in the sample size or the origin of the material, demonstrating highly conserved traits of the species. Finally, in general, the measurements based on binary counting demonstrated robustness for modeling embryonic growth.
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