Developing vision-based analytic algorithms and software to dynamically measure key traits in seed germination

[Objectives] Seed is one of the most important research topics in plant research. The ability of dynamically detecting key seed germination traits provides important phenotypic evidence for researchers to understand plant survival, growth, development, and reproduction. Here, we proposed a set of algorithms for quantifying germination-related traits by combining automated image analysis, graph theory and supervised machine learning techniques. [Methods] Utilizing Poaceae such as wheat (Triticum aestivum) as a model plant, we applied automated image analysis together with machine learning algorithms (e.g. K-Nearest Neighbors, Support Vector Machine, Random forests) to train foreground and background objects, followed by background segmentation and object extraction based on image series collected from three weak gluten wheat varieties. Then, graph theory and two-dimensional skeletonization were employed to dynamically analyze changes of radicles and radicle tip positions to measure key germination-related traits in a high- throughput manner. [Results] We have collected a range of phenotypic traits in this study that were difficult to obtain through traditional approaches, including seed length, width, area, perimeter, radicle and seedling length, and their growth rates. We applied a linear regression analysis to validate the computational results with manual scoring, the square of the correlation coefficient, R2, computed for traits such as radical length, radical growth rate and seedling length are 0.922 (n=188, P<0.001, ，RMSE=1.727), 0.719 (n=191, P<0.001, RMSE=0.406), 0.897 (n=115, P<0.001, RMSE=2.726), respectively. [Conclusions] The results suggest that the algorithm and open-source software presented here can reliably obtain dynamic seed germination traits, which can also be extended to other crop species such as cotton (Gossypium barbadense) and oilseed rape (Brassica napus), providing phenotypic evidence and smart analytic solutions to enable studies in plant genetics and crop breeding

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton

Anthropogenic Noise Aggravates the Toxicity of Cadmium on Some Physiological Characteristics of the Blood Clam Tegillarca granosa

Widespread applications of cadmium (Cd) in various products have caused Cd contamination in marine ecosystems. Meanwhile, human activities in the ocean have also generated an increasing amount of noise in recent decades. Although anthropogenic noise and Cd contaminants could be present simultaneously in marine environments, the physiological responses of marine bivalve mollusks upon coexposure to anthropogenic noise and toxic metal contaminants, including Cd remain unclear. Therefore, the combined effects of anthropogenic noise and Cd on the physiological characteristics of the blood clam Tegillarca granosa were investigated in this study. The results showed that 10 days of coexposure to anthropogenic noise and Cd can enhance adverse impacts on metabolic processes, as indicated by the clearance rate, respiration rate, ammonium excretion rate, and O:N ratio of T. granosa. In addition, both the ATP content, ATP synthase activity and genes encoding important enzymes in ATP synthesis significantly declined after coexposures to anthropogenic noise and Cd, which have resulted from reduced feeding activity and respiration. Furthermore, the expressions of neurotransmitter-related genes (MAO, AChE, and mAChR3) were all significantly down-regulated after coexposure to anthropogenic noise and Cd, which suggests an enhanced neurotoxicity under coexposure. In conclusion, our study demonstrated that anthropogenic noise and Cd would have synergetic effects on the feeding activity, metabolism, and ATP synthesis of T. granosa, which may be due to the add-on of stress responses and neurotransmitter disturbances

Metabolomic and Transcriptomic Insights into How Cotton Fiber Transitions to Secondary Wall Synthesis, Represses Lignification, and Prolongs Elongation

The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber. Results: Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA. Conclusions: The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.National Science Foundation grant 1025947Cellular and Molecular Biolog

Вихретоковый анизотропный термоэлектрический первичный преобразователь лучистого потока

Представлена оригинальная конструкция первичного преобразователя лучистого потока, который может служить основой для создания приемника неселективного излучения с повышенной чувствительностью

Spontaneous order of Chinese travel associations

The theory of spontaneous order by F. A. Hayek shows an effective system within society, where individuals can effectively act without external interference. An example of this theory can be seen in the system of Chinese travel associations, that are active in the sphere of tourism, specifically with Chinese tourists. In my thesis I analyze spontaneous order of Chinese travel associations, which exist inside local community. Because of the special circumstances they face and because of different culture and mentality that can be found in the leaders of the association and also members, they had to form a different type of cooperation – a cooperation that is flexible and can constantly adapt to new circumstances, since those rules and agreements are not written down. My bachelor thesis provides a view of economic constraints that are today active inside of the Chinese community in the sphere of tourism. Due to the need of enforcing these rules and agreements, there was a room for Chinese travel associations to exist, so they can effectively protect the right of their members towards the third party.Teorie spontánního řádu od F.A. Hayeka ukazuje možnost efektivního fungování systému ve společnosti, kdy jedinec dokáže sám efektivně jednat bez vnějšího zásahu. Danou teorii lze vidět na systému čínské cestovní asociace, která dnes aktivně působí v oblasti cestovního ruchu s čínskými turisty. V práci analyzuji spontánní řád čínské cestovní asociace, která působí v rámci místní společnosti, avšak z důvodu specifických okolností, jako je odlišná kultura a mentalita jak u vedení asociací, tak i u členů, si vytvořili odlišnou formu spolupráce. Kooperace bude flexibilní z důvodu nepsaných pravidel a dohod, které se neustále přizpůsobují novým okolnostem. Práce poskytuje pohled do ekonomickýchvazeb, které dnes aktivně fungují mezi čínskou komunitou v oblasti cestovního ruchu. Kvůli potřebě vynucování těchto pravidel a dohod vznikl prostor pro existenci čínských cestovních asociací, které dokáží efektivně chránit práva svých členů vůči třetí straně